DB code: T00057

RLCP classification 1.30.36000.3 : Hydrolysis
CATH domain 3.20.20.80 : TIM Barrel Catalytic domain
2.40.31.10 :
2.60.40.1180 : Immunoglobulin-like
E.C. 3.2.1.1
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
2.60.40.1180 : Immunoglobulin-like M00113 T00307 D00165 D00176 D00664 D00665 D00863 D00864 M00112 M00193 M00314 T00062 T00067
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 D00165 D00166 D00169 D00176 D00501 D00502 D00503 D00844 D00861 D00864 M00026 M00112 M00193 M00346 T00062 T00063 T00066 T00067

Uniprot Enzyme Name
UniprotKB Protein name Synonyms CAZy Pfam
P06278 Alpha-amylase
EC 3.2.1.1
1,4-alpha-D-glucan glucanohydrolase
BLA
GH13 (Glycoside Hydrolase Family 13)
PF00128 (Alpha-amylase)
PF09154 (DUF1939)
[Graphical View]
P06279 Alpha-amylase
EC 3.2.1.1
1,4-alpha-D-glucan glucanohydrolase
GH13 (Glycoside Hydrolase Family 13)
PF00128 (Alpha-amylase)
PF09154 (DUF1939)
[Graphical View]

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
P06279 AMY_BACST Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides. Monomer. Binds 3 calcium ions per subunit. Binds 1 sodium ion per subunit.
P06278 AMY_BACLI Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides. Monomer. Binds 3 calcium ions per subunit. Binds 1 sodium ion per subunit.

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

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00076 C01330 C00420 C00001 C00930
E.C.
Compound Calcium Sodium Polysaccharide H2O Oligosaccharide
Type divalent metal (Ca2+, Mg2+) univalent metal (Na+, K+) polysaccharide H2O polysaccharide
ChEBI 29108
29101
15377
PubChem 271
923
871
22247451
962
1bplB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1bliA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_CA Unbound Unbound Unbound
1ob0A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_CA Unbound Unbound Unbound
1vjsA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1hvxA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:3x_CA Bound:_NA Unbound Unbound
1bplA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1bliA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_CA Bound:_NA Unbound Unbound
1ob0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_CA Bound:_NA Unbound Unbound
1vjsA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1hvxA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Bound:_NA Unbound Unbound
1bliA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Unbound Unbound Unbound
1ob0A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Unbound Unbound Unbound
1vjsA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1hvxA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
PDB;1bli, 1hvx & Swiss-prot;P06278, P06279 & literature [11],[17]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1bplB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 231;GLU 261;ASP 328 ASP 194;ASP 200;HIS 235(Calcium-1 binding);ASP 202;ASP 204(Calcium-2 binding);GLY 300;TYR 302;HIS 406;ASP 407;ASP 430(Calcium-3 binding);ASP 194;ASP 200;ILE 201(Sodium binding)
1bliA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 231;GLU 261;ASP 328 ASN 104;HIS 235(Calcium-1 binding);GLY 300(Calcium-3 binding)
1ob0A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 231;GLU 261;ASP 328 ASN 104;HIS 235(Calcium-1 binding);GLY 300(Calcium-3 binding) mutant A209V, Q264S, N265Y
1vjsA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 231;GLU 261;ASP 328 ASN 104;HIS 235(Calcium-1 binding);GLY 300(Calcium-3 binding)
1hvxA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 234;GLU 264;ASP 331 ASP 105;ASP 197;ASP 203;HIS 238(Calcium-1 binding);ASP 205(Calcium-2 binding);GLY 303;PHE 305(Calcium-3 binding);ASP 197;ASP 203;LEU 204(Sodium binding)
1bplA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 104;(Calcium-1 binding);ASP 161;ALA 181;(Calcium-2 binding);ASP 161; (Sodium binding) invisible D183
1bliA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 194;ASP 200(Calcium-1 binding);ASP 161;ALA 181;ASP 183;ASP 202;ASP 204(Calcium-2 binding);ASP 161;ASP 183;ASP 194;ASP 200;ILE 201(Sodium binding)
1ob0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 194;ASP 200(Calcium-1 binding);ASP 161;ALA 181;ASP 183;ASP 202;ASP 204(Calcium-2 binding);ASP 161;ASP 183;ASP 194;ASP 200;ILE 201(Sodium binding) mutant H133V, N190F
1vjsA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 194;ASP 200(Calcium-1 binding);ASP 161;ALA 181;;ASP 202;ASP 204(Calcium-2 binding);ASP 161;;ASP 194;ASP 200;ILE 201(Sodium binding) invisible 182-192
1hvxA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 162;ALA 184;ASP 186(Calcium-2 binding);ASP 162;ASP 186(Sodium binding)
1bliA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 406;ASP 407;ASP 430(Calcium-3 binding)
1ob0A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 406;ASP 407;ASP 430(Calcium-3 binding)
1vjsA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 406;ASP 407;ASP 430(Calcium-3 binding)
1hvxA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 406;ASP 407;ASP 430(Calcium-3 binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[3]
p.187-188
[11]
Fig.2
[12]
p.9106
[13]
Fig.5, p.261-264

References
[1]
Resource
Comments
Medline ID
PubMed ID 3125174
Journal J Biol Chem
Year 1988
Volume 263
Pages 3092-6
Authors Tomazic SJ, Klibanov AM
Title Why is one Bacillus alpha-amylase more resistant against irreversible thermoinactivation than another?
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 2277029
Journal J Biochem (Tokyo)
Year 1990
Volume 108
Pages 379-81
Authors Suzuki A, Yamane T, Ito Y, Nishio T, Fujiwara H, Ashida T
Title Crystallization and preliminary crystallographic study of bacterial alpha-amylases.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 2330367
Journal Protein Eng
Year 1990
Volume 3
Pages 181-91
Authors Holm L, Koivula AK, Lehtovaara PM, Hemminki A, Knowles JK
Title Random mutagenesis used to probe the structure and function of Bacillus stearothermophilus alpha-amylase.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 1952938
Journal Arch Biochem Biophys
Year 1991
Volume 291
Pages 255-7
Authors Lee SY, Kim S, Sweet RM, Suh SW
Title Crystallization and a preliminary X-ray crystallographic study of alpha-amylase from Bacillus licheniformis.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 7926034
Journal FEBS Lett
Year 1994
Volume 353
Pages 119-23
Authors Janecek S
Title Parallel beta/alpha-barrels of alpha-amylase, cyclodextrin glycosyltransferase and oligo-1,6-glucosidase versus the barrel of beta-amylase: evolutionary distance is a reflection of unrelated sequences.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
Medline ID 95182462
PubMed ID 7877175
Journal J Mol Biol
Year 1995
Volume 246
Pages 545-59
Authors Machius M, Wiegand G, Huber R
Title Crystal structure of calcium-depleted Bacillus licheniformis alpha-amylase at 2.2 A resolution.
Related PDB 1bpl
Related UniProtKB P06278
[7]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 9163741
Journal Mol Cells
Year 1997
Volume 7
Pages 251-8
Authors Hwang KY, Song HK, Chang C, Lee J, Lee SY, Kim KK, Choe S, Sweet RM, Suh SW
Title Crystal structure of thermostable alpha-amylase from Bacillus licheniformis refined at 1.7 A resolution.
Related PDB 1vjs
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 9401418
Journal Prog Biophys Mol Biol
Year 1997
Volume 67
Pages 67-97
Authors Janecek S
Title alpha-Amylase family: molecular biology and evolution.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 9215572
Journal Protein Eng
Year 1997
Volume 10
Pages 541-9
Authors Declerck N, Machius M, Chambert R, Wiegand G, Huber R, Gaillardin C
Title Hyperthermostable mutants of Bacillus licheniformis alpha-amylase: thermodynamic studies and structural interpretation.
Related PDB
Related UniProtKB
[10]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID 98212915
PubMed ID 9551551
Journal Structure
Year 1998
Volume 6
Pages 281-92
Authors Machius M, Declerck N, Huber R, Wiegand G
Title Activation of Bacillus licheniformis alpha-amylase through a disorder-->order transition of the substrate-binding site mediated by a calcium-sodium-calcium metal triad.
Related PDB 1bli
Related UniProtKB P06278
[11]
Resource
Comments
Medline ID
PubMed ID 10491128
Journal Eur J Biochem
Year 1999
Volume 264
Pages 816-24
Authors Nielsen JE, Beier L, Otzen D, Borchert TV, Frantzen HB, Andersen KV, Svendsen A
Title Electrostatics in the active site of an alpha-amylase.
Related PDB
Related UniProtKB
[12]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 330-512.
Medline ID 20384196
PubMed ID 10924103
Journal Biochemistry
Year 2000
Volume 39
Pages 9099-107
Authors Brzozowski AM, Lawson DM, Turkenburg JP, Bisgaard-Frantzen H, Svendsen A, Borchert TV, Dauter Z, Wilson KS, Davies GJ
Title Structural analysis of a chimeric bacterial alpha-amylase. High-resolution analysis of native and ligand complexes.
Related PDB 1e3x 1e3z 1e40 1e43
Related UniProtKB P06278
[13]
Resource
Comments
Medline ID
PubMed ID 11150610
Journal Biochim Biophys Acta
Year 2000
Volume 1543
Pages 253-274
Authors Nielsen JE, Borchert TV
Title Protein engineering of bacterial alpha-amylases.
Related PDB
Related UniProtKB
[14]
Resource
Comments MUTAGENESIS OF ASP-150; ASN-155; ARG-175; ASP-193; ASN-201; GLN-207; ASN-217; ASN-219; ASN-221; ASP-229; ASP-233; ALA-298; GLU-300; GLN-359 AND GLU-365.
Medline ID
PubMed ID 10966804
Journal J Mol Biol
Year 2000
Volume 301
Pages 1041-57
Authors Declerck N, Machius M, Wiegand G, Huber R, Gaillardin C
Title Probing structural determinants specifying high thermostability in Bacillus licheniformis alpha-amylase.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 11456297
Journal Appl Biochem Biotechnol
Year 2001
Volume 94
Pages 97-109
Authors Khajeh K, Khezre-Barati S, Nemat-Gorgani M
Title Proteolysis of mesophilic and thermophilic alpha-amylases: a comparative study.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 11524019
Journal Biochemistry
Year 2001
Volume 40
Pages 10723-31
Authors Fitter J, Herrmann R, Dencher NA, Blume A, Hauss T
Title Activity and stability of a thermostable alpha-amylase compared to its mesophilic homologue: mechanisms of thermal adaptation.
Related PDB
Related UniProtKB
[17]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID
PubMed ID 11226887
Journal J Biochem (Tokyo)
Year 2001
Volume 129
Pages 461-8
Authors Suvd D, Fujimoto Z, Takase K, Matsumura M, Mizuno H
Title Crystal structure of Bacillus stearothermophilus alpha-amylase: possible factors determining the thermostability.
Related PDB 1hvx
Related UniProtKB P06279
[18]
Resource
Comments
Medline ID
PubMed ID 11994016
Journal Biochemistry
Year 2002
Volume 41
Pages 6193-201
Authors Savchenko A, Vieille C, Kang S, Zeikus JG
Title Pyrococcus furiosus alpha-amylase is stabilized by calcium and zinc.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 11997021
Journal FEBS Lett
Year 2002
Volume 518
Pages 79-82
Authors Kandra L, Gyemant G, Remenyik J, Hovanszki G, Liptak A
Title Action pattern and subsite mapping of Bacillus licheniformis alpha-amylase (BLA) with modified maltooligosaccharide substrates.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 11796168
Journal J Biotechnol
Year 2002
Volume 94
Pages 137-55
Authors van der Maarel MJ, van der Veen B, Uitdehaag JC, Leemhuis H, Dijkhuizen L
Title Properties and applications of starch-converting enzymes of the alpha-amylase family.
Related PDB
Related UniProtKB
[21]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF MUTANT H162V/N219F/A238V/Q293S/N294Y.
Medline ID 22538505
PubMed ID 12540849
Journal J Biol Chem
Year 2003
Volume 278
Pages 11546-53
Authors Machius M, Declerck N, Huber R, Wiegand G
Title Kinetic stabilization of Bacillus licheniformis alpha-amylase through introduction of hydrophobic residues at the surface.
Related PDB 1ob0
Related UniProtKB P06278
[22]
Resource
Comments
Medline ID
PubMed ID 12719434
Journal J Biol Chem
Year 2003
Volume 278
Pages 24818-24
Authors Nonaka T, Fujihashi M, Kita A, Hagihara H, Ozaki K, Ito S, Miki K
Title Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites.
Related PDB
Related UniProtKB
[23]
Resource
Comments MUTAGENESIS OF TRP-292 AND VAL-315.
Medline ID
PubMed ID 12915728
Journal Protein Eng
Year 2003
Volume 16
Pages 505-14
Authors Rivera MH, Lopez-Munguia A, Soberon X, Saab-Rincon G
Title Alpha-amylase from Bacillus licheniformis mutants near to the catalytic site: effects on hydrolytic and transglycosylation activity.
Related PDB
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 15681870
Journal Acta Crystallogr D Biol Crystallogr
Year 2005
Volume 61
Pages 190-3
Authors Davies GJ, Brzozowski AM, Dauter Z, Rasmussen MD, Borchert TV, Wilson KS
Title Structure of a Bacillus halmapalus family 13 alpha-amylase, BHA, in complex with an acarbose-derived nonasaccharide at 2.1 A resolution.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to the glycosyl hydrolase family-13. Although this enzyme binds three calcium ions and a sodium ion, they are not involved in catalytic reaction. The catalytic mechanism of this enzyme must be the same as that of the other alpha-amylase (D00165 in EzCatDB).
####
Chain A and B of PDB;1bpl are parts of the enzyme. Cleaved after GLU 189, chain A is N-terminal side and chain B is C-terminal side.
As 1e3x, 1e3z, 1e40, 1e43 of PDB are chimaeric protein consisting of residues 1-300 of Swiss-prot;P00692(residues 32-331) and residues 301-483 of Swiss-prot;P06278(residues 330-512), these entries are not included in this entry.

Created Updated
2005-04-19 2009-02-26