EzCatDB: D00166

DB codeD00166
RLCP classification1.30.5100.2
CATH domainDomain 13.20.20.80Catalytic domain
Domain 22.60.40.10
E.C.3.2.1.2
CSA1bya

CATH domainRelated DB codes (homologues)
2.60.40.10M00131,T00257,T00005,M00113,M00127,M00132,M00323,M00325,M00327,M00329,M00330,M00331,M00332,T00307,D00500,M00112,M00193,T00063,T00065,T00067,T00245
3.20.20.80S00202,S00210,S00748,S00906,S00907,S00911,S00912,S00915,M00134,M00160,D00479,S00204,S00205,S00206,S00207,S00203,S00208,S00209,S00211,S00213,S00214,M00113,T00307,D00165,D00169,D00176,D00501,D00502,D00503,D00844,D00861,D00864,M00026,M00112,M00193,M00346,T00057,T00062,T00063,T00066,T00067

Enzyme Name
Swiss-protKEGG

P10537P10538P16098P36924
Protein nameBeta-amylaseBeta-amylaseBeta-amylaseBeta-amylasebeta-amylase
saccharogen amylase
glycogenase
beta amylase, beta-amylase
1,4-alpha-D-glucan maltohydrolase
SynonymsEC 3.2.1.2
1,4-alpha-D-glucan maltohydrolase
EC 3.2.1.2
1,4-alpha-D-glucan maltohydrolase
EC 3.2.1.2
1,4-alpha-D-glucan maltohydrolase
EC 3.2.1.2
1,4-alpha-D-glucan maltohydrolase

KEGG pathways
MAP codePathways
MAP00500Starch and sucrose metabolism

Swiss-prot:Accession NumberP10537P10538P16098P36924
Entry nameAMYB_IPOBAAMYB_SOYBNAMYB_HORVUAMYB_BACCE
ActivityHydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides so as to remove successive maltose units from the non-reducing ends of the chains.Hydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides so as to remove successive maltose units from the non-reducing ends of the chains.Hydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides so as to remove successive maltose units from the non-reducing ends of the chains.Hydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides so as to remove successive maltose units from the non-reducing ends of the chains.
SubunitHomotetramer.Monomer.Monomer.Monomer (By similarity).
Subcellular location



Cofactor


Binds 1 calcium ion per subunit.


SubstratesProducts
KEGG-idC00420C00001C00208C01935
CompoundPolysaccharideH2OMaltoseMaltodextrin
TypepolysaccharideH2Opolysaccharidepolysaccharide
1b90A01Unbound
UnboundUnbound
1b9zA01Unbound
Bound:MALBound:MAL
5bcaA01Unbound
UnboundUnbound
5bcaB01Unbound
UnboundUnbound
5bcaC01Unbound
UnboundUnbound
5bcaD01Unbound
UnboundUnbound
1b1yAUnbound
Analogue:GLCBound:GLC-GLC
1bfnAUnbound
UnboundUnbound
1btcAUnbound
UnboundUnbound
1byaAUnbound
UnboundUnbound
1bybABound:GLC-GLC-GLC-GLC
UnboundUnbound
1bycABound:GLC-GLC-GLC-GLC
UnboundUnbound
1bydAUnbound
Analogue:DOMAnalogue:DOM
1fa2AUnbound
UnboundAnalogue:DOM
1b90A02Unbound
UnboundUnbound
1b9zA02Unbound
UnboundUnbound
5bcaA02Unbound
UnboundUnbound
5bcaB02Unbound
UnboundUnbound
5bcaC02Unbound
UnboundUnbound
5bcaD02Unbound
UnboundUnbound

Active-site residues
resource
Swiss-prot;P36924 & PDB;1b90, 1b9z & literature[14]
pdbCatalytic residuesCofactor-binding residues
1b90A01GLU 172;GLU 367
GLU 56;ASP 60;      ;TRP 106;LYS 140;GLU 141;GLU 144(Calcium binding)
1b9zA01GLU 172;GLU 367
GLU 56;ASP 60;GLN 61;       ;       ;GLU 141;GLU 144(Calcium binding)
5bcaA01GLU 172;GLU 367
GLU 56;ASP 60;GLN 61;       ;       ;GLU 141;GLU 144(Calcium binding)
5bcaB01GLU 172;GLU 367
GLU 56;ASP 60;GLN 61;       ;       ;GLU 141;GLU 144(Calcium binding)
5bcaC01GLU 172;GLU 367
GLU 56;ASP 60;GLN 61;       ;LYS 140;GLU 141;GLU 144(Calcium binding)
5bcaD01GLU 172;GLU 367
GLU 56;ASP 60;GLN 61;       ;LYS 140;GLU 141;GLU 144(Calcium binding)
1b1yAGLU 184;GLU 378

1bfnAGLU 186;GLU 380

1btcAGLU 186;GLU 380

1byaAGLU 186;GLU 380

1bybAGLU 186;GLU 380

1bycAGLU 186;GLU 380

1bydAGLU 186;GLU 380

1fa2AGLU 187;GLU 382

1b90A02

1b9zA02

5bcaA02

5bcaB02

5bcaC02

5bcaD02


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]Scheme 2, p.5948-59491
[3]p.28
[7]p.7786-7787
[19]Scheme 2, p.5892

references
[1]
PubMed ID156183
JournalJ Biol Chem
Year1979
Volume254
Pages5942-50
AuthorsHehre EJ, Brewer CF, Genghof DS
TitleScope and mechanism of carbohydrase action. Hydrolytic and nonhydrolytic actions of beta-amylase on alpha- and beta-maltosyl fluoride.
[2]
PubMed ID2449255
JournalBiopolymers
Year1988
Volume27
Pages123-38
AuthorsHenis YI, Yaron T, Lamed R, Rishpon J, Sahar E, Katchalski-Katzir E
TitleMobility of enzymes on insoluble substrates: the beta-amylase-starch gel system.
[3]
PubMed ID1476373
JournalAnn N Y Acad Sci
Year1992
Volume672
Pages24-8
AuthorsUozumi N
TitleFunctional roles of active site residues of Bacillus polymyxa beta-amylase.
[4]
PubMed ID1491009
JournalJ Biochem (Tokyo)
Year1992
Volume112
Pages541-6
AuthorsMikami B, Sato M, Shibata T, Hirose M, Aibara S, Katsube Y, Morita Y
TitleThree-dimensional structure of soybean beta-amylase determined at 3.0 A resolution: preliminary chain tracing of the complex with alpha-cyclodextrin.
Related Swiss-protP10538
[5]
PubMed ID8334116
JournalBiochemistry
Year1993
Volume32
Pages6836-45
AuthorsMikami B, Hehre EJ, Sato M, Katsube Y, Hirose M, Morita Y, Sacchettini JC
TitleThe 2.0-A resolution structure of soybean beta-amylase complexed with alpha-cyclodextrin.
Related PDB1bya,1byb,1byc,1byd
Related Swiss-protP10538
[6]
PubMed ID8174545
JournalEur J Biochem
Year1994
Volume221
Pages649-54
AuthorsTotsuka A, Nong VH, Kadokawa H, Kim CS, Itoh Y, Fukazawa C
TitleResidues essential for catalytic activity of soybean beta-amylase.
Related Swiss-protP10538
[7]
PubMed ID8011643
JournalBiochemistry
Year1994
Volume33
Pages7779-87
AuthorsMikami B, Degano M, Hehre EJ, Sacchettini JC
TitleCrystal structures of soybean beta-amylase reacted with beta-maltose and maltal: active site components and their apparent roles in catalysis.
Related PDB1fa2
Related Swiss-protP10537
[8]
PubMed ID7777485
JournalProteins
Year1995
Volume21
Pages105-17
AuthorsCheong CG, Eom SH, Chang C, Shin DH, Song HK, Min K, Moon JH, Kim KK, Hwang KY, Suh SW
TitleCrystallization, molecular replacement solution, and refinement of tetrameric beta-amylase from sweet potato.
[9]
PubMed ID8720125
JournalJ Biochem (Tokyo)
Year1995
Volume118
Pages1124-30
AuthorsNomura K, Yoneda I, Nanmori T, Shinke R, Morita Y, Mikami B
TitleThe role of SH and S-S groups in Bacillus cereus beta-amylase.
[10]
PubMed ID9677422
JournalJ Biol Chem
Year1998
Volume273
Pages19859-65
AuthorsAdachi M, Mikami B, Katsube T, Utsumi S
TitleCrystal structure of recombinant soybean beta-amylase complexed with beta-cyclodextrin.
Related PDB1bfn
Related Swiss-protP10538
[11]
PubMed ID9918723
JournalJ Mol Biol
Year1999
Volume285
Pages1235-43
AuthorsMikami B, Yoon HJ, Yoshigi N
TitleThe crystal structure of the sevenfold mutant of barley beta-amylase with increased thermostability at 2.5 A resolution.
Related Swiss-protP16098
[12]
CommentsX-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS)
PubMed ID10353816
JournalBiochemistry
Year1999
Volume38
Pages7050-61
AuthorsMikami B, Adachi M, Kage T, Sarikaya E, Nanmori T, Shinke R, Utsumi S
TitleStructure of raw starch-digesting Bacillus cereus beta-amylase complexed with maltose.
Related PDB1b90,1b9z
Related Swiss-protP36924
[13]
PubMed ID10452542
JournalFEBS Lett
Year1999
Volume456
Pages119-25
AuthorsJanecek S, Sevcik J
TitleThe evolution of starch-binding domain.
[14]
CommentsX-ray crystallography
PubMed ID10348915
JournalJ Biochem (Tokyo)
Year1999
Volume125
Pages1120-30
AuthorsOyama T, Kusunoki M, Kishimoto Y, Takasaki Y, Nitta Y
TitleCrystal structure of beta-amylase from Bacillus cereus var. mycoides at 2.2 A resolution.
Related PDB5bca
[15]
PubMed ID11468361
JournalProtein Sci
Year2001
Volume10
Pages1645-57
AuthorsPujadas G, Palau J
TitleMolecular mimicry of substrate oxygen atoms by water molecules in the beta-amylase active site.
[16]
PubMed ID11733023
JournalEur J Biochem
Year2001
Volume268
Pages6263-73
AuthorsVan Damme EJ, Hu J, Barre A, Hause B, Baggerman G, Rouge P, Peumans WJ
TitlePurification, characterization, immunolocalization and structural analysis of the abundant cytoplasmic beta-amylase from Calystegia sepium (hedge bindweed) rhizomes.
[17]
PubMed ID11508823
JournalGen Physiol Biophys
Year2001
Volume20
Pages7-32
AuthorsHorvathova V, Janecek S, Sturdik E
TitleAmylolytic enzymes: molecular aspects of their properties.
[18]
PubMed ID11713664
JournalMol Genet Genomics
Year2001
Volume266
Pages345-52
AuthorsMa YF, Evans DE, Logue SJ, Langridge P
TitleMutations of barley beta-amylase that improve substrate-binding affinity and thermostability.
[19]
PubMed ID11926997
JournalJ Biochem (Tokyo)
Year2002
Volume131
Pages587-91
AuthorsMiyake H, Otsuka C, Nishimura S, Nitta Y
TitleCatalytic mechanism of beta-amylase from Bacillus cereus var. mycoides: chemical rescue of hydrolytic activity for a catalytic site mutant (Glu367-->Ala) by azide.

comments
This enzyme belongs to the glycosyl hydrolase family-14. This is an inverting enzyme that hydrolyzes the alpha-1,4-glucosidic linkage of a substrate, producing the beta-anomer of maltose.
Although the catalytic domain binds calcium ion, the ion does not contribute to the catalysis as a cofactor.
According to the literature [19], Glu367 (PDB, 1b90) acts as a general base, whilst Glu172 acts as a general acid. At the first step, the general acid, Glu172, protonates the leaving oxygen atom of the glycosidic linkage, resulting in the formation of carbonium ion intermediate. At the next stage, the general base, Glu367, abstracts the proton from a nearby water molecule to produce an activated hydroxide ion, which makes a nucleophilic attack on the carbonium ion intermediate to produce beta-maltose.

createdupdated
2004-04-012009-02-26
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 2010)
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)

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