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
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 28087
PubChem		439177 439177

1m7xA01	Unbound	Unbound
1m7xB01	Unbound	Unbound
1m7xC01	Unbound	Unbound
1m7xD01	Unbound	Unbound
3o7yA01	Unbound	Unbound
3o7yB01	Unbound	Unbound
3o7yC01	Unbound	Unbound
3o7yD01	Unbound	Unbound
3o7zA01	Unbound	Unbound
3o7zB01	Unbound	Unbound
3o7zC01	Unbound	Unbound
3o7zD01	Unbound	Unbound
3k1dA01	Unbound	Unbound
3amkA01	Unbound	Unbound
3amlA01	Unbound	Unbound
1m7xA02	Unbound	Unbound
1m7xB02	Unbound	Unbound
1m7xC02	Unbound	Unbound
1m7xD02	Unbound	Unbound
3o7yA02	Unbound	Unbound
3o7yB02	Unbound	Unbound
3o7yC02	Unbound	Unbound
3o7yD02	Unbound	Unbound
3o7zA02	Unbound	Unbound
3o7zB02	Unbound	Unbound
3o7zC02	Unbound	Unbound
3o7zD02	Unbound	Unbound
3k1dA02	Unbound	Unbound
3amkA02	Unbound	Unbound
3amlA02	Unbound	Unbound
1m7xA03	Unbound	Unbound
1m7xB03	Unbound	Unbound
1m7xC03	Unbound	Unbound
1m7xD03	Unbound	Unbound
3o7yA03	Unbound	Unbound
3o7yB03	Unbound	Unbound
3o7yC03	Unbound	Unbound
3o7yD03	Unbound	Unbound
3o7zA03	Unbound	Unbound
3o7zB03	Unbound	Unbound
3o7zC03	Unbound	Unbound
3o7zD03	Unbound	Unbound
3k1dA03	Unbound	Unbound
3amkA03	Unbound	Unbound
3amlA03	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
1m7xB01
1m7xC01
1m7xD01
3o7yA01
3o7yB01
3o7yC01
3o7yD01
3o7zA01
3o7zB01
3o7zC01
3o7zD01
3k1dA01
3amkA01
3amlA01
1m7xA02	ASP 405;GLU 458;HIS 525;ASP 526
1m7xB02	ASP 405;GLU 458;HIS 525;ASP 526
1m7xC02	ASP 405;GLU 458;HIS 525;ASP 526
1m7xD02	ASP 405;GLU 458;HIS 525;ASP 526
3o7yA02	ASP 405;GLU 458;HIS 525;ASP 526
3o7yB02	ASP 405;GLU 458;HIS 525;ASP 526
3o7yC02	ASP 405;GLU 458;HIS 525;ASP 526
3o7yD02	ASP 405;GLU 458;HIS 525;ASP 526
3o7zA02	ASP 405;GLU 458;HIS 525;ASP 526
3o7zB02	ASP 405;GLU 458;HIS 525;ASP 526
3o7zC02	ASP 405;GLU 458;HIS 525;ASP 526
3o7zD02	ASP 405;GLU 458;HIS 525;ASP 526
3k1dA02	ASP 411;GLU 464;HIS 531;ASP 532
3amkA02	ASP 344;GLU 399;HIS 467;ASP 468
3amlA02	ASP 344;GLU 399;HIS 467;ASP 468
1m7xA03
1m7xB03
1m7xC03
1m7xD03
3o7yA03
3o7yB03
3o7yC03
3o7yD03
3o7zA03
3o7zB03
3o7zC03
3o7zD03
3k1dA03
3amkA03
3amlA03

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

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.

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