DB code: T00307

RLCP classification 3.900.275800.990 : Transfer
CATH domain 2.60.40.10 : Immunoglobulin-like
3.20.20.80 : TIM Barrel Catalytic domain
2.60.40.1180 : Immunoglobulin-like
E.C. 2.4.1.18
CSA
M-CSA
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 D00166 D00500 M00112 M00193 T00063 T00065 T00067 T00245
2.60.40.1180 : Immunoglobulin-like M00113 D00165 D00176 D00664 D00665 D00863 D00864 M00112 M00193 M00314 T00057 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 D00165 D00166 D00169 D00176 D00501 D00502 D00503 D00844 D00861 D00864 M00026 M00112 M00193 M00346 T00057 T00062 T00063 T00066 T00067

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq CAZy Pfam
P07762 1,4-alpha-glucan branching enzyme GlgB
EC 2.4.1.18
1,4-alpha-D-glucan:1,4-alpha-D-glucan 6-glucosyl-transferase
Alpha-(1->4)-glucan branching enzyme
Glycogen branching enzyme
BE
NP_417890.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_492001.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
CBM48 (Carbohydrate-Binding Module Family 48)
GH13 (Glycoside Hydrolase Family 13)
PF00128 (Alpha-amylase)
PF02806 (Alpha-amylase_C)
PF02922 (CBM_48)
[Graphical View]
Q10625 1,4-alpha-glucan branching enzyme GlgB
EC 2.4.1.18
1,4-alpha-D-glucan:1,4-alpha-D-glucan 6-glucosyl-transferase
Alpha-(1->4)-glucan branching enzyme
Glycogen-branching enzyme
BE
NP_215842.1 (Protein)
NC_000962.3 (DNA/RNA sequence)
NP_335818.1 (Protein)
NC_002755.2 (DNA/RNA sequence)
YP_006514704.1 (Protein)
NC_018143.1 (DNA/RNA sequence)
CBM48 (Carbohydrate-Binding Module Family 48)
GH13 (Glycoside Hydrolase Family 13)
PF00128 (Alpha-amylase)
PF02806 (Alpha-amylase_C)
PF02922 (CBM_48)
[Graphical View]
Q01401 1,4-alpha-glucan-branching enzyme, chloroplastic/amyloplastic
EC 2.4.1.18
Q-enzyme
Starch-branching enzyme
NP_001058629.1 (Protein)
NM_001065164.1 (DNA/RNA sequence)
CBM48 (Carbohydrate-Binding Module Family 48)
GH13 (Glycoside Hydrolase Family 13)
PF00128 (Alpha-amylase)
PF02806 (Alpha-amylase_C)
PF02922 (CBM_48)
[Graphical View]

KEGG enzyme name
1,4-alpha-glucan branching enzyme
Branching enzyme
Amylo-(1,4->1,6)-transglycosylase
Q-enzyme
Alpha-glucan-branching glycosyltransferase
Amylose isomerase
Enzymatic branching factor
Branching glycosyltransferase
Enzyme Q
Glucosan transglycosylase
Glycogen branching enzyme
Plant branching enzyme
Alpha-1,4-glucan:alpha-1,4-glucan-6-glycosyltransferase
Starch branching enzyme

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P07762 GLGB_ECOLI Transfers a segment of a (1->4)-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain. Monomer.
Q10625 GLGB_MYCTU Transfers a segment of a (1->4)-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain. Monomer.
Q01401 GLGB_ORYSJ Transfers a segment of a (1->4)-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain. Monomer. Plastid, chloroplast. Plastid, amyloplast.

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

Compound table
Substrates Products Intermediates
KEGG-id C00718 C00182
E.C.
Compound Amylose Glycogen
Type polysaccharide polysaccharide
ChEBI 28087
PubChem 439177
1m7xA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1m7xB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1m7xC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1m7xD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7yA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7yB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7yC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7yD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7zA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7zB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7zC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7zD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3k1dA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3amkA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3amlA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1m7xA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1m7xB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1m7xC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1m7xD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7yA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7yB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7yC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7yD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7zA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7zB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7zC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7zD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3k1dA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3amkA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3amlA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1m7xA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1m7xB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1m7xC03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1m7xD03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7yA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7yB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7yC03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7yD03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7zA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7zB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7zC03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3o7zD03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3k1dA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3amkA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
3amlA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound

Reference for Active-site residues
resource references E.C.
Literature [7], [13] & Swiss-prot;P07762, Q10625

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1m7xA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1m7xB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1m7xC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1m7xD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3o7yA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3o7yB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3o7yC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3o7yD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3o7zA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3o7zB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3o7zC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3o7zD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3k1dA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3amkA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3amlA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1m7xA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 405;GLU 458;HIS 525;ASP 526
1m7xB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 405;GLU 458;HIS 525;ASP 526
1m7xC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 405;GLU 458;HIS 525;ASP 526
1m7xD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 405;GLU 458;HIS 525;ASP 526
3o7yA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 405;GLU 458;HIS 525;ASP 526
3o7yB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 405;GLU 458;HIS 525;ASP 526
3o7yC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 405;GLU 458;HIS 525;ASP 526
3o7yD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 405;GLU 458;HIS 525;ASP 526
3o7zA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 405;GLU 458;HIS 525;ASP 526
3o7zB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 405;GLU 458;HIS 525;ASP 526
3o7zC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 405;GLU 458;HIS 525;ASP 526
3o7zD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 405;GLU 458;HIS 525;ASP 526
3k1dA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 411;GLU 464;HIS 531;ASP 532
3amkA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 344;GLU 399;HIS 467;ASP 468
3amlA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 344;GLU 399;HIS 467;ASP 468
1m7xA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1m7xB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1m7xC03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1m7xD03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3o7yA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3o7yB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3o7yC03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3o7yD03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3o7zA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3o7zB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3o7zC03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3o7zD03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3k1dA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3amkA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3amlA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[13]
p.1112
[1]
[7]
p.42169
[8]
p.141-143
[9]
Fig.2,p.297-300
[12]
SCHEME 2

References
[1]
Resource
Comments
Medline ID
PubMed ID 8329389
Journal Biochemistry
Year 1993
Volume 32
Pages 6624-31
Authors Nakamura A, Haga K, Yamane K
Title Three histidine residues in the active center of cyclodextrin glucanotransferase from alkalophilic Bacillus sp. 1011: effects of the replacement on pH dependence and transition-state stabilization.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 8018865
Journal Plant Mol Biol
Year 1994
Volume 25
Pages 141-57
Authors Svensson B
Title Protein engineering in the alpha-amylase family: catalytic mechanism, substrate specificity, and stability.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 8804578
Journal J Protein Chem
Year 1996
Volume 15
Pages 305-13
Authors Kuriki T, Guan H, Sivak M, Preiss J
Title Analysis of the active center of branching enzyme II from maize endosperm.
Related PDB
Related UniProtKB
[4]
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
[5]
Resource
Comments
Medline ID
PubMed ID 9699264
Journal Adv Food Nutr Res
Year 1998
Volume 41
Pages 89-106
Authors
Title Branching enzymes.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID
Journal Biologia
Year 2002
Volume 57
Pages 109-18
Authors Lo Leggio L, Ernst HA, Hilden I, Larsen S
Title A structural model for the N-terminal N1 module of E-coli glycogen branching enzyme.
Related PDB
Related UniProtKB
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 113-728.
Medline ID
PubMed ID 12196524
Journal J Biol Chem
Year 2002
Volume 277
Pages 42164-70
Authors Abad MC, Binderup K, Rios-Steiner J, Arni RK, Preiss J, Geiger JH
Title The X-ray crystallographic structure of Escherichia coli branching enzyme.
Related PDB 1m7x
Related UniProtKB P07762
[8]
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
[9]
Resource
Comments
Medline ID
PubMed ID
Journal Enzyme Microb Technol
Year 2002
Volume 30
Pages 295-304
Authors Uitdehaag JC, van der Veen B, Dijkhuizen L, Dijkstra BW
Title Catalytic mechanism and product specificity of cyclodextrin glycosyltransferase, a prototypical transglycosylase from the alpha-amylase family.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 13679080
Journal Arch Biochem Biophys
Year 2003
Volume 418
Pages 34-8
Authors Devillers CH, Piper ME, Ballicora MA, Preiss J
Title Characterization of the branching patterns of glycogen branching enzyme truncated on the N-terminus.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 17005418
Journal Protein Expr Purif
Year 2007
Volume 51
Pages 198-208
Authors Garg SK, Alam MS, Kishan KV, Agrawal P
Title Expression and characterization of alpha-(1,4)-glucan branching enzyme Rv1326c of Mycobacterium tuberculosis H37Rv.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 20444687
Journal J Biol Chem
Year 2010
Volume 285
Pages 20897-903
Authors Pal K, Kumar S, Sharma S, Garg SK, Alam MS, Xu HE, Agrawal P, Swaminathan K
Title Crystal structure of full-length Mycobacterium tuberculosis H37Rv glycogen branching enzyme: insights of N-terminal beta-sandwich in substrate specificity and enzymatic activity.
Related PDB 3k1d
Related UniProtKB Q10625
[13]
Resource
Comments
Medline ID
PubMed ID 21493662
Journal Glycobiology
Year 2011
Volume 21
Pages 1108-16
Authors Noguchi J, Chaen K, Vu NT, Akasaka T, Shimada H, Nakashima T, Nishi A, Satoh H, Omori T, Kakuta Y, Kimura M
Title Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.
Related PDB 3amk 3aml
Related UniProtKB

Comments
This enzyme belongs to the glycosidase family-13.
This enzyme must have the same catalytic mechanism as those homologous enzymes, such as cyclodextrin transferase (M00113 in EzCatDB) and 4-alpha-glucanotransferase (S00202 in EzCatDB).
According to the literature [1], [7], [8], [9], [12] & [13], the reaction proceeds as follows:
(1) Asp526 (or/and His525) modulates the activity of Glu458 by raising its pKa, so that the carboxylate of Glu458 is protonated to act as a general acid.
(2) Glu458 acts as a general acid, to protonate the leaving O4 atom, leading to the formation of oxocarbonium transition-state (SN1-like reaction). This transition state is stabilized by Asp526 and His525.
(3) Asp405 acts as a nucleophile, attacking the C1 atom to form a covalent bond with it, which is an intermediate.
(4) The acceptor group, O6 hydroxyl group, approaches the active site.
(5) Glu257 acts as a general base to deprotonate the acceptor, O6 hydroxyl group of the glucose at subsite +1.
(6) The O6 hydroxyl group makes a nucleophilic attack on the C1 atom, leading to the formation of oxocarbonium transition-state (SN1-like reaction). This transition state is stabilized by Asp526 and His525.
(7) Finally, Asp405 is released.

Created Updated
2010-09-22 2011-11-30