EzCatDB: T00307
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DB codeT00307
RLCP classification3.900.275800.990 : Transfer
CATH domainDomain 12.60.40.10 : Immunoglobulin-like
Domain 23.20.20.80 : TIM BarrelCatalytic domain
Domain 32.60.40.1180 : Immunoglobulin-like
E.C.2.4.1.18

CATH domainRelated DB codes (homologues)
2.60.40.10 : Immunoglobulin-likeM00131,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-likeM00113,D00165,D00176,D00664,D00665,D00863,D00864,M00112,M00193,M00314,T00057,T00062,T00067
3.20.20.80 : TIM BarrelS00202,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

Enzyme Name
UniProtKBKEGG

P07762Q10625Q01401
Protein name1,4-alpha-glucan branching enzyme GlgB1,4-alpha-glucan branching enzyme GlgB1,4-alpha-glucan-branching enzyme, chloroplastic/amyloplastic1,4-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
SynonymsEC 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
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
EC 2.4.1.18
Q-enzyme
Starch-branching enzyme
RefSeqNP_417890.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_492001.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
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)
NP_001058629.1 (Protein)
NM_001065164.1 (DNA/RNA sequence)
PfamPF00128 (Alpha-amylase)
PF02806 (Alpha-amylase_C)
PF02922 (CBM_48)
[Graphical view]
PF00128 (Alpha-amylase)
PF02806 (Alpha-amylase_C)
PF02922 (CBM_48)
[Graphical view]
PF00128 (Alpha-amylase)
PF02806 (Alpha-amylase_C)
PF02922 (CBM_48)
[Graphical view]
CAZyGH13 (Glycoside Hydrolase Family)
GH13 (Glycoside Hydrolase Family)
GH13 (Glycoside Hydrolase Family)

KEGG pathways
MAP codePathways
MAP00500Starch and sucrose metabolism

UniProtKB:Accession NumberP07762Q10625Q01401
Entry nameGLGB_ECOLIGLGB_MYCTUGLGB_ORYSJ
ActivityTransfers a segment of a (1->4)-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain.Transfers a segment of a (1->4)-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain.Transfers a segment of a (1->4)-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain.
SubunitMonomer.Monomer.Monomer.
Subcellular location

Plastid, chloroplast. Plastid, amyloplast.
Cofactor



Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC00718C00182
CompoundAmyloseGlycogen
Typepolysaccharidepolysaccharide
ChEBI
28087
PubChem
439177
          
1m7xA01UnboundUnbound
1m7xB01UnboundUnbound
1m7xC01UnboundUnbound
1m7xD01UnboundUnbound
3o7yA01UnboundUnbound
3o7yB01UnboundUnbound
3o7yC01UnboundUnbound
3o7yD01UnboundUnbound
3o7zA01UnboundUnbound
3o7zB01UnboundUnbound
3o7zC01UnboundUnbound
3o7zD01UnboundUnbound
3k1dA01UnboundUnbound
3amkA01UnboundUnbound
3amlA01UnboundUnbound
1m7xA02UnboundUnbound
1m7xB02UnboundUnbound
1m7xC02UnboundUnbound
1m7xD02UnboundUnbound
3o7yA02UnboundUnbound
3o7yB02UnboundUnbound
3o7yC02UnboundUnbound
3o7yD02UnboundUnbound
3o7zA02UnboundUnbound
3o7zB02UnboundUnbound
3o7zC02UnboundUnbound
3o7zD02UnboundUnbound
3k1dA02UnboundUnbound
3amkA02UnboundUnbound
3amlA02UnboundUnbound
1m7xA03UnboundUnbound
1m7xB03UnboundUnbound
1m7xC03UnboundUnbound
1m7xD03UnboundUnbound
3o7yA03UnboundUnbound
3o7yB03UnboundUnbound
3o7yC03UnboundUnbound
3o7yD03UnboundUnbound
3o7zA03UnboundUnbound
3o7zB03UnboundUnbound
3o7zC03UnboundUnbound
3o7zD03UnboundUnbound
3k1dA03UnboundUnbound
3amkA03UnboundUnbound
3amlA03UnboundUnbound

Active-site residues
resource
Literature [7], [13] & Swiss-prot;P07762, Q10625
pdbCatalytic residues
         
1m7xA01 
1m7xB01 
1m7xC01 
1m7xD01 
3o7yA01 
3o7yB01 
3o7yC01 
3o7yD01 
3o7zA01 
3o7zB01 
3o7zC01 
3o7zD01 
3k1dA01 
3amkA01 
3amlA01 
1m7xA02ASP 405;GLU 458;HIS 525;ASP 526
1m7xB02ASP 405;GLU 458;HIS 525;ASP 526
1m7xC02ASP 405;GLU 458;HIS 525;ASP 526
1m7xD02ASP 405;GLU 458;HIS 525;ASP 526
3o7yA02ASP 405;GLU 458;HIS 525;ASP 526
3o7yB02ASP 405;GLU 458;HIS 525;ASP 526
3o7yC02ASP 405;GLU 458;HIS 525;ASP 526
3o7yD02ASP 405;GLU 458;HIS 525;ASP 526
3o7zA02ASP 405;GLU 458;HIS 525;ASP 526
3o7zB02ASP 405;GLU 458;HIS 525;ASP 526
3o7zC02ASP 405;GLU 458;HIS 525;ASP 526
3o7zD02ASP 405;GLU 458;HIS 525;ASP 526
3k1dA02ASP 411;GLU 464;HIS 531;ASP 532
3amkA02ASP 344;GLU 399;HIS 467;ASP 468
3amlA02ASP 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
ReferencesSectionsNo. 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]
PubMed ID8329389
JournalBiochemistry
Year1993
Volume32
Pages6624-31
AuthorsNakamura A, Haga K, Yamane K
TitleThree 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.
[2]
PubMed ID8018865
JournalPlant Mol Biol
Year1994
Volume25
Pages141-57
AuthorsSvensson B
TitleProtein engineering in the alpha-amylase family: catalytic mechanism, substrate specificity, and stability.
[3]
PubMed ID8804578
JournalJ Protein Chem
Year1996
Volume15
Pages305-13
AuthorsKuriki T, Guan H, Sivak M, Preiss J
TitleAnalysis of the active center of branching enzyme II from maize endosperm.
[4]
PubMed ID9401418
JournalProg Biophys Mol Biol
Year1997
Volume67
Pages67-97
AuthorsJanecek S
Titlealpha-Amylase family: molecular biology and evolution.
[5]
PubMed ID9699264
JournalAdv Food Nutr Res
Year1998
Volume41
Pages89-106
Authors
TitleBranching enzymes.
[6]
JournalBiologia
Year2002
Volume57
Pages109-18
AuthorsLo Leggio L, Ernst HA, Hilden I, Larsen S
TitleA structural model for the N-terminal N1 module of E-coli glycogen branching enzyme.
[7]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 113-728.
PubMed ID12196524
JournalJ Biol Chem
Year2002
Volume277
Pages42164-70
AuthorsAbad MC, Binderup K, Rios-Steiner J, Arni RK, Preiss J, Geiger JH
TitleThe X-ray crystallographic structure of Escherichia coli branching enzyme.
Related PDB1m7x
Related UniProtKBP07762
[8]
PubMed ID11796168
JournalJ Biotechnol
Year2002
Volume94
Pages137-55
Authorsvan der Maarel MJ, van der Veen B, Uitdehaag JC, Leemhuis H, Dijkhuizen L
TitleProperties and applications of starch-converting enzymes of the alpha-amylase family.
[9]
JournalEnzyme Microb Technol
Year2002
Volume30
Pages295-304
AuthorsUitdehaag JC, van der Veen B, Dijkhuizen L, Dijkstra BW
TitleCatalytic mechanism and product specificity of cyclodextrin glycosyltransferase, a prototypical transglycosylase from the alpha-amylase family.
[10]
PubMed ID13679080
JournalArch Biochem Biophys
Year2003
Volume418
Pages34-8
AuthorsDevillers CH, Piper ME, Ballicora MA, Preiss J
TitleCharacterization of the branching patterns of glycogen branching enzyme truncated on the N-terminus.
[11]
PubMed ID17005418
JournalProtein Expr Purif
Year2007
Volume51
Pages198-208
AuthorsGarg SK, Alam MS, Kishan KV, Agrawal P
TitleExpression and characterization of alpha-(1,4)-glucan branching enzyme Rv1326c of Mycobacterium tuberculosis H37Rv.
[12]
PubMed ID20444687
JournalJ Biol Chem
Year2010
Volume285
Pages20897-903
AuthorsPal K, Kumar S, Sharma S, Garg SK, Alam MS, Xu HE, Agrawal P, Swaminathan K
TitleCrystal structure of full-length Mycobacterium tuberculosis H37Rv glycogen branching enzyme: insights of N-terminal beta-sandwich in substrate specificity and enzymatic activity.
Related PDB3k1d
Related UniProtKBQ10625
[13]
PubMed ID21493662
JournalGlycobiology
Year2011
Volume21
Pages1108-16
AuthorsNoguchi J, Chaen K, Vu NT, Akasaka T, Shimada H, Nakashima T, Nishi A, Satoh H, Omori T, Kakuta Y, Kimura M
TitleCrystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.
Related PDB3amk,3aml

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.

createdupdated
2010-09-222011-11-30


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Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
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)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
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