DB code: T00245

RLCP classification 1.30.5050.993 : Hydrolysis
CATH domain 2.60.40.10 : Immunoglobulin-like
1.50.10.10 : Glycosyltransferase Catalytic domain
1.10.1330.10 : Type 1 dockerin domain
E.C. 3.2.1.4
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
1.10.1330.10 : Type 1 dockerin domain D00167 D00503 T00246
1.50.10.10 : Glycosyltransferase S00531 S00048 S00845 D00167 D00500 M00192 T00246
2.60.40.10 : Immunoglobulin-like M00131 T00257 T00005 M00113 M00127 M00132 M00323 M00325 M00327 M00329 M00330 M00331 M00332 T00307 D00166 D00500 M00112 M00193 T00063 T00065 T00067

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P0C2S4 Endoglucanase D
EGD
EC 3.2.1.4
Endo-1,4-beta-glucanase
Cellulase D
PF02927 (CelD_N)
PF00404 (Dockerin_1)
PF00759 (Glyco_hydro_9)
[Graphical View]

KEGG enzyme name
cellulase
endo-1,4-beta-D-glucanase
beta-1,4-glucanase
beta-1,4-endoglucan hydrolase
celluase A
cellulosin AP
endoglucanase D
alkali cellulase
cellulase A 3
celludextrinase
9.5 cellulase
avicelase
pancellase SS
1,4-(1,3
1,4)-beta-D-glucan 4-glucanohydrolase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P0C2S4 GUND_CLOTM Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans. Calcium.

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

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00038 C00076 C00760 C00478 C00551 C00001 C00760 C00551
E.C.
Compound Zinc Calcium Cellulose Lichenin beta-D-Glucan H2O Cellulose beta-D-Glucan
Type heavy metal divalent metal (Ca2+, Mg2+) polysaccharide carbohydrate polysaccharide H2O polysaccharide polysaccharide
ChEBI 29105
29108
15377
PubChem 32051
271
439241
46173706
962
22247451
46173706
1clcA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1clcA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Bound:3x_CA Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
PDB;1clc & literature [5], [6], [8], [14]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1clcA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1clcA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 198;ASP 201;TYR 205;TYR 354;GLU 555 CYS 155;CYS 173;HIS 174;HIS 197(Zinc binding);GLU 236;ASN 239;ILE 241;ASP 243;ASP 246(Calcium-1 binding);THR 356;SER 358;ASP 361;ASP 362;ASP 401(Calcium-2 binding);SER 520;ASP 523;ILE 525(Calcium-3 binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[5]
p.91
[8]
Fig.4, p.814815
[10]
p.657-658

References
[1]
Resource
Comments CALCIUM-BINDING DATA.
Medline ID 90147577
PubMed ID 2302168
Journal Biochem J
Year 1990
Volume 265
Pages 261-5
Authors Chauvaux S, Beguin P, Aubert JP, Bhat KM, Gow LA, Wood TM, Bairoch A
Title Calcium-binding affinity and calcium-enhanced activity of Clostridium thermocellum endoglucanase D.
Related PDB
Related UniProtKB P04954
[2]
Resource
Comments ACTIVE SITE HIS-516, AND MUTAGENESIS OF ALL HISTIDINE RESIDUES.
Medline ID 91244802
PubMed ID 2037583
Journal J Biol Chem
Year 1991
Volume 266
Pages 10313-8
Authors Tomme P, Chauvaux S, Beguin P, Millet J, Aubert JP, Claeyssens M
Title Identification of a histidyl residue in the active center of endoglucanase D from Clostridium thermocellum.
Related PDB
Related UniProtKB P04954
[3]
Resource
Comments ACTIVE SITE ASP-546.
Medline ID 92344589
PubMed ID 1637316
Journal Biochem J
Year 1992
Volume 285
Pages 319-24
Authors Tomme P, van Beeumen J, Claeyssens M
Title Modification of catalytically important carboxy residues in endoglucanase D from Clostridium thermocellum.
Related PDB
Related UniProtKB P04954
[4]
Resource
Comments ACTIVE SITE GLU-555, AND MUTAGENESIS OF ASPARTIC ACID AND GLUTAMIC ACID RESIDUES.
Medline ID 92165798
PubMed ID 1537833
Journal J Biol Chem
Year 1992
Volume 267
Pages 4472-8
Authors Chauvaux S, Beguin P, Aubert JP
Title Site-directed mutagenesis of essential carboxylic residues in Clostridium thermocellum endoglucanase CelD.
Related PDB
Related UniProtKB P04954
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID
PubMed ID
Journal Nature
Year 1992
Volume 357
Pages 89-91
Authors Juy M, Amit AG, Alzari PM, Poljak RJ, Claeyssens M, Beguin P, Aubert J-P
Title Three-dimensional structure of a thermostable bacterial cellulase.
Related PDB
Related UniProtKB P04954
[6]
Resource
Comments
Medline ID
PubMed ID 7730353
Journal J Biol Chem
Year 1995
Volume 270
Pages 9757-62
Authors Chauvaux S, Souchon H, Alzari PM, Chariot P, Beguin P
Title Structural and functional analysis of the metal-binding sites of Clostridium thermocellum endoglucanase CelD.
Related PDB
Related UniProtKB
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID
PubMed ID 7739036
Journal J Mol Biol
Year 1995
Volume 248
Pages 225-32
Authors Chitarra V, Souchon H, Spinelli S, Juy M, Beguin P, Alzari PM
Title Multiple crystal forms of endoglucanase CelD: signal peptide residues modulate lattice formation.
Related PDB
Related UniProtKB P04954
[8]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 47-651
Medline ID 9334746
PubMed ID 9334746
Journal Nat Struct Biol
Year 1997
Volume 4
Pages 810-8
Authors Sakon J, Irwin D, Wilson DB, Karplus PA
Title Structure and mechanism of endo/exocellulase E4 from Thermomonospora fusca.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 11273698
Journal J Mol Biol
Year 2001
Volume 307
Pages 745-53
Authors Lytle BL, Volkman BF, Westler WM, Heckman MP, Wu JH
Title Solution structure of a type I dockerin domain, a novel prokaryotic, extracellular calcium-binding domain.
Related PDB
Related UniProtKB
[10]
Resource
Comments X-ray crystallography (1.4 Angstroms)
Medline ID
PubMed ID 11914490
Journal Acta Crystallogr D Biol Crystallogr
Year 2002
Volume 58
Pages 653-659
Authors Khademi S, Guarino LA, Watanabe H, Tokuda G, Meyer EF
Title Structure of an endoglucanase from termite, Nasutitermes takasagoensis.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 11844767
Journal J Bacteriol
Year 2002
Volume 184
Pages 1378-84
Authors Belaich A, Parsiegla G, Gal L, Villard C, Haser R, Belaich JP
Title Cel9M, a new family 9 cellulase of the Clostridium cellulolyticum cellulosome.
Related PDB
Related UniProtKB
[12]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 12837787
Journal J Bacteriol
Year 2003
Volume 185
Pages 4127-35
Authors Mandelman D, Belaich A, Belaich JP, Aghajari N, Driguez H, Haser R
Title X-Ray crystal structure of the multidomain endoglucanase Cel9G from Clostridium cellulolyticum complexed with natural and synthetic cello-oligosaccharides.
Related PDB
Related UniProtKB
[13]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 14756552
Journal Biochemistry
Year 2004
Volume 43
Pages 1163-70
Authors Schubot FD, Kataeva IA, Chang J, Shah AK, Ljungdahl LG, Rose JP, Wang BC
Title Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 15274620
Journal Biochemistry
Year 2004
Volume 43
Pages 9655-63
Authors Zhou W, Irwin DC, Escovar-Kousen J, Wilson DB
Title Kinetic studies of Thermobifida fusca Cel9A active site mutant enzymes.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to the glycosidase family-9, with an inverting mechanism.
Although the structure of the domain 3 (dockerin repeat region) has not been determined yet, it must have a similar structure to that of type-I dockerin domain (PDB;1daq).
Althoug this enzyme binds a zinc ion and three calcium ions, they are not involved in catalysis. They must play structural roles (see [1] & [6]).
Although a catalytic histdine residue is not conserved in this enzyme, the catalytic domain of this enzyme is homologous to those of the other glycosidase family-9 enzymes (S00531, D00167, T00245, M00192 in EzCatDB). Considering the active-site structure of this enzyme, instead of a catalytic histidine residue, Tyr205 must act as a modulator for Asp201.
The reaction of this enzyme may proceeds as follows:
(0) Tyr354 modulates the pKa of Asp198, whereas Tyr205 modulates the pKa of Asp201.
(1) Glu555 acts as a general acid to protonate the leaving group, the glycosidic oxygen, forming an oxocarbonium ion in the transition state. (SN1-like reaction)
(2) Both Asp198 and Asp201 act as general bases to deprotonate the nucleophilic water. (Here, Asp201 seems more likely to be the base.)
(3) The activated water makes a nucleophilic attack on the anomeric carbon to complete the reaction.

Created Updated
2004-08-18 2009-02-26