DB code: D00166

RLCP classification	1.30.5100.2 : Hydrolysis
CATH domain	3.20.20.80 : TIM Barrel	Catalytic domain
CATH 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)
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
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

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	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 15377	17306 17306
PubChem	871 871	22247451 962 22247451 962	439186 439186

1b90A01	Unbound		Unbound	Unbound
1b9zA01	Unbound		Bound:MAL	Bound:MAL
5bcaA01	Unbound		Unbound	Unbound
5bcaB01	Unbound		Unbound	Unbound
5bcaC01	Unbound		Unbound	Unbound
5bcaD01	Unbound		Unbound	Unbound
1b1yA	Unbound		Analogue:GLC	Bound:GLC-GLC
1bfnA	Unbound		Unbound	Unbound
1btcA	Unbound		Unbound	Unbound
1byaA	Unbound		Unbound	Unbound
1bybA	Bound:GLC-GLC-GLC-GLC		Unbound	Unbound
1bycA	Bound:GLC-GLC-GLC-GLC		Unbound	Unbound
1bydA	Unbound		Analogue:DOM	Analogue:DOM
1fa2A	Unbound		Unbound	Analogue:DOM
1b90A02	Unbound		Unbound	Unbound
1b9zA02	Unbound		Unbound	Unbound
5bcaA02	Unbound		Unbound	Unbound
5bcaB02	Unbound		Unbound	Unbound
5bcaC02	Unbound		Unbound	Unbound
5bcaD02	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	GLU 172;GLU 367	GLU 56;ASP 60; ;TRP 106;LYS 140;GLU 141;GLU 144(Calcium binding)
1b9zA01	GLU 172;GLU 367	GLU 56;ASP 60;GLN 61; ; ;GLU 141;GLU 144(Calcium binding)
5bcaA01	GLU 172;GLU 367	GLU 56;ASP 60;GLN 61; ; ;GLU 141;GLU 144(Calcium binding)
5bcaB01	GLU 172;GLU 367	GLU 56;ASP 60;GLN 61; ; ;GLU 141;GLU 144(Calcium binding)
5bcaC01	GLU 172;GLU 367	GLU 56;ASP 60;GLN 61; ;LYS 140;GLU 141;GLU 144(Calcium binding)
5bcaD01	GLU 172;GLU 367	GLU 56;ASP 60;GLN 61; ;LYS 140;GLU 141;GLU 144(Calcium binding)
1b1yA	GLU 184;GLU 378
1bfnA	GLU 186;GLU 380
1btcA	GLU 186;GLU 380
1byaA	GLU 186;GLU 380
1bybA	GLU 186;GLU 380
1bycA	GLU 186;GLU 380
1bydA	GLU 186;GLU 380
1fa2A	GLU 187;GLU 382
1b90A02
1b9zA02
5bcaA02
5bcaB02
5bcaC02
5bcaD02

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.

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