DB code: D00165

RLCP classification 1.30.36000.3 : Hydrolysis
CATH domain 3.20.20.80 : TIM Barrel Catalytic domain
2.60.40.1180 : Immunoglobulin-like
E.C. 3.2.1.1
CSA 1amy
M-CSA 1amy
MACiE

CATH domain Related DB codes (homologues)
3.20.20.80 : TIM Barrel S00202 S00210 S00748 S00906 S00907 S00911 S00912 S00915 M00134 M00160 D00479 S00204 S00205 S00206 S00207 S00203 S00208 S00209 S00211 S00213 S00214 M00113 T00307 D00166 D00169 D00176 D00501 D00502 D00503 D00844 D00861 D00864 M00026 M00112 M00193 M00346 T00057 T00062 T00063 T00066 T00067
2.60.40.1180 : Immunoglobulin-like M00113 T00307 D00176 D00664 D00665 D00863 D00864 M00112 M00193 M00314 T00057 T00062 T00067

Uniprot Enzyme Name
UniprotKB Protein name Synonyms CAZy Pfam RefSeq
P04063 Alpha-amylase type B isozyme
EC 3.2.1.1
1,4-alpha-D-glucan glucanohydrolase
AMY2-2
High pI alpha-amylase
GH13 (Glycoside Hydrolase Family 13)
PF07821 (Alpha-amyl_C2)
PF00128 (Alpha-amylase)
[Graphical View]
P00691 Alpha-amylase
EC 3.2.1.1
1,4-alpha-D-glucan glucanohydrolase
CBM26 (Carbohydrate-Binding Module Family 26)
GH13 (Glycoside Hydrolase Family 13)
PF00128 (Alpha-amylase)
[Graphical View]
NP_388186.2 (Protein)
NC_000964.3 (DNA/RNA sequence)
P56271 Acid alpha-amylase
EC 3.2.1.1
1,4-alpha-D-glucan glucanohydrolase
GH13 (Glycoside Hydrolase Family 13)
PF00128 (Alpha-amylase)
PF09260 (DUF1966)
[Graphical View]
P0C1B3 Alpha-amylase A type-1/2
EC 3.2.1.1
1,4-alpha-D-glucan glucanohydrolase
Taka-amylase A
TAA
GH13 (Glycoside Hydrolase Family 13)
PF00128 (Alpha-amylase)
PF09260 (DUF1966)
[Graphical View]
XP_001821436.1 (Protein)
XM_001821384.2 (DNA/RNA sequence)
XP_001823941.1 (Protein)
XM_001823889.2 (DNA/RNA sequence)
P29957 Alpha-amylase
EC 3.2.1.1
1,4-alpha-D-glucan glucanohydrolase
GH13 (Glycoside Hydrolase Family 13)
PF00128 (Alpha-amylase)
PF02806 (Alpha-amylase_C)
[Graphical View]
P56634 Alpha-amylase
EC 3.2.1.1
1,4-alpha-D-glucan glucanohydrolase
GH13 (Glycoside Hydrolase Family 13)
PF00128 (Alpha-amylase)
PF02806 (Alpha-amylase_C)
[Graphical View]
P00690 Pancreatic alpha-amylase
PA
EC 3.2.1.1
1,4-alpha-D-glucan glucanohydrolase
GH13 (Glycoside Hydrolase Family 13)
PF00128 (Alpha-amylase)
PF02806 (Alpha-amylase_C)
[Graphical View]
NP_999360.1 (Protein)
NM_214195.1 (DNA/RNA sequence)
P04745 Alpha-amylase 1
EC 3.2.1.1
1,4-alpha-D-glucan glucanohydrolase 1
Salivary alpha-amylase
GH13 (Glycoside Hydrolase Family 13)
PF00128 (Alpha-amylase)
PF02806 (Alpha-amylase_C)
[Graphical View]
NP_001008219.1 (Protein)
NM_001008218.1 (DNA/RNA sequence)
NP_001008220.1 (Protein)
NM_001008219.1 (DNA/RNA sequence)
NP_001008222.1 (Protein)
NM_001008221.1 (DNA/RNA sequence)
NP_004029.2 (Protein)
NM_004038.3 (DNA/RNA sequence)
P04746 Pancreatic alpha-amylase
PA
EC 3.2.1.1
1,4-alpha-D-glucan glucanohydrolase
GH13 (Glycoside Hydrolase Family 13)
PF00128 (Alpha-amylase)
PF02806 (Alpha-amylase_C)
[Graphical View]
NP_000690.1 (Protein)
NM_000699.2 (DNA/RNA sequence)

KEGG enzyme name
alpha-amylase
glycogenase
alpha amylase, alpha-amylase
endoamylase
Taka-amylase A
1,4-alpha-D-glucan glucanohydrolase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P04063 AMY2_HORVU Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides. Monomer. Binds 3 calcium ions per subunit.
P00691 AMY_BACSU Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides. Monomer. Secreted. Binds 2 calcium ions per subunit.
P56271 AMYA_ASPNG Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides. Monomer. Binds 2 calcium ions per subunit. Calcium is inhibitory at high concentrations.
P0C1B3 AMYA1_ASPOR Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides. Monomer. Binds 2 calcium ions per subunit. Calcium is inhibitory at high concentrations.
P29957 AMY_PSEHA Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides. Monomer. Binds 1 calcium ion per subunit. Binds 1 chloride ion per subunit.
P56634 AMY_TENMO Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides. Monomer. Binds 1 calcium ion per subunit. Binds 1 chloride ion per subunit.
P00690 AMYP_PIG Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides. Secreted, extracellular space. Binds 1 calcium ion per subunit. Binds 1 chloride ion per subunit.
P04745 AMY1_HUMAN Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides. Monomer. Secreted. Binds 1 calcium ion per subunit. Binds 1 chloride ion per subunit.
P04746 AMYP_HUMAN Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides. Monomer. Secreted, extracellular space. Binds 1 calcium ion per subunit. Binds 1 chloride ion per subunit.

KEGG Pathways
Map code Pathways E.C.
MAP00500 Starch and sucrose metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00076 C00115 C00369 C00001 C00369 C00721
E.C.
Compound Calcium Chloride Starch H2O Starch Dextrin
Type divalent metal (Ca2+, Mg2+) halide polysaccharide H2O polysaccharide polysaccharide
ChEBI 29108
15377
PubChem 271
22247451
962
1amyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:3x_CA Unbound Unbound Unbound Unbound Unbound
1avaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:3x_CA Unbound Unbound Unbound Unbound Unbound
1avaB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:3x_CA Unbound Unbound Unbound Unbound Unbound
1bg9A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:3x_CA Unbound Unbound Unbound Unbound Transition-state-analogue:DAF-GLC
1bagA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:3x_CA Unbound Bound:GLC-GLC-GLC-GLC-GLC Unbound Unbound Unbound
2aaaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Unbound Unbound Unbound Unbound Unbound
2taaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Unbound Unbound Unbound Unbound Unbound
6taaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_CA Unbound Unbound Unbound Unbound Unbound
7taaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Unbound Unbound Unbound Unbound Transition-state-analogue:ABC
1aqhA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Bound:_CL Unbound Unbound Unbound Unbound
1aqmA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Bound:_CL Unbound Unbound Unbound Unbound
1b0iA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Bound:_CL Unbound Unbound Unbound Unbound
1clvA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Bound:_CL Unbound Unbound Unbound Unbound
1jaeA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Bound:_CL Unbound Unbound Unbound Unbound
1tmqA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Bound:_CL Unbound Unbound Unbound Unbound
1viwA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Bound:_CL Unbound Unbound Unbound Unbound
1bvnP01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Bound:_CL Unbound Unbound Unbound Unbound
1dhkA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_CA Bound:_CL Unbound Unbound Unbound Unbound
1jfhA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Bound:_CL Unbound Analogue:MA2-MA3 Analogue:MAN-MA1 Unbound
1oseA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Bound:_CL Unbound Unbound Unbound Transition-state-analogue:AC1-GLC-AC1-GLC
1pifA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Bound:_CL Unbound Unbound Unbound Unbound
1pigA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Bound:_CL Unbound Unbound Unbound Transition-state-analogue:AGL-GLC-HMC-AGL-GLC-GLC
1ppiA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Bound:_CL Unbound Unbound Unbound Transition-state-analogue:GLC-GLC-DAF-GLC
1smdA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Bound:_CL Unbound Unbound Unbound Unbound
1bsiA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Bound:_CL Unbound Unbound Unbound Unbound
1cpuA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Bound:_CL Unbound Unbound Unbound Transition-state-analogue:GLC-GLC-HMC-AGL-GLC
1hnyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Bound:_CL Unbound Unbound Unbound Unbound
1amyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1avaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1avaB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1bg9A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1bagA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
2aaaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
2taaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
6taaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
7taaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1aqhA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1aqmA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1b0iA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1clvA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1jaeA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1tmqA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1viwA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1bvnP02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1dhkA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1jfhA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1oseA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1pifA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1pigA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1ppiA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1smdA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1bsiA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1cpuA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1hnyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P04063, P00691, P56271, P10529, P29957, P29957, P56634, P00690, P04745, P04746

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1amyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 179;GLU 204;ASP 289 ASN 91;PHE 143;ASP 148;ASP 142(Calcium binding);GLU 108;THR 111;ASP 113;ASP 117(2nd calcium);ASP 127;ASP 138;ALA 141;ALA 146(3rd calcium)
1avaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 179;GLU 204;ASP 289 ASN 91;PHE 143;ASP 148;ASP 142(Calcium binding);GLU 108;THR 111;ASP 113;ASP 117(2nd calcium);ASP 127;ASP 138;ALA 141;ALA 146(3rd calcium)
1avaB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 179;GLU 204;ASP 289 ASN 91;PHE 143;ASP 148;ASP 142(Calcium binding);GLU 108;THR 111;ASP 113;ASP 117(2nd calcium);ASP 127;ASP 138;ALA 141;ALA 146(3rd calcium)
1bg9A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 179;GLU 204;ASP 289 ASN 91;ASP 142;PHE 143;ASP 148(Calcium binding);GLU 108;THR 111;ASP 113;ASP 117(2nd calcium);ASP 127;ASP 138;ALA 141;ALA 146(3rd calcium)
1bagA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 176;;ASP 269 ASN 101;THR 137;ASP 146;HIS 180(Calcium binding);GLY 169;ASP 171(2nd calcium) mutant E208Q
2aaaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 206;GLU 230;ASP 297 ASP 121;GLU 162;ASP 175;GLU 210(Calcium binding);ASP 206;GLU 230(Inhibitory calcium binding)
2taaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 206;GLU 230;ASP 297 ASN 121;GLU 162;ASP 175;HIS 210(Calcium binding);ASP 206;GLU 230(Inhibitory calcium binding)
6taaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 206;GLU 230;ASP 297 ASN 121;GLU 162;ASP 175;HIS 210(Calcium binding);ASP 206;GLU 230(Inhibitory calcium binding)
7taaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 206;GLU 230;ASP 297 ASN 121;GLU 162;ASP 175;HIS 210(Calcium binding);ASP 206;GLU 230(Inhibitory calcium binding)
1aqhA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 174;GLU 200;ASP 264 ASN 88;GLN 135;ASP 144;HIS 178(Calcium binding);ARG 172;ASN 262;LYS 300(Chloride binding)
1aqmA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 174;GLU 200;ASP 264 ASN 88;GLN 135;ASP 144;HIS 178(Calcium binding);ARG 172;ASN 262;LYS 300(Chloride binding)
1b0iA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 174;GLU 200;ASP 264 ASN 88;GLN 135;ASP 144;HIS 178(Calcium binding);ARG 172;ASN 262;LYS 300(Chloride binding)
1clvA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 185;GLU 222;ASP 287 ASN 98;ARG 146;ASP 155;HIS 189(Calcium binding);ARG 183;ASN 285;ARG 321(Chloride binding)
1jaeA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 185;GLU 222;ASP 287 ASN 98;ARG 146;ASP 155;HIS 189(Calcium binding);ARG 183;ASN 285;ARG 321(Chloride binding)
1tmqA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 185;GLU 222;ASP 287 ASN 98;ARG 146;ASP 155;HIS 189(Calcium binding);ARG 183;ASN 285;ARG 321(Chloride binding)
1viwA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 185;GLU 222;ASP 287 ASN 98;ARG 146;ASP 155;HIS 189(Calcium binding);ARG 183;ASN 285;ARG 321(Chloride binding)
1bvnP01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 197;GLU 233;ASP 300 ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding)
1dhkA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 197;GLU 233;ASP 300 ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding)
1jfhA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 197;GLU 233;ASP 300 ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding)
1oseA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 197;GLU 233;ASP 300 ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding)
1pifA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 197;GLU 233;ASP 300 ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding)
1pigA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 197;GLU 233;ASP 300 ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding)
1ppiA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 197;GLU 233;ASP 300 ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding)
1smdA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 197;GLU 233;ASP 300 ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding) ASN 350(Deamidation)
1bsiA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 197;GLU 233;ASP 300 ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding)
1cpuA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 197;GLU 233;ASP 300 ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding)
1hnyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 197;GLU 233;ASP 300 ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding)
1amyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1avaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1avaB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1bg9A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1bagA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2aaaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2taaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
6taaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
7taaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1aqhA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1aqmA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1b0iA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1clvA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1jaeA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1tmqA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1viwA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1bvnP02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dhkA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1jfhA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1oseA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1pifA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1pigA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ppiA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1smdA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 412;ASN 459(Deamidation)
1bsiA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1cpuA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1hnyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
p.699-700
[9]
Fig. 1, Fig. 2, p.215, p.219-220 3
[18]
Fig. 6, p.207-208 3
[22]
Fig. 2, p.298-301 5
[23]
p.6292-6293
[27]
p.1580-1582
[37]
Scheme 2 4
[38]
Fig. 2, p.10843-10845 4
[43]
Fig. 1, p.201-203 2
[44]
p.403-404
[45]
p.211-214
[46]
p.620-622
[47]
p.565-568
[61]
Fig. 2, p.4785-4789 10
[62]
Fig. 5, p.261-264 2
[69]
Fig. 2, Fig. 8A, p.7707 4
[70]
Fig. 2, p.4-5 8
[77]
Fig. 3, p.4277-4278 8
[78]
Scheme 1, p.4500-4502 10
[79]
Fig. 3 4

References
[1]
Resource
Comments X-RAY CRYSTALLOGRAPHY (5 ANGSTROMS)
Medline ID
PubMed ID
Journal Acta Crystallogr B
Year 1980
Volume 36
Pages 416-21
Authors Payan F, Haser R, Pierrot M, Frey M, Astier JP, Abadie B, Duee B, Buisson G
Title The three-dimensional structure of [alpha]-amylase from porcine pancreas at 5 A resolution - the active-site location.
Related PDB
Related UniProtKB P00690
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (3 ANGSTROMS)
Medline ID
PubMed ID 6156152
Journal J Biochem (Tokyo)
Year 1980
Volume 87
Pages 1555-8
Authors Matsuura Y, Kusunoki M, Harada W, Tanaka N, Iga Y, Yasuoka N, Toda H, Narita K, Kakudo M
Title Molecular structure of taka-amylase A. I. Backbone chain folding at 3 A resolution.
Related PDB
Related UniProtKB P10529
[3]
Resource
Comments
Medline ID
PubMed ID 6611158
Journal Biochem Biophys Res Commun
Year 1984
Volume 122
Pages 75-81
Authors Prodanov E, Seigner C, Marchis-Mouren G
Title Subsite profile of the active center of porcine pancreatic alpha-amylase. Kinetic studies using maltooligosaccharides as substrates.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (3 ANGSTROMS)
Medline ID
PubMed ID 6609921
Journal J Biochem (Tokyo)
Year 1984
Volume 95
Pages 697-702
Authors Matsuura Y, Kusunoki M, Harada W, Kakudo M
Title Structure and possible catalytic residues of Taka-amylase A.
Related PDB 2taa
Related UniProtKB P10529
[5]
Resource
Comments
Medline ID
PubMed ID 3872211
Journal Eur J Biochem
Year 1985
Volume 148
Pages 161-8
Authors Seigner C, Prodanov E, Marchis-Mouren G
Title On porcine pancreatic alpha-amylase action: kinetic evidence for the binding of two maltooligosaccharide molecules (maltose, maltotriose and o-nitrophenylmaltoside) by inhibition studies. Correlation with the five-subsite energy profile.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 3496084
Journal Biochem J
Year 1987
Volume 242
Pages 681-7
Authors Reddy MK, Heda GD, Reddy JK
Title Purification and characterization of alpha-amylase from rat pancreatic acinar carcinoma. Comparison with pancreatic alpha-amylase.
Related PDB
Related UniProtKB
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS)
Medline ID
PubMed ID 3502087
Journal EMBO J
Year 1987
Volume 6
Pages 3909-16
Authors Buisson G, Duee E, Haser R, Payan F
Title Three dimensional structure of porcine pancreatic alpha-amylase at 2.9 A resolution. Role of calcium in structure and activity.
Related PDB
Related UniProtKB P00690
[8]
Resource
Comments
Medline ID
PubMed ID 3267138
Journal J Protein Chem
Year 1988
Volume 7
Pages 399-415
Authors MacGregor EA
Title Alpha-amylase structure and activity.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 2784982
Journal Biochim Biophys Acta
Year 1989
Volume 995
Pages 214-20
Authors Tao BY, Reilly PJ, Robyt JF
Title Detection of a covalent intermediate in the mechanism of action of porcine pancreatic alpha-amylase by using 13C nuclear magnetic resonance.
Related PDB
Related UniProtKB
[10]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS)
Medline ID
PubMed ID 2207069
Journal Biochemistry
Year 1990
Volume 29
Pages 6244-9
Authors Boel E, Brady L, Brzozowski AM, Derewenda Z, Dodson GG, Jensen VJ, Petersen SB, Swift H, Thim L, Woldike HF
Title Calcium binding in alpha-amylases: an X-ray diffraction study at 2.1-A resolution of two enzymes from Aspergillus.
Related PDB 2aaa
Related UniProtKB P56271
[11]
Resource
Comments
Medline ID
PubMed ID 2143471
Journal Eur J Biochem
Year 1990
Volume 191
Pages 287-95
Authors Hayashi M, Tsuru A, Mitsui T, Takahashi N, Hanzawa H, Arata Y, Akazawa T
Title Structure and biosynthesis of the xylose-containing carbohydrate moiety of rice alpha-amylase.
Related PDB
Related UniProtKB
[12]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 1930835
Journal Acta Crystallogr B
Year 1991
Volume 47
Pages 535-44
Authors Swift HJ, Brady L, Derewenda ZS, Dodson EJ, Dodson GG, Turkenburg JP, Wilkinson AJ
Title Structure and molecular model refinement of Aspergillus oryzae (TAKA) alpha-amylase: an application of the simulated-annealing method.
Related PDB 6taa
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 1806988
Journal Scand J Clin Lab Invest
Year 1991
Volume 51
Pages 735-8
Authors Huguet J, Fuentes-Arderiu X
Title Biological variation in the catalytic concentration of pancreatic alpha-amylase and triacylglycerol lipase in serum.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 1606147
Journal Biochemistry
Year 1992
Volume 31
Pages 5232-6
Authors Matsui I, Ishikawa K, Miyairi S, Fukui S, Honda K
Title Alteration of bond-cleavage pattern in the hydrolysis catalyzed by Saccharomycopsis alpha-amylase altered by site-directed mutagenesis.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 1576155
Journal Biochim Biophys Acta
Year 1992
Volume 1120
Pages 281-8
Authors Takase K, Matsumoto T, Mizuno H, Yamane K
Title Site-directed mutagenesis of active site residues in Bacillus subtilis alpha-amylase.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 1369074
Journal Biosci Biotechnol Biochem
Year 1992
Volume 56
Pages 1792-6
Authors Kawaguchi T, Nagae H, Murao S, Arai M
Title Purification and some properties of a Haim-sensitive alpha-amylase from newly isolated Bacillus sp. No. 195.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 1377974
Journal Biosci Biotechnol Biochem
Year 1992
Volume 56
Pages 207-10
Authors Nagashima T, Tada S, Kitamoto K, Gomi K, Kumagai C, Toda H
Title Site-directed mutagenesis of catalytic active-site residues of Taka-amylase A.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 1569044
Journal J Biochem (Tokyo)
Year 1992
Volume 111
Pages 204-9
Authors Isoda Y, Shimizu Y, Hashimoto A, Fujiwara H, Nitta Y, Kagemoto A
Title Mechanism of hydrolyses of phenyl alpha-maltosides catalyzed by taka-amylase A.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 8421303
Journal J Mol Biol
Year 1993
Volume 229
Pages 235-8
Authors Chang C, Kim KK, Hwang KY, Choi MU, Suh SW
Title Crystallization and preliminary X-ray crystallographic analysis of alpha-amylase from Bacillus subtilis.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 8263932
Journal J Mol Biol
Year 1993
Volume 234
Pages 1282-3
Authors Mizuno H, Morimoto Y, Tsukihara T, Matsumoto T, Takase K
Title Crystallization and preliminary X-ray studies of wild type and catalytic-site mutant alpha-amylase from Bacillus subtilis.
Related PDB
Related UniProtKB
[21]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS), AND REVISIONS
Medline ID
PubMed ID 8515451
Journal J Mol Biol
Year 1993
Volume 231
Pages 785-99
Authors Qian M, Haser R, Payan F
Title Structure and molecular model refinement of pig pancreatic alpha-amylase at 2.1 A resolution.
Related PDB
Related UniProtKB P00690
[22]
Resource
Comments
Medline ID
PubMed ID 7945374
Journal Biochem Biophys Res Commun
Year 1994
Volume 204
Pages 297-302
Authors Mazur AK, Haser R, Payan F
Title The catalytic mechanism of alpha-amylases based upon enzyme crystal structures and model building calculations.
Related PDB
Related UniProtKB
[23]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS)
Medline ID
PubMed ID 8193143
Journal Biochemistry
Year 1994
Volume 33
Pages 6284-94
Authors Qian M, Haser R, Buisson G, Duee E, Payan F
Title The active center of a mammalian alpha-amylase. Structure of the complex of a pancreatic alpha-amylase with a carbohydrate inhibitor refined to 2.2-A resolution.
Related PDB 1ppi
Related UniProtKB P00690
[24]
Resource
Comments
Medline ID
PubMed ID 7822101
Journal Int J Pept Protein Res
Year 1994
Volume 44
Pages 245-52
Authors Hansen G, Heese O, Hohne WE, Hofemeister B
Title alpha-Amylases from Thermoactinomyces vulgaris: characteristics, primary structure and structure prediction.
Related PDB
Related UniProtKB
[25]
Resource
Comments
Medline ID
PubMed ID 8206864
Journal J Biochem (Tokyo)
Year 1994
Volume 115
Pages 179-81
Authors Miyazaki T, Morimoto T, Fukuyama K, Matsubara H
Title Crystallization and preliminary X-ray diffraction studies of the alpha-amylase inhibitor coded 0.19 from wheat kernel.
Related PDB
Related UniProtKB
[26]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS)
Medline ID
PubMed ID 8196040
Journal J Mol Biol
Year 1994
Volume 239
Pages 104-21
Authors Kadziola A, Abe J, Svensson B, Haser R
Title Crystal and molecular structure of barley alpha-amylase.
Related PDB 1amy
Related UniProtKB P04063
[27]
Resource
Comments
Medline ID
PubMed ID 8107092
Journal J Mol Biol
Year 1994
Volume 235
Pages 1560-84
Authors Larson SB, Greenwood A, Cascio D, Day J, McPherson A
Title Refined molecular structure of pig pancreatic alpha-amylase at 2.1 A resolution.
Related PDB
Related UniProtKB
[28]
Resource
Comments
Medline ID
PubMed ID 8107117
Journal J Mol Biol
Year 1994
Volume 236
Pages 368-71
Authors Vallee F, Kadziola A, Bourne Y, Abe J, Svensson B, Haser R
Title Characterization, crystallization and preliminary X-ray crystallographic analysis of the complex between barley alpha-amylase and the bifunctional alpha-amylase/subtilisin inhibitor from barley seeds.
Related PDB
Related UniProtKB
[29]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF COMPLEX WITH INHIBITOR
Medline ID
PubMed ID 7897663
Journal J Mol Biol
Year 1995
Volume 247
Pages 99-110
Authors Wiegand G, Epp O, Huber R
Title The crystal structure of porcine pancreatic alpha-amylase in complex with the microbial inhibitor Tendamistat.
Related PDB 1bvn
Related UniProtKB P00690
[30]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS)
Medline ID
PubMed ID 8528071
Journal Protein Sci
Year 1995
Volume 4
Pages 1730-42
Authors Brayer GD, Luo Y, Withers SG
Title The structure of human pancreatic alpha-amylase at 1.8 A resolution and comparisons with related enzymes.
Related PDB 1hny
Related UniProtKB P04746
[31]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS)
Medline ID
PubMed ID
Journal Acta Crystallogr D Biol Crystallogr
Year 1996
Volume 52
Pages 435-46
Authors Ramasubbu N, Paloth V, Luo Y, Brayer GD, Levine MJ
Title Structure of Human Salivary [alpha]-Amylase at 1.6 A Resolution: Implications for its Role in the Oral Cavity.
Related PDB 1smd
Related UniProtKB P04745
[32]
Resource
Comments
Medline ID
PubMed ID 8862470
Journal Clin Chim Acta
Year 1996
Volume 251
Pages 145-62
Authors Gubern G, Canalias F, Gella FJ, Colinet E, Profilis C, Calam DH, Ceriotti F, Dufaux J, Hadjivassiliou AG, Lessinger JM, Lorentz K, Vassault A
Title Production and certification of an enzyme reference material for pancreatic alpha-amylase (CRM 476).
Related PDB
Related UniProtKB
[33]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS), AND REVISIONS
Medline ID
PubMed ID 8681972
Journal Eur J Biochem
Year 1996
Volume 238
Pages 561-9
Authors Gilles C, Astier JP, Marchis-Mouren G, Cambillau C, Payan F
Title Crystal structure of pig pancreatic alpha-amylase isoenzyme II, in complex with the carbohydrate inhibitor acarbose.
Related PDB 1ose
Related UniProtKB P00690
[34]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS)
Medline ID
PubMed ID 8757803
Journal J Mol Biol
Year 1996
Volume 260
Pages 409-21
Authors Machius M, Vertesy L, Huber R, Wiegand G
Title Carbohydrate and protein-based inhibitors of porcine pancreatic alpha-amylase: structure analysis and comparison of their binding characteristics.
Related PDB 1pif 1pig
Related UniProtKB P00690
[35]
Resource
Comments
Medline ID
PubMed ID 8897615
Journal Protein Sci
Year 1996
Volume 5
Pages 2128-9
Authors Aghajari N, Feller G, Gerday C, Haser R
Title Crystallization and preliminary X-ray diffraction studies of alpha-amylase from the antarctic psychrophile Alteromonas haloplanctis A23.
Related PDB
Related UniProtKB
[36]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF COMPLEX WITH INHIBITOR
Medline ID
PubMed ID 8994970
Journal Structure
Year 1996
Volume 4
Pages 1441-52
Authors Bompard-Gilles C, Rousseau P, Rouge P, Payan F
Title Substrate mimicry in the active center of a mammalian alpha-amylase: structural analysis of an enzyme-inhibitor complex.
Related PDB 1dhk
Related UniProtKB P00690
[37]
Resource
Comments
Medline ID
PubMed ID 8636115
Journal J Biol Chem
Year 1996
Volume 271
Pages 6889-94
Authors McCarter JD, Withers SG
Title Unequivocal identification of Asp-214 as the catalytic nucleophile of Saccharomyces cerevisiae alpha-glucosidase using 5-fluoro glycosyl fluorides.
Related PDB
Related UniProtKB
[38]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.98 ANGSTROMS)
Medline ID
PubMed ID 9283074
Journal Biochemistry
Year 1997
Volume 36
Pages 10837-45
Authors Brzozowski AM, Davies GJ
Title Structure of the Aspergillus oryzae alpha-amylase complexed with the inhibitor acarbose at 2.0 A resolution.
Related PDB 7taa
Related UniProtKB P10529
[39]
Resource
Comments
Medline ID
PubMed ID 9434115
Journal Biochim Biophys Acta
Year 1997
Volume 1343
Pages 243-50
Authors Matsumoto T, Makimoto S, Taniguchi Y
Title Effect of pressure on the mechanism of hydrolysis of maltotetraose, maltopentaose, and maltohexose catalyzed by porcine pancreatic alpha-amylase.
Related PDB
Related UniProtKB
[40]
Resource
Comments
Medline ID
PubMed ID 9199514
Journal FEBS Lett
Year 1997
Volume 409
Pages 109-14
Authors Strobl S, Gomis-Ruth FX, Maskos K, Frank G, Huber R, Glockshuber R
Title The alpha-amylase from the yellow meal worm: complete primary structure, crystallization and preliminary X-ray analysis.
Related PDB
Related UniProtKB
[41]
Resource
Comments
Medline ID
PubMed ID 9278396
Journal J Biol Chem
Year 1997
Volume 272
Pages 22456-63
Authors Matsui I, Svensson B
Title Improved activity and modulated action pattern obtained by random mutagenesis at the fourth beta-alpha loop involved in substrate binding to the catalytic (beta/alpha)8-barrel domain of barley alpha-amylase 1.
Related PDB
Related UniProtKB
[42]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.03 ANGSTROMS)
Medline ID
PubMed ID 9385631
Journal Protein Sci
Year 1997
Volume 6
Pages 2285-96
Authors Qian M, Spinelli S, Driguez H, Payan F
Title Structure of a pancreatic alpha-amylase bound to a substrate analogue at 2.03 A resolution.
Related PDB 1jfh
Related UniProtKB P00690
[43]
Resource
Comments
Medline ID
PubMed ID 9649747
Journal Biochem Soc Trans
Year 1998
Volume 26
Pages 198-204
Authors Gottschalk TE, Fierobe HP, Mirgorodskaya E, Clarke AJ, Tull D, Sigurskjold BW, Christensen T, Payre N, Frandsen TP, Juge N, McGuire KA, Cottaz S, Roepstorff P, Driguez H, Williamson G, Svensson B
Title Structure, function and protein engineering of starch-degrading enzymes.
Related PDB
Related UniProtKB
[44]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 42-466
Medline ID
PubMed ID 9514750
Journal J Mol Biol
Year 1998
Volume 277
Pages 393-407
Authors Fujimoto Z, Takase K, Doui N, Momma M, Matsumoto T, Mizuno H
Title Crystal structure of a catalytic-site mutant alpha-amylase from Bacillus subtilis complexed with maltopentaose.
Related PDB 1bag
Related UniProtKB P00691
[45]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 9571044
Journal J Mol Biol
Year 1998
Volume 278
Pages 205-17
Authors Kadziola A, Sogaard M, Svensson B, Haser R
Title Molecular structure of a barley alpha-amylase-inhibitor complex: implications for starch binding and catalysis.
Related PDB 1bg9
Related UniProtKB
[46]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS)
Medline ID
PubMed ID 9600843
Journal J Mol Biol
Year 1998
Volume 278
Pages 617-28
Authors Strobl S, Maskos K, Betz M, Wiegand G, Huber R, Gomis-Ruth FX, Glockshuber R
Title Crystal structure of yellow meal worm alpha-amylase at 1.64 A resolution.
Related PDB 1jae
Related UniProtKB P56634
[47]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 25-477
Medline ID
PubMed ID 9541387
Journal Protein Sci
Year 1998
Volume 7
Pages 564-72
Authors Aghajari N, Feller G, Gerday C, Haser R
Title Crystal structures of the psychrophilic alpha-amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor.
Related PDB 1aqh 1aqm
Related UniProtKB P29957
[48]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 9862804
Journal Structure
Year 1998
Volume 6
Pages 1503-16
Authors Aghajari N, Feller G, Gerday C, Haser R
Title Structures of the psychrophilic Alteromonas haloplanctis alpha-amylase give insights into cold adaptation at a molecular level.
Related PDB 1b0i
Related UniProtKB
[49]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS)
Medline ID
PubMed ID 9687373
Journal Structure
Year 1998
Volume 6
Pages 911-21
Authors Strobl S, Maskos K, Wiegand G, Huber R, Gomis-Ruth FX, Glockshuber R
Title A novel strategy for inhibition of alpha-amylases: yellow meal worm alpha-amylase in complex with the Ragi bifunctional inhibitor at 2.5 A resolution.
Related PDB 1tmq
Related UniProtKB P56634
[50]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF COMPLEX WITH BASI
Medline ID
PubMed ID 9634702
Journal Structure
Year 1998
Volume 6
Pages 649-59
Authors Vallee F, Kadziola A, Bourne Y, Juy M, Rodenburg KW, Svensson B, Haser R
Title Barley alpha-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9 A resolution.
Related PDB 1ava
Related UniProtKB P04063
[51]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10089450
Journal Acta Crystallogr D Biol Crystallogr
Year 1999
Volume 55
Pages 360-2
Authors Nahoum V, Farisei F, Le-Berre-Anton V, Egloff MP, Rouge P, Poerio E, Payan F
Title A plant-seed inhibitor of two classes of alpha-amylases: X-ray analysis of Tenebrio molitor larvae alpha-amylase in complex with the bean Phaseolus vulgaris inhibitor.
Related PDB 1viw
Related UniProtKB
[52]
Resource
Comments
Medline ID
PubMed ID 10547530
Journal Biopolymers
Year 1999
Volume 50
Pages 751-62
Authors Andre G, Buleon A, Haser R, Tran V
Title Amylose chain behavior in an interacting context. III. Complete occupancy of the AMY2 barley alpha-amylase cleft and comparison with biochemical data.
Related PDB
Related UniProtKB
[53]
Resource
Comments
Medline ID 99198742
PubMed ID 10100643
Journal FEBS Lett
Year 1999
Volume 446
Pages 203-6
Authors Young NM, Thibault P, Watson DC, Chrispeels MJ
Title Post-translational processing of two alpha-amylase inhibitors and an arcelin from the common bean, Phaseolus vulgaris.
Related PDB
Related UniProtKB
[54]
Resource
Comments
Medline ID
PubMed ID 10650713
Journal Indian J Biochem Biophys
Year 1999
Volume 36
Pages 150-7
Authors Dey S, Agarwal SO
Title Characterization of a thermostable alpha-amylase from a thermophilic Streptomyces megasporus strain SD12.
Related PDB
Related UniProtKB
[55]
Resource
Comments
Medline ID
PubMed ID 10222200
Journal J Mol Biol
Year 1999
Volume 287
Pages 907-21
Authors Kamitori S, Kondo S, Okuyama K, Yokota T, Shimura Y, Tonozuka T, Sakano Y
Title Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVAII) hydrolyzing cyclodextrins and pullulan at 2.6 A resolution.
Related PDB
Related UniProtKB
[56]
Resource
Comments
Medline ID
PubMed ID 10556241
Journal Protein Eng
Year 1999
Volume 12
Pages 819-24
Authors Hasegawa K, Kubota M, Matsuura Y
Title Roles of catalytic residues in alpha-amylases as evidenced by the structures of the product-complexed mutants of a maltotetraose-forming amylase.
Related PDB
Related UniProtKB
[57]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10091666
Journal Protein Sci
Year 1999
Volume 8
Pages 635-43
Authors Rydberg EH, Sidhu G, Vo HC, Hewitt J, Cote HC, Wang Y, Numao S, MacGillivray RT, Overall CM, Brayer GD, Withers SG
Title Cloning, mutagenesis, and structural analysis of human pancreatic alpha-amylase expressed in Pichia pastoris.
Related PDB 1bsi
Related UniProtKB
[58]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10508777
Journal Structure Fold Des
Year 1999
Volume 7
Pages 1079-88
Authors Pereira PJ, Lozanov V, Patthy A, Huber R, Bode W, Pongor S, Strobl S
Title Specific inhibition of insect alpha-amylases: yellow meal worm alpha-amylase in complex with the amaranth alpha-amylase inhibitor at 2.0 A resolution.
Related PDB 1clv
Related UniProtKB
[59]
Resource
Comments
Medline ID
PubMed ID 10657258
Journal Biochem J
Year 2000
Volume 346 Pt 1
Pages 201-8
Authors Nahoum V, Roux G, Anton V, Rouge P, Puigserver A, Bischoff H, Henrissat B, Payan F
Title Crystal structures of human pancreatic alpha-amylase in complex with carbohydrate and proteinaceous inhibitors.
Related PDB
Related UniProtKB
[60]
Resource
Comments
Medline ID
PubMed ID 10947962
Journal Biochem J
Year 2000
Volume 350 Pt 2
Pages 477-84
Authors Sumitani J, Tottori T, Kawaguchi T, Arai M
Title New type of starch-binding domain: the direct repeat motif in the C-terminal region of Bacillus sp. no. 195 alpha-amylase contributes to starch binding and raw starch degrading.
Related PDB
Related UniProtKB
[61]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10769135
Journal Biochemistry
Year 2000
Volume 39
Pages 4778-91
Authors Brayer GD, Sidhu G, Maurus R, Rydberg EH, Braun C, Wang Y, Nguyen NT, Overall CM, Withers SG
Title Subsite mapping of the human pancreatic alpha-amylase active site through structural, kinetic, and mutagenesis techniques.
Related PDB 1cpu
Related UniProtKB
[62]
Resource
Comments
Medline ID
PubMed ID 11150610
Journal Biochim Biophys Acta
Year 2000
Volume 1543
Pages 253-74
Authors Nielsen JE, Borchert TV
Title Protein engineering of bacterial alpha-amylases.
Related PDB
Related UniProtKB
[63]
Resource
Comments
Medline ID
PubMed ID 10969023
Journal Biophys J
Year 2000
Volume 79
Pages 1629-36
Authors Fitter J, Heberle J
Title Structural equilibrium fluctuations in mesophilic and thermophilic alpha-amylase.
Related PDB
Related UniProtKB
[64]
Resource
Comments
Medline ID
PubMed ID 11210138
Journal Biosci Biotechnol Biochem
Year 2000
Volume 64
Pages 2692-5
Authors Ichikawa K, Tonozuka T, Yokota T, Shimura Y, Sakano Y
Title Analysis of catalytic residues of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) by site-directed mutagenesis.
Related PDB
Related UniProtKB
[65]
Resource
Comments
Medline ID
PubMed ID 10925206
Journal Gene
Year 2000
Volume 253
Pages 95-105
Authors D'Amico S, Gerday C, Feller G
Title Structural similarities and evolutionary relationships in chloride-dependent alpha-amylases.
Related PDB
Related UniProtKB
[66]
Resource
Comments
Medline ID
PubMed ID 11307950
Journal J Protein Chem
Year 2000
Volume 19
Pages 663-9
Authors Tibbot BK, Wong DW, Robertson GH
Title A functional raw starch-binding domain of barley alpha-amylase expressed in Escherichia coli.
Related PDB
Related UniProtKB
[67]
Resource
Comments
Medline ID
PubMed ID 10775658
Journal Protein Eng
Year 2000
Volume 13
Pages 167-77
Authors Da Silva MC, de Sa MF, Chrispeels MJ, Togawa RC, Neshich G
Title Analysis of structural and physico-chemical parameters involved in the specificity of binding between alpha-amylases and their inhibitors.
Related PDB
Related UniProtKB
[68]
Resource
Comments
Medline ID
PubMed ID 11669621
Journal Biochemistry
Year 2001
Volume 40
Pages 12844-54
Authors Gottschalk TE, Tull D, Aghajari N, Haser R, Svensson B
Title Specificity modulation of barley alpha-amylase through biased random mutagenesis involving a conserved tripeptide in beta --> alpha loop 7 of the catalytic (beta/alpha)(8)-barrel domain.
Related PDB
Related UniProtKB
[69]
Resource
Comments
Medline ID
PubMed ID 11412124
Journal Biochemistry
Year 2001
Volume 40
Pages 7700-9
Authors Qian M, Nahoum V, Bonicel J, Bischoff H, Henrissat B, Payan F
Title Enzyme-catalyzed condensation reaction in a mammalian alpha-amylase. High-resolution structural analysis of an enzyme-inhibitor complex.
Related PDB
Related UniProtKB
[70]
Resource
Comments
Medline ID
PubMed ID 11257505
Journal Biochim Biophys Acta
Year 2001
Volume 1546
Pages 1-20
Authors MacGregor EA, Janecek S, Svensson B
Title Relationship of sequence and structure to specificity in the alpha-amylase family of enzymes.
Related PDB
Related UniProtKB
[71]
Resource
Comments
Medline ID
PubMed ID 11342250
Journal Biochim Biophys Acta
Year 2001
Volume 1525
Pages 29-36
Authors Slaughter SL, Ellis PR, Butterworth PJ
Title An investigation of the action of porcine pancreatic alpha-amylase on native and gelatinised starches.
Related PDB
Related UniProtKB
[72]
Resource
Comments
Medline ID
PubMed ID 11527532
Journal Carbohydr Res
Year 2001
Volume 334
Pages 309-13
Authors Ohtaki A, Kondo S, Shimura Y, Tonozuka T, Sakano Y, Kamitori S
Title Role of Phe286 in the recognition mechanism of cyclomaltooligosaccharides (cyclodextrins) by Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII). X-ray structures of the mutant TVAIIs, F286A and F286Y, and kinetic analyses of the Phe286-replaced mutant TVAIIs.
Related PDB
Related UniProtKB
[73]
Resource
Comments
Medline ID
PubMed ID 11508823
Journal Gen Physiol Biophys
Year 2001
Volume 20
Pages 7-32
Authors Horvathova V, Janecek S, Sturdik E
Title Amylolytic enzymes: molecular aspects of their properties.
Related PDB
Related UniProtKB
[74]
Resource
Comments
Medline ID
PubMed ID 11226882
Journal J Biochem (Tokyo)
Year 2001
Volume 129
Pages 423-8
Authors Kondo S, Ohtaki A, Tonozuka T, Sakano Y, Kamitori S
Title Studies on the hydrolyzing mechanism for cyclodextrins of Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII). X-ray structure of the mutant E354A complexed with beta-cyclodextrin, and kinetic analyses on cyclodextrins.
Related PDB
Related UniProtKB
[75]
Resource
Comments
Medline ID
PubMed ID 11522925
Journal Protein Eng
Year 2001
Volume 14
Pages 505-12
Authors Nielsen JE, Borchert TV, Vriend G
Title The determinants of alpha-amylase pH-activity profiles.
Related PDB
Related UniProtKB
[76]
Resource
Comments
Medline ID
PubMed ID 12115056
Journal Arch Microbiol
Year 2002
Volume 178
Pages 115-23
Authors Lo HF, Lin LL, Chiang WY, Chie MC, Hsu WH, Chang CT
Title Deletion analysis of the C-terminal region of the alpha-amylase of Bacillus sp. strain TS-23.
Related PDB
Related UniProtKB
[77]
Resource
Comments
Medline ID
PubMed ID 11914073
Journal Biochemistry
Year 2002
Volume 41
Pages 4273-80
Authors Aghajari N, Roth M, Haser R
Title Crystallographic evidence of a transglycosylation reaction: ternary complexes of a psychrophilic alpha-amylase.
Related PDB
Related UniProtKB
[78]
Resource
Comments
Medline ID
PubMed ID 11914097
Journal Biochemistry
Year 2002
Volume 41
Pages 4492-502
Authors Rydberg EH, Li C, Maurus R, Overall CM, Brayer GD, Withers SG
Title Mechanistic analyses of catalysis in human pancreatic alpha-amylase: detailed kinetic and structural studies of mutants of three conserved carboxylic acids.
Related PDB
Related UniProtKB
[79]
Resource
Comments
Medline ID
PubMed ID 12423336
Journal Eur J Biochem
Year 2002
Volume 269
Pages 5377-90
Authors Mori H, Bak-Jensen KS, Svensson B
Title Barley alpha-amylase Met53 situated at the high-affinity subsite -2 belongs to a substrate binding motif in the beta-->alpha loop 2 of the catalytic (beta/alpha)8-barrel and is critical for activity and substrate specificity.
Related PDB
Related UniProtKB
[80]
Resource
Comments
Medline ID
PubMed ID 12379350
Journal J Immunol Methods
Year 2002
Volume 269
Pages 29-37
Authors Goncalves O, Dintinger T, Blanchard D, Tellier C
Title Functional mimicry between anti-Tendamistat antibodies and alpha-amylase.
Related PDB
Related UniProtKB
[81]
Resource
Comments
Medline ID
PubMed ID 12051850
Journal J Mol Biol
Year 2002
Volume 318
Pages 443-53
Authors Kamitori S, Abe A, Ohtaki A, Kaji A, Tonozuka T, Sakano Y
Title Crystal structures and structural comparison of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) at 1.6 A resolution and alpha-amylase 2 (TVAII) at 2.3 A resolution.
Related PDB
Related UniProtKB
[82]
Resource
Comments
Medline ID
PubMed ID 12578360
Journal Biochemistry
Year 2003
Volume 42
Pages 1478-87
Authors Nielsen PK, Bonsager BC, Berland CR, Sigurskjold BW, Svensson B
Title Kinetics and energetics of the binding between barley alpha-amylase/subtilisin inhibitor and barley alpha-amylase 2 analyzed by surface plasmon resonance and isothermal titration calorimetry.
Related PDB
Related UniProtKB
[83]
Resource
Comments
Medline ID
PubMed ID 12581203
Journal Eur J Biochem
Year 2003
Volume 270
Pages 635-45
Authors Janecek S, Svensson B, MacGregor EA
Title Relation between domain evolution, specificity, and taxonomy of the alpha-amylase family members containing a C-terminal starch-binding domain.
Related PDB
Related UniProtKB

Comments
The enzyme belongs to the glycosyl hydrolase family-13.
The polysaccharide substrate/product data contained in the PDB data are described from the non-reducing end to the reducing end.
The Swiss-prot data are corresponding to the PDB data as follows:
AMY2_HORVU;P04063: 1amy, 1ava, 1bg9
AMY_BACSU;P00691 : 1bag
AMYA_ASPNG;P56271: 2aaa
AMYA_ASPOR;P10529: 2taa, 6taa, 7taa
AMY_ALTHA;P29957 : 1aqh, 1aqm, 1b0i
AMY_TENMO;P56634 : 1clv, 1jae, 1tmq, 1viw
AMYP_PIG;P00690 : 1bvn, 1dhk, 1jfh, 1ose, 1pif, 1pig, 1ppi
AMYS_HUMAN;P04745: 1smd
AMYP_HUMAN;P04746: 1bsi, 1cpu, 1hny
Binding modes of calcium and chloride ions are various among the alpha-amylase enzymes. However, the first calcium ion binding sites can be superimposed, except for those from barley (Swiss-prot; P04063). The enzyme from barley has got the distinct binding sites for three calcium ions. Although the calcium ions are necessary for the catalytic activities, they are not involved in catalysis, and may stabilize the enzyme structures. On the other hand, in chloride-dependent alpha-amlyases, the chloride ion seems to be involved in catalysis, by raising the pKa of the catalytic glutamic acid by its electrostatic effect (see [47]).
A variety of catalytic mechanisms has been proposed. In the proposed mechanisms, three acidic residues at the active site (Asp at beta-4, Glu at beta-5 and Asp at beta-7 of (alpha/beta)8 barrel structure) seemed to be involved in catalysis.
Paper [22] proposed a ring-opening mechanism, in which opening of glucose ring is induced by a nucleophilic attack by a catalytic water. However, this mechanism is more complicated and unlikely than any other proposed ones, as no experimental evidence has been reported so far.
On the other hand, a single displacement mechanism and a double displacement mechanism have been proposed and discussed. In both the mechanisms, an oxocarbenium ion seems to be formed either as a long-lived intermediate, or as a transition state.
Papers ([4], [23], [27], [44] & [46]) proposed and supported a single displacement mechanism, in which a catalytic water would hydrolyze the glycosidic bond of the substrate directly, assisted by the acid-base catalysis. In this mechanism, the Glu resiue at the C-terminal end of beta-5 acts as a general acid, protonating the leaving oxygen atom(O4). This protonation results in the formation of oxocarbenium ion intermediate (dissociative mechanism). Next, the general base activates the catalytic water, which would make a nucleophilic attack on the C1 atom of the intermediate.
On the other hand, the other papers ([9], [18], [37], [38], [43], [45], [47], [61], [62], [69], [70], [77] & [78]) supported a double displacement mechanism, in which a covalent enzyme-glycosyl intermediate would be formed prior to the hydrolysis by a catalytic water. Moreover, the papers, [18], [45], [47], [70] & [77], mentioned that protonation to the glycosidic oxygen (O4) by a general base, the Glu residue at beta-5, would occur, forming an oxocarbenium ion-like transtion state, prior to the nucleophilic attack by the Asp residue at beta-4 (suggesting a dissociative mechanism instead of an associative mechanism). After the formation of the covalent intermediate, Glu at beta-5 acts as a general base to activate a water molecule. The activated water makes a nucleophilic attack on the intermediate to complete the reaction.
Considering that the anomeric configuration of the glycosidic bond is retatined, the double displacement mechanism is more compelling than the single displacement mechanism. Moreover, the papers, [9] & [37], reproted that the experimental identification of the enzyme-glycosyl intermediate could be carried out. Taken together, the double displacement mechanism seems to be supported. In this reaction mechanism, the third acidic residue, Asp at beta-7, seems to stabilize the half-chair conformation during the transition state, and raise the pKa of the catalytic acid, Glu at beta-5. However, to acts as a modulator for Glu at beta-5, Asp at beta-7 is a bit too distant.

Created Updated
2003-11-04 2009-02-26