DB code: D00166

RLCP classification 1.30.5100.2 : Hydrolysis
CATH domain 3.20.20.80 : TIM Barrel Catalytic domain
2.60.40.10 : Immunoglobulin-like
E.C. 3.2.1.2
CSA 1bya
M-CSA 1bya
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 D00165 D00169 D00176 D00501 D00502 D00503 D00844 D00861 D00864 M00026 M00112 M00193 M00346 T00057 T00062 T00063 T00066 T00067
2.60.40.10 : Immunoglobulin-like M00131 T00257 T00005 M00113 M00127 M00132 M00323 M00325 M00327 M00329 M00330 M00331 M00332 T00307 D00500 M00112 M00193 T00063 T00065 T00067 T00245

Uniprot Enzyme Name
UniprotKB Protein name Synonyms CAZy Pfam RefSeq
P10537 Beta-amylase
EC 3.2.1.2
1,4-alpha-D-glucan maltohydrolase
GH14 (Glycoside Hydrolase Family 14)
PF01373 (Glyco_hydro_14)
[Graphical View]
P10538 Beta-amylase
EC 3.2.1.2
1,4-alpha-D-glucan maltohydrolase
GH14 (Glycoside Hydrolase Family 14)
PF01373 (Glyco_hydro_14)
[Graphical View]
NP_001236247.1 (Protein)
NM_001249318.1 (DNA/RNA sequence)
P16098 Beta-amylase
EC 3.2.1.2
1,4-alpha-D-glucan maltohydrolase
GH14 (Glycoside Hydrolase Family 14)
PF01373 (Glyco_hydro_14)
[Graphical View]
P36924 Beta-amylase
EC 3.2.1.2
1,4-alpha-D-glucan maltohydrolase
CBM20 (Carbohydrate-Binding Module Family 20)
GH14 (Glycoside Hydrolase Family 14)
PF00686 (CBM_20)
PF01373 (Glyco_hydro_14)
[Graphical View]

KEGG enzyme name
beta-amylase
saccharogen amylase
glycogenase
beta amylase, beta-amylase
1,4-alpha-D-glucan maltohydrolase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P10537 AMYB_IPOBA 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. Homotetramer.
P10538 AMYB_SOYBN 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. Monomer.
P16098 AMYB_HORVU 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. Monomer.
P36924 AMYB_BACCE 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. Monomer (By similarity). Binds 1 calcium ion per subunit.

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

Compound table
Substrates Products Intermediates
KEGG-id C00420 C00001 C00208 C01935
E.C.
Compound Polysaccharide H2O Maltose Maltodextrin
Type polysaccharide H2O polysaccharide polysaccharide
ChEBI 15377
17306
PubChem 871
22247451
962
439186
1b90A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1b9zA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:MAL Bound:MAL
5bcaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
5bcaB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
5bcaC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
5bcaD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1b1yA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:GLC Bound:GLC-GLC
1bfnA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1btcA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1byaA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1bybA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:GLC-GLC-GLC-GLC Unbound Unbound
1bycA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:GLC-GLC-GLC-GLC Unbound Unbound
1bydA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:DOM Analogue:DOM
1fa2A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:DOM
1b90A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1b9zA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
5bcaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
5bcaB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
5bcaC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
5bcaD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P36924 & PDB;1b90, 1b9z & literature[14]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1b90A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 172;GLU 367 GLU 56;ASP 60; ;TRP 106;LYS 140;GLU 141;GLU 144(Calcium binding)
1b9zA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 172;GLU 367 GLU 56;ASP 60;GLN 61; ; ;GLU 141;GLU 144(Calcium binding)
5bcaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 172;GLU 367 GLU 56;ASP 60;GLN 61; ; ;GLU 141;GLU 144(Calcium binding)
5bcaB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 172;GLU 367 GLU 56;ASP 60;GLN 61; ; ;GLU 141;GLU 144(Calcium binding)
5bcaC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 172;GLU 367 GLU 56;ASP 60;GLN 61; ;LYS 140;GLU 141;GLU 144(Calcium binding)
5bcaD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 172;GLU 367 GLU 56;ASP 60;GLN 61; ;LYS 140;GLU 141;GLU 144(Calcium binding)
1b1yA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 184;GLU 378
1bfnA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 186;GLU 380
1btcA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 186;GLU 380
1byaA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 186;GLU 380
1bybA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 186;GLU 380
1bycA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 186;GLU 380
1bydA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 186;GLU 380
1fa2A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 187;GLU 382
1b90A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1b9zA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
5bcaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
5bcaB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
5bcaC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
5bcaD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
Scheme 2, p.5948-5949 1
[3]
p.28
[7]
p.7786-7787
[19]
Scheme 2, p.589 2

References
[1]
Resource
Comments
Medline ID
PubMed ID 156183
Journal J Biol Chem
Year 1979
Volume 254
Pages 5942-50
Authors Hehre EJ, Brewer CF, Genghof DS
Title Scope and mechanism of carbohydrase action. Hydrolytic and nonhydrolytic actions of beta-amylase on alpha- and beta-maltosyl fluoride.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 2449255
Journal Biopolymers
Year 1988
Volume 27
Pages 123-38
Authors Henis YI, Yaron T, Lamed R, Rishpon J, Sahar E, Katchalski-Katzir E
Title Mobility of enzymes on insoluble substrates: the beta-amylase-starch gel system.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 1476373
Journal Ann N Y Acad Sci
Year 1992
Volume 672
Pages 24-8
Authors Uozumi N
Title Functional roles of active site residues of Bacillus polymyxa beta-amylase.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 1491009
Journal J Biochem (Tokyo)
Year 1992
Volume 112
Pages 541-6
Authors Mikami B, Sato M, Shibata T, Hirose M, Aibara S, Katsube Y, Morita Y
Title Three-dimensional structure of soybean beta-amylase determined at 3.0 A resolution: preliminary chain tracing of the complex with alpha-cyclodextrin.
Related PDB
Related UniProtKB P10538
[5]
Resource
Comments
Medline ID
PubMed ID 8334116
Journal Biochemistry
Year 1993
Volume 32
Pages 6836-45
Authors Mikami B, Hehre EJ, Sato M, Katsube Y, Hirose M, Morita Y, Sacchettini JC
Title The 2.0-A resolution structure of soybean beta-amylase complexed with alpha-cyclodextrin.
Related PDB 1bya 1byb 1byc 1byd
Related UniProtKB P10538
[6]
Resource
Comments
Medline ID
PubMed ID 8174545
Journal Eur J Biochem
Year 1994
Volume 221
Pages 649-54
Authors Totsuka A, Nong VH, Kadokawa H, Kim CS, Itoh Y, Fukazawa C
Title Residues essential for catalytic activity of soybean beta-amylase.
Related PDB
Related UniProtKB P10538
[7]
Resource
Comments
Medline ID
PubMed ID 8011643
Journal Biochemistry
Year 1994
Volume 33
Pages 7779-87
Authors Mikami B, Degano M, Hehre EJ, Sacchettini JC
Title Crystal structures of soybean beta-amylase reacted with beta-maltose and maltal: active site components and their apparent roles in catalysis.
Related PDB 1fa2
Related UniProtKB P10537
[8]
Resource
Comments
Medline ID
PubMed ID 7777485
Journal Proteins
Year 1995
Volume 21
Pages 105-17
Authors Cheong CG, Eom SH, Chang C, Shin DH, Song HK, Min K, Moon JH, Kim KK, Hwang KY, Suh SW
Title Crystallization, molecular replacement solution, and refinement of tetrameric beta-amylase from sweet potato.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 8720125
Journal J Biochem (Tokyo)
Year 1995
Volume 118
Pages 1124-30
Authors Nomura K, Yoneda I, Nanmori T, Shinke R, Morita Y, Mikami B
Title The role of SH and S-S groups in Bacillus cereus beta-amylase.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 9677422
Journal J Biol Chem
Year 1998
Volume 273
Pages 19859-65
Authors Adachi M, Mikami B, Katsube T, Utsumi S
Title Crystal structure of recombinant soybean beta-amylase complexed with beta-cyclodextrin.
Related PDB 1bfn
Related UniProtKB P10538
[11]
Resource
Comments
Medline ID
PubMed ID 9918723
Journal J Mol Biol
Year 1999
Volume 285
Pages 1235-43
Authors Mikami B, Yoon HJ, Yoshigi N
Title The crystal structure of the sevenfold mutant of barley beta-amylase with increased thermostability at 2.5 A resolution.
Related PDB
Related UniProtKB P16098
[12]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS)
Medline ID
PubMed ID 10353816
Journal Biochemistry
Year 1999
Volume 38
Pages 7050-61
Authors Mikami B, Adachi M, Kage T, Sarikaya E, Nanmori T, Shinke R, Utsumi S
Title Structure of raw starch-digesting Bacillus cereus beta-amylase complexed with maltose.
Related PDB 1b90 1b9z
Related UniProtKB P36924
[13]
Resource
Comments
Medline ID
PubMed ID 10452542
Journal FEBS Lett
Year 1999
Volume 456
Pages 119-25
Authors Janecek S, Sevcik J
Title The evolution of starch-binding domain.
Related PDB
Related UniProtKB
[14]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10348915
Journal J Biochem (Tokyo)
Year 1999
Volume 125
Pages 1120-30
Authors Oyama T, Kusunoki M, Kishimoto Y, Takasaki Y, Nitta Y
Title Crystal structure of beta-amylase from Bacillus cereus var. mycoides at 2.2 A resolution.
Related PDB 5bca
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 11468361
Journal Protein Sci
Year 2001
Volume 10
Pages 1645-57
Authors Pujadas G, Palau J
Title Molecular mimicry of substrate oxygen atoms by water molecules in the beta-amylase active site.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 11733023
Journal Eur J Biochem
Year 2001
Volume 268
Pages 6263-73
Authors Van Damme EJ, Hu J, Barre A, Hause B, Baggerman G, Rouge P, Peumans WJ
Title Purification, characterization, immunolocalization and structural analysis of the abundant cytoplasmic beta-amylase from Calystegia sepium (hedge bindweed) rhizomes.
Related PDB
Related UniProtKB
[17]
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
[18]
Resource
Comments
Medline ID
PubMed ID 11713664
Journal Mol Genet Genomics
Year 2001
Volume 266
Pages 345-52
Authors Ma YF, Evans DE, Logue SJ, Langridge P
Title Mutations of barley beta-amylase that improve substrate-binding affinity and thermostability.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 11926997
Journal J Biochem (Tokyo)
Year 2002
Volume 131
Pages 587-91
Authors Miyake H, Otsuka C, Nishimura S, Nitta Y
Title Catalytic mechanism of beta-amylase from Bacillus cereus var. mycoides: chemical rescue of hydrolytic activity for a catalytic site mutant (Glu367-->Ala) by azide.
Related PDB
Related UniProtKB

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.

Created Updated
2004-04-01 2009-02-26