EzCatDB: T00057
Related links:    PDB-formatted query search system Fasta-formatted query search system Fasta-formatted query search system

DB codeT00057
RLCP classification1.30.36000.3 : Hydrolysis
CATH domainDomain 13.20.20.80 : TIM BarrelCatalytic domain
Domain 22.40.31.10
Domain 32.60.40.1180 : Immunoglobulin-like
E.C.3.2.1.1

CATH domainRelated DB codes (homologues)
2.60.40.1180 : Immunoglobulin-likeM00113,T00307,D00165,D00176,D00664,D00665,D00863,D00864,M00112,M00193,M00314,T00062,T00067
3.20.20.80 : TIM BarrelS00202,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

Enzyme Name
UniProtKBKEGG

P06278P06279
Protein nameAlpha-amylaseAlpha-amylasealpha-amylase
glycogenase
alpha amylase, alpha-amylase
endoamylase
Taka-amylase A
1,4-alpha-D-glucan glucanohydrolase
SynonymsEC 3.2.1.1
1,4-alpha-D-glucan glucanohydrolase
BLA
EC 3.2.1.1
1,4-alpha-D-glucan glucanohydrolase
PfamPF00128 (Alpha-amylase)
PF09154 (DUF1939)
[Graphical view]
PF00128 (Alpha-amylase)
PF09154 (DUF1939)
[Graphical view]
CAZyGH13 (Glycoside Hydrolase Family)
GH13 (Glycoside Hydrolase Family)

KEGG pathways
MAP codePathways
MAP00500Starch and sucrose metabolism

UniProtKB:Accession NumberP06278P06279
Entry nameAMY_BACLIAMY_BACST
ActivityEndohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides.Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides.
SubunitMonomer.Monomer.
Subcellular location

CofactorBinds 3 calcium ions per subunit.,Binds 1 sodium ion per subunit.Binds 3 calcium ions per subunit.,Binds 1 sodium ion per subunit.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00076C01330C00420C00001C00930
CompoundCalciumSodiumPolysaccharideH2OOligosaccharide
Typedivalent metal (Ca2+, Mg2+)univalent metal (Na+, K+)polysaccharideH2Opolysaccharide
ChEBI29108
29101

15377

PubChem271
923
871
962
22247451

             
1bplBUnboundUnboundUnbound Unbound
1bliA01Bound:2x_CAUnboundUnbound Unbound
1ob0A01Bound:2x_CAUnboundUnbound Unbound
1vjsA01UnboundUnboundUnbound Unbound
1hvxA01Bound:3x_CABound:_NAUnbound Unbound
1bplAUnboundUnboundUnbound Unbound
1bliA02Bound:2x_CABound:_NAUnbound Unbound
1ob0A02Bound:2x_CABound:_NAUnbound Unbound
1vjsA02UnboundUnboundUnbound Unbound
1hvxA03Bound:_CABound:_NAUnbound Unbound
1bliA03Bound:_CAUnboundUnbound Unbound
1ob0A03Bound:_CAUnboundUnbound Unbound
1vjsA03UnboundUnboundUnbound Unbound
1hvxA02Bound:_CAUnboundUnbound Unbound

Active-site residues
resource
PDB;1bli, 1hvx & Swiss-prot;P06278, P06279 & literature [11],[17]
pdbCatalytic residuesCofactor-binding residuescomment
           
1bplBASP 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)
 
1bliA01ASP 231;GLU 261;ASP 328
ASN 104;HIS 235(Calcium-1 binding);GLY 300(Calcium-3 binding)
 
1ob0A01ASP 231;GLU 261;ASP 328
ASN 104;HIS 235(Calcium-1 binding);GLY 300(Calcium-3 binding)
mutant A209V, Q264S, N265Y
1vjsA01ASP 231;GLU 261;ASP 328
ASN 104;HIS 235(Calcium-1 binding);GLY 300(Calcium-3 binding)
 
1hvxA01ASP 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 
ASN 104;(Calcium-1 binding);ASP 161;ALA 181;       (Calcium-2 binding);ASP 161;       (Sodium binding)
invisible D183
1bliA02 
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 
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 
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 
ASP 162;ALA 184;ASP 186(Calcium-2 binding);ASP 162;ASP 186(Sodium binding)
 
1bliA03 
HIS 406;ASP 407;ASP 430(Calcium-3 binding)
 
1ob0A03 
HIS 406;ASP 407;ASP 430(Calcium-3 binding)
 
1vjsA03 
HIS 406;ASP 407;ASP 430(Calcium-3 binding)
 
1hvxA02 
SER 406;ASP 407;ASP 430(Calcium-3 binding)
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]p.187-188
[11]Fig.2
[12]p.9106
[13]Fig.5, p.261-264

references
[1]
PubMed ID3125174
JournalJ Biol Chem
Year1988
Volume263
Pages3092-6
AuthorsTomazic SJ, Klibanov AM
TitleWhy is one Bacillus alpha-amylase more resistant against irreversible thermoinactivation than another?
[2]
PubMed ID2277029
JournalJ Biochem (Tokyo)
Year1990
Volume108
Pages379-81
AuthorsSuzuki A, Yamane T, Ito Y, Nishio T, Fujiwara H, Ashida T
TitleCrystallization and preliminary crystallographic study of bacterial alpha-amylases.
[3]
PubMed ID2330367
JournalProtein Eng
Year1990
Volume3
Pages181-91
AuthorsHolm L, Koivula AK, Lehtovaara PM, Hemminki A, Knowles JK
TitleRandom mutagenesis used to probe the structure and function of Bacillus stearothermophilus alpha-amylase.
[4]
PubMed ID1952938
JournalArch Biochem Biophys
Year1991
Volume291
Pages255-7
AuthorsLee SY, Kim S, Sweet RM, Suh SW
TitleCrystallization and a preliminary X-ray crystallographic study of alpha-amylase from Bacillus licheniformis.
[5]
PubMed ID7926034
JournalFEBS Lett
Year1994
Volume353
Pages119-23
AuthorsJanecek S
TitleParallel 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.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
Medline ID95182462
PubMed ID7877175
JournalJ Mol Biol
Year1995
Volume246
Pages545-59
AuthorsMachius M, Wiegand G, Huber R
TitleCrystal structure of calcium-depleted Bacillus licheniformis alpha-amylase at 2.2 A resolution.
Related PDB1bpl
Related UniProtKBP06278
[7]
CommentsX-ray crystallography
PubMed ID9163741
JournalMol Cells
Year1997
Volume7
Pages251-8
AuthorsHwang KY, Song HK, Chang C, Lee J, Lee SY, Kim KK, Choe S, Sweet RM, Suh SW
TitleCrystal structure of thermostable alpha-amylase from Bacillus licheniformis refined at 1.7 A resolution.
Related PDB1vjs
[8]
PubMed ID9401418
JournalProg Biophys Mol Biol
Year1997
Volume67
Pages67-97
AuthorsJanecek S
Titlealpha-Amylase family: molecular biology and evolution.
[9]
PubMed ID9215572
JournalProtein Eng
Year1997
Volume10
Pages541-9
AuthorsDeclerck N, Machius M, Chambert R, Wiegand G, Huber R, Gaillardin C
TitleHyperthermostable mutants of Bacillus licheniformis alpha-amylase: thermodynamic studies and structural interpretation.
[10]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID98212915
PubMed ID9551551
JournalStructure
Year1998
Volume6
Pages281-92
AuthorsMachius M, Declerck N, Huber R, Wiegand G
TitleActivation of Bacillus licheniformis alpha-amylase through a disorder-->order transition of the substrate-binding site mediated by a calcium-sodium-calcium metal triad.
Related PDB1bli
Related UniProtKBP06278
[11]
PubMed ID10491128
JournalEur J Biochem
Year1999
Volume264
Pages816-24
AuthorsNielsen JE, Beier L, Otzen D, Borchert TV, Frantzen HB, Andersen KV, Svendsen A
TitleElectrostatics in the active site of an alpha-amylase.
[12]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 330-512.
Medline ID20384196
PubMed ID10924103
JournalBiochemistry
Year2000
Volume39
Pages9099-107
AuthorsBrzozowski AM, Lawson DM, Turkenburg JP, Bisgaard-Frantzen H, Svendsen A, Borchert TV, Dauter Z, Wilson KS, Davies GJ
TitleStructural analysis of a chimeric bacterial alpha-amylase. High-resolution analysis of native and ligand complexes.
Related PDB1e3x,1e3z,1e40,1e43
Related UniProtKBP06278
[13]
PubMed ID11150610
JournalBiochim Biophys Acta
Year2000
Volume1543
Pages253-274
AuthorsNielsen JE, Borchert TV
TitleProtein engineering of bacterial alpha-amylases.
[14]
CommentsMUTAGENESIS 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.
PubMed ID10966804
JournalJ Mol Biol
Year2000
Volume301
Pages1041-57
AuthorsDeclerck N, Machius M, Wiegand G, Huber R, Gaillardin C
TitleProbing structural determinants specifying high thermostability in Bacillus licheniformis alpha-amylase.
[15]
PubMed ID11456297
JournalAppl Biochem Biotechnol
Year2001
Volume94
Pages97-109
AuthorsKhajeh K, Khezre-Barati S, Nemat-Gorgani M
TitleProteolysis of mesophilic and thermophilic alpha-amylases: a comparative study.
[16]
PubMed ID11524019
JournalBiochemistry
Year2001
Volume40
Pages10723-31
AuthorsFitter J, Herrmann R, Dencher NA, Blume A, Hauss T
TitleActivity and stability of a thermostable alpha-amylase compared to its mesophilic homologue: mechanisms of thermal adaptation.
[17]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
PubMed ID11226887
JournalJ Biochem (Tokyo)
Year2001
Volume129
Pages461-8
AuthorsSuvd D, Fujimoto Z, Takase K, Matsumura M, Mizuno H
TitleCrystal structure of Bacillus stearothermophilus alpha-amylase: possible factors determining the thermostability.
Related PDB1hvx
Related UniProtKBP06279
[18]
PubMed ID11994016
JournalBiochemistry
Year2002
Volume41
Pages6193-201
AuthorsSavchenko A, Vieille C, Kang S, Zeikus JG
TitlePyrococcus furiosus alpha-amylase is stabilized by calcium and zinc.
[19]
PubMed ID11997021
JournalFEBS Lett
Year2002
Volume518
Pages79-82
AuthorsKandra L, Gyemant G, Remenyik J, Hovanszki G, Liptak A
TitleAction pattern and subsite mapping of Bacillus licheniformis alpha-amylase (BLA) with modified maltooligosaccharide substrates.
[20]
PubMed ID11796168
JournalJ Biotechnol
Year2002
Volume94
Pages137-55
Authorsvan der Maarel MJ, van der Veen B, Uitdehaag JC, Leemhuis H, Dijkhuizen L
TitleProperties and applications of starch-converting enzymes of the alpha-amylase family.
[21]
CommentsX-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF MUTANT H162V/N219F/A238V/Q293S/N294Y.
Medline ID22538505
PubMed ID12540849
JournalJ Biol Chem
Year2003
Volume278
Pages11546-53
AuthorsMachius M, Declerck N, Huber R, Wiegand G
TitleKinetic stabilization of Bacillus licheniformis alpha-amylase through introduction of hydrophobic residues at the surface.
Related PDB1ob0
Related UniProtKBP06278
[22]
PubMed ID12719434
JournalJ Biol Chem
Year2003
Volume278
Pages24818-24
AuthorsNonaka T, Fujihashi M, Kita A, Hagihara H, Ozaki K, Ito S, Miki K
TitleCrystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites.
[23]
CommentsMUTAGENESIS OF TRP-292 AND VAL-315.
PubMed ID12915728
JournalProtein Eng
Year2003
Volume16
Pages505-14
AuthorsRivera MH, Lopez-Munguia A, Soberon X, Saab-Rincon G
TitleAlpha-amylase from Bacillus licheniformis mutants near to the catalytic site: effects on hydrolytic and transglycosylation activity.
[24]
PubMed ID15681870
JournalActa Crystallogr D Biol Crystallogr
Year2005
Volume61
Pages190-3
AuthorsDavies GJ, Brzozowski AM, Dauter Z, Rasmussen MD, Borchert TV, Wilson KS
TitleStructure of a Bacillus halmapalus family 13 alpha-amylase, BHA, in complex with an acarbose-derived nonasaccharide at 2.1 A resolution.

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.

createdupdated
2005-04-192009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
© Biotechnology Research Institute for Drug Discovery, AIST, 2015-2016 All Rights Reserved.
© Computational Biology Research Center, AIST, 2004-2016 All Rights Reserved.