DB code: D00175

RLCP classification 1.30.36040.982 : Hydrolysis
CATH domain 3.20.20.300 : TIM Barrel Catalytic domain
3.40.50.1700 : Rossmann fold Catalytic domain
E.C. 3.2.1.-
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms CAZy Pfam
Q9XEI3
Beta-D-glucan exohydrolase isoenzyme ExoI
GH3 (Glycoside Hydrolase Family 3)
PF00933 (Glyco_hydro_3)
PF01915 (Glyco_hydro_3_C)
[Graphical View]

KEGG enzyme name

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q9XEI3 Q9XEI3_HORVD

KEGG Pathways
Map code Pathways E.C.

Compound table
Substrates Products Intermediates
KEGG-id C00965 C00001 C00221 C00965
E.C.
Compound 1,3-beta-D-Glucan H2O beta-D-Glucose 1,3-beta-D-Glucan Transition-state in glycosylation Glycosyl-enzyme intermediate Transition-state in deglycosylation
Type polysaccharide H2O carbohydrate polysaccharide
ChEBI 15377
15903
PubChem 22247451
962
64689
1ex1A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:GLC Unbound Unbound Unbound Unbound
1ieqA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:GLC Unbound Unbound Unbound Unbound
1ievA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Intermediate-analogue:INS Unbound
1iewA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Intermediate-analogue:G2F Unbound
1iexA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:TCB Unbound Unbound Unbound Unbound Unbound
1j8vA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:LAM Unbound Unbound Unbound Unbound Unbound
1lq2A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Transition-state-analogue:IDD Unbound Unbound
1x38A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Transition-state-analogue:IDD Unbound Unbound
1x39A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Transition-state-analogue:IDE Unbound Unbound
1ex1A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1ieqA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1ievA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1iewA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1iexA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1j8vA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1lq2A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1x38A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1x39A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
PDB;1ex1 & literature [3], [6]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1ex1A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 158;ASP 285
1ieqA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 158;ASP 285
1ievA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 158;ASP 285
1iewA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 158;ASP 285
1iexA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 158;ASP 285
1j8vA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 158;ASP 285
1lq2A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 158;ASP 285
1x38A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 158;ASP 285
1x39A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 158;ASP 285
1ex1A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 430;TRP 434;GLU 491
1ieqA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 430;TRP 434;GLU 491
1ievA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 430;TRP 434;GLU 491
1iewA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 430;TRP 434;GLU 491
1iexA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 430;TRP 434;GLU 491
1j8vA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 430;TRP 434;GLU 491
1lq2A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 430;TRP 434;GLU 491
1x38A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 430;TRP 434;GLU 491
1x39A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 430;TRP 434;GLU 491

References for Catalytic Mechanism
References Sections No. 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]
Resource
Comments
Medline ID
PubMed ID 8617814
Journal J Biol Chem
Year 1996
Volume 271
Pages 5277-86
Authors Hrmova M, Harvey AJ, Wang J, Shirley NJ, Jones GP, Stone BA, Hoj PB, Fincher GB
Title Barley beta-D-glucan exohydrolases with beta-D-glucosidase activity. Purification, characterization, and determination of primary structure from a cDNA clone.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID
Journal Carbohydr Res
Year 1998
Volume 305
Pages 209-21
Authors Hrmova M, Fincher GB
Title Barley beta-D-glucan exohydrolases. Substrate specificity and kinetic properties.
Related PDB
Related UniProtKB
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 26-630.
Medline ID
PubMed ID 10368285
Journal Structure Fold Des
Year 1999
Volume 7
Pages 179-90
Authors Varghese JN, Hrmova M, Fincher GB
Title Three-dimensional structure of a barley beta-D-glucan exohydrolase, a family 3 glycosyl hydrolase.
Related PDB 1ex1
Related UniProtKB Q9XEI3
[4]
Resource
Comments
Medline ID
PubMed ID 10966578
Journal Proteins
Year 2000
Volume 41
Pages 257-69
Authors Harvey AJ, Hrmova M, De Gori R, Varghese JN, Fincher GB
Title Comparative modeling of the three-dimensional structures of family 3 glycoside hydrolases.
Related PDB
Related UniProtKB
[5]
Resource
Comments structure-function relationships (review)
Medline ID
PubMed ID 11554481
Journal Plant Mol Biol
Year 2001
Volume 47
Pages 73-91
Authors Hrmova M, Fincher GB
Title Structure-function relationships of beta-D-glucan endo- and exohydrolases from higher plants.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11709165
Journal Structure
Year 2001
Volume 9
Pages 1005-16
Authors Hrmova M, Varghese JN, De Gori R, Smith BJ, Driguez H, Fincher GB
Title Catalytic mechanisms and reaction intermediates along the hydrolytic pathway of a plant beta-D-glucan glucohydrolase.
Related PDB 1ieq 1iev 1iew 1iex
Related UniProtKB
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 26-630.
Medline ID
PubMed ID 12034895
Journal Plant Cell
Year 2002
Volume 14
Pages 1033-52
Authors Hrmova M, De Gori R, Smith BJ, Fairweather JK, Driguez H, Varghese JN, Fincher GB
Title Structural basis for broad substrate specificity in higher plant beta-D-glucan glucohydrolases.
Related PDB 1j8v
Related UniProtKB Q9XEI3
[8]
Resource
Comments
Medline ID
PubMed ID 12932786
Journal J Mol Graph Model
Year 2003
Volume 22
Pages 151-9
Authors Smith BJ
Title Can thioglycosides imitate the oxonium intermediate in glycosyl hydrolases?
Related PDB
Related UniProtKB
[9]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 26-627.
Medline ID
PubMed ID 14597633
Journal J Biol Chem
Year 2004
Volume 279
Pages 4970-80
Authors Hrmova M, De Gori R, Smith BJ, Vasella A, Varghese JN, Fincher GB
Title Three-dimensional structure of the barley beta-D-glucan glucohydrolase in complex with a transition state mimic.
Related PDB 1lq2
Related UniProtKB Q9XEI3
[10]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 16342944
Journal Biochemistry
Year 2005
Volume 44
Pages 16529-39
Authors Hrmova M, Streltsov VA, Smith BJ, Vasella A, Varghese JN, Fincher GB
Title Structural rationale for low-nanomolar binding of transition state mimics to a family GH3 beta-D-glucan glucohydrolase from barley.
Related PDB 1x38 1x39
Related UniProtKB

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.

Created Updated
2004-05-07 2009-02-26