EzCatDB: D00175
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DB codeD00175
RLCP classification1.30.36040.982 : Hydrolysis
CATH domainDomain 13.20.20.300 : TIM BarrelCatalytic domain
Domain 23.40.50.1700 : Rossmann foldCatalytic domain
E.C.3.2.1.-


Enzyme Name
UniProtKB

Q9XEI3
Protein name
SynonymsBeta-D-glucan exohydrolase isoenzyme ExoI
PfamPF00933 (Glyco_hydro_3)
PF01915 (Glyco_hydro_3_C)
[Graphical view]
CAZyGH3 (Glycoside Hydrolase Family)


UniProtKB:Accession NumberQ9XEI3
Entry nameQ9XEI3_HORVD
Activity
Subunit
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idC00965C00001C00221C00965


Compound1,3-beta-D-GlucanH2Obeta-D-Glucose1,3-beta-D-GlucanTransition-state in glycosylationGlycosyl-enzyme intermediateTransition-state in deglycosylation
TypepolysaccharideH2Ocarbohydratepolysaccharide


ChEBI
15377
15903




PubChem
962
22247451
64689




               
1ex1A01Unbound Analogue:GLCUnboundUnboundUnboundUnbound
1ieqA01Unbound Bound:GLCUnboundUnboundUnboundUnbound
1ievA01Unbound UnboundUnboundUnboundIntermediate-analogue:INSUnbound
1iewA01Unbound UnboundUnboundUnboundIntermediate-analogue:G2FUnbound
1iexA01Analogue:TCB UnboundUnboundUnboundUnboundUnbound
1j8vA01Analogue:LAM UnboundUnboundUnboundUnboundUnbound
1lq2A01Unbound UnboundUnboundTransition-state-analogue:IDDUnboundUnbound
1x38A01Unbound UnboundUnboundTransition-state-analogue:IDDUnboundUnbound
1x39A01Unbound UnboundUnboundTransition-state-analogue:IDEUnboundUnbound
1ex1A02Unbound UnboundUnboundUnboundUnboundUnbound
1ieqA02Unbound UnboundUnboundUnboundUnboundUnbound
1ievA02Unbound UnboundUnboundUnboundUnboundUnbound
1iewA02Unbound UnboundUnboundUnboundUnboundUnbound
1iexA02Unbound UnboundUnboundUnboundUnboundUnbound
1j8vA02Unbound UnboundUnboundUnboundUnboundUnbound
1lq2A02Unbound UnboundUnboundUnboundUnboundUnbound
1x38A02Unbound UnboundUnboundUnboundUnboundUnbound
1x39A02Unbound UnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
PDB;1ex1 & literature [3], [6]
pdbCatalytic residues
         
1ex1A01ARG 158;ASP 285
1ieqA01ARG 158;ASP 285
1ievA01ARG 158;ASP 285
1iewA01ARG 158;ASP 285
1iexA01ARG 158;ASP 285
1j8vA01ARG 158;ASP 285
1lq2A01ARG 158;ASP 285
1x38A01ARG 158;ASP 285
1x39A01ARG 158;ASP 285
1ex1A02TRP 430;TRP 434;GLU 491
1ieqA02TRP 430;TRP 434;GLU 491
1ievA02TRP 430;TRP 434;GLU 491
1iewA02TRP 430;TRP 434;GLU 491
1iexA02TRP 430;TRP 434;GLU 491
1j8vA02TRP 430;TRP 434;GLU 491
1lq2A02TRP 430;TRP 434;GLU 491
1x38A02TRP 430;TRP 434;GLU 491
1x39A02TRP 430;TRP 434;GLU 491

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]p.186-187
[4]p.263-266
[5]Fig.3, p.85-86
[6]Fig.8, p.1013-1014
[9]p.4976-4979
[10]p.16536-16538

references
[1]
PubMed ID8617814
JournalJ Biol Chem
Year1996
Volume271
Pages5277-86
AuthorsHrmova M, Harvey AJ, Wang J, Shirley NJ, Jones GP, Stone BA, Hoj PB, Fincher GB
TitleBarley beta-D-glucan exohydrolases with beta-D-glucosidase activity. Purification, characterization, and determination of primary structure from a cDNA clone.
[2]
JournalCarbohydr Res
Year1998
Volume305
Pages209-21
AuthorsHrmova M, Fincher GB
TitleBarley beta-D-glucan exohydrolases. Substrate specificity and kinetic properties.
[3]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 26-630.
PubMed ID10368285
JournalStructure Fold Des
Year1999
Volume7
Pages179-90
AuthorsVarghese JN, Hrmova M, Fincher GB
TitleThree-dimensional structure of a barley beta-D-glucan exohydrolase, a family 3 glycosyl hydrolase.
Related PDB1ex1
Related UniProtKBQ9XEI3
[4]
PubMed ID10966578
JournalProteins
Year2000
Volume41
Pages257-69
AuthorsHarvey AJ, Hrmova M, De Gori R, Varghese JN, Fincher GB
TitleComparative modeling of the three-dimensional structures of family 3 glycoside hydrolases.
[5]
Commentsstructure-function relationships (review)
PubMed ID11554481
JournalPlant Mol Biol
Year2001
Volume47
Pages73-91
AuthorsHrmova M, Fincher GB
TitleStructure-function relationships of beta-D-glucan endo- and exohydrolases from higher plants.
[6]
CommentsX-ray crystallography
PubMed ID11709165
JournalStructure
Year2001
Volume9
Pages1005-16
AuthorsHrmova M, Varghese JN, De Gori R, Smith BJ, Driguez H, Fincher GB
TitleCatalytic mechanisms and reaction intermediates along the hydrolytic pathway of a plant beta-D-glucan glucohydrolase.
Related PDB1ieq,1iev,1iew,1iex
[7]
CommentsX-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 26-630.
PubMed ID12034895
JournalPlant Cell
Year2002
Volume14
Pages1033-52
AuthorsHrmova M, De Gori R, Smith BJ, Fairweather JK, Driguez H, Varghese JN, Fincher GB
TitleStructural basis for broad substrate specificity in higher plant beta-D-glucan glucohydrolases.
Related PDB1j8v
Related UniProtKBQ9XEI3
[8]
PubMed ID12932786
JournalJ Mol Graph Model
Year2003
Volume22
Pages151-9
AuthorsSmith BJ
TitleCan thioglycosides imitate the oxonium intermediate in glycosyl hydrolases?
[9]
CommentsX-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 26-627.
PubMed ID14597633
JournalJ Biol Chem
Year2004
Volume279
Pages4970-80
AuthorsHrmova M, De Gori R, Smith BJ, Vasella A, Varghese JN, Fincher GB
TitleThree-dimensional structure of the barley beta-D-glucan glucohydrolase in complex with a transition state mimic.
Related PDB1lq2
Related UniProtKBQ9XEI3
[10]
CommentsX-ray crystallography
PubMed ID16342944
JournalBiochemistry
Year2005
Volume44
Pages16529-39
AuthorsHrmova M, Streltsov VA, Smith BJ, Vasella A, Varghese JN, Fincher GB
TitleStructural rationale for low-nanomolar binding of transition state mimics to a family GH3 beta-D-glucan glucohydrolase from barley.
Related PDB1x38,1x39

comments
This enzyme belongs to the glycosidase family-3, with a retaining mechanism.
According to the literature [1], although the reactions by this enzyme are similar to those by (1,3)-beta-glucan exohydrolases that have been classified in E.C. 3.2.1.58, this enzyme can hydrolyze substrates with linkages other than those in the (1,3)-position.
Furthermore, whilst the glycosidases that are classified in the E.C. 3.2.1.58 must have an inverting mechanism, releaseing alpha-D-Glucose, this enzyme has got a retaining mechanism, releasing beta-D-glucose. Thus, the E.C. number of this enzyme is not completely assigned yet.
According to the literature [2] & [6], the reaction of this enzyme proceeds as follows:
(1) Trp430 and Trp434 may act as modulator by increasing the pKa of Glu491, whereas Arg158 may decrease the pKa of Glu491 as a modulator.
(2) Glu491 acts as a general acid to protonate the leaving oxygen atom, leading to the formation of an oxocarbonium ion-like transition-state. Here, Asp285 may stabilize the positive charge on the C1 carbon of the oxocarbonium ion-like transition-state.
(3) Asp285 makes a nucleophilic attack on the C1 carbon, forming a glycosyl-enzyme intermediate.
(4) Glu491 acts as a general base to activate a water molecule.
(5) The activated water molecule makes a nucleophilic attack on the C1 carbon of the intermediate, completing the hydrolysis reaction through the formation of an oxocarbonium ion-like transition-state.

createdupdated
2004-05-072009-02-26


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