EzCatDB: T00245
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DB codeT00245
RLCP classification1.30.5050.993 : Hydrolysis
CATH domainDomain 12.60.40.10 : Immunoglobulin-like
Domain 21.50.10.10 : GlycosyltransferaseCatalytic domain
Domain 31.10.1330.10 : Type 1 dockerin domain
E.C.3.2.1.4

CATH domainRelated DB codes (homologues)
1.10.1330.10 : Type 1 dockerin domainD00167,D00503,T00246
1.50.10.10 : GlycosyltransferaseS00531,S00048,S00845,D00167,D00500,M00192,T00246
2.60.40.10 : Immunoglobulin-likeM00131,T00257,T00005,M00113,M00127,M00132,M00323,M00325,M00327,M00329,M00330,M00331,M00332,T00307,D00166,D00500,M00112,M00193,T00063,T00065,T00067

Enzyme Name
UniProtKBKEGG

P0C2S4
Protein nameEndoglucanase Dcellulase
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
SynonymsEGD
EC 3.2.1.4
Endo-1,4-beta-glucanase
Cellulase D
PfamPF02927 (CelD_N)
PF00404 (Dockerin_1)
PF00759 (Glyco_hydro_9)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00500Starch and sucrose metabolism

UniProtKB:Accession NumberP0C2S4
Entry nameGUND_CLOTM
ActivityEndohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
Subunit
Subcellular location
CofactorCalcium.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00038C00076C00760C00478C00551C00001C00760C00551
CompoundZincCalciumCelluloseLicheninbeta-D-GlucanH2OCellulosebeta-D-Glucan
Typeheavy metaldivalent metal (Ca2+, Mg2+)polysaccharidecarbohydratepolysaccharideH2Opolysaccharidepolysaccharide
ChEBI29105
29108



15377


PubChem32051
271

439241
46173706
962
22247451

46173706
                
1clcA01UnboundUnboundUnboundUnboundUnbound UnboundUnbound
1clcA02Bound:_ZNBound:3x_CAUnboundUnboundUnbound UnboundUnbound

Active-site residues
resource
PDB;1clc & literature [5], [6], [8], [14]
pdbCatalytic residuesCofactor-binding residues
          
1clcA01 
 
1clcA02ASP 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
ReferencesSectionsNo. of steps in catalysis
[5]p.91
[8]Fig.4, p.814815
[10]p.657-658

references
[1]
CommentsCALCIUM-BINDING DATA.
Medline ID90147577
PubMed ID2302168
JournalBiochem J
Year1990
Volume265
Pages261-5
AuthorsChauvaux S, Beguin P, Aubert JP, Bhat KM, Gow LA, Wood TM, Bairoch A
TitleCalcium-binding affinity and calcium-enhanced activity of Clostridium thermocellum endoglucanase D.
Related UniProtKBP04954
[2]
CommentsACTIVE SITE HIS-516, AND MUTAGENESIS OF ALL HISTIDINE RESIDUES.
Medline ID91244802
PubMed ID2037583
JournalJ Biol Chem
Year1991
Volume266
Pages10313-8
AuthorsTomme P, Chauvaux S, Beguin P, Millet J, Aubert JP, Claeyssens M
TitleIdentification of a histidyl residue in the active center of endoglucanase D from Clostridium thermocellum.
Related UniProtKBP04954
[3]
CommentsACTIVE SITE ASP-546.
Medline ID92344589
PubMed ID1637316
JournalBiochem J
Year1992
Volume285
Pages319-24
AuthorsTomme P, van Beeumen J, Claeyssens M
TitleModification of catalytically important carboxy residues in endoglucanase D from Clostridium thermocellum.
Related UniProtKBP04954
[4]
CommentsACTIVE SITE GLU-555, AND MUTAGENESIS OF ASPARTIC ACID AND GLUTAMIC ACID RESIDUES.
Medline ID92165798
PubMed ID1537833
JournalJ Biol Chem
Year1992
Volume267
Pages4472-8
AuthorsChauvaux S, Beguin P, Aubert JP
TitleSite-directed mutagenesis of essential carboxylic residues in Clostridium thermocellum endoglucanase CelD.
Related UniProtKBP04954
[5]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
JournalNature
Year1992
Volume357
Pages89-91
AuthorsJuy M, Amit AG, Alzari PM, Poljak RJ, Claeyssens M, Beguin P, Aubert J-P
TitleThree-dimensional structure of a thermostable bacterial cellulase.
Related UniProtKBP04954
[6]
PubMed ID7730353
JournalJ Biol Chem
Year1995
Volume270
Pages9757-62
AuthorsChauvaux S, Souchon H, Alzari PM, Chariot P, Beguin P
TitleStructural and functional analysis of the metal-binding sites of Clostridium thermocellum endoglucanase CelD.
[7]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
PubMed ID7739036
JournalJ Mol Biol
Year1995
Volume248
Pages225-32
AuthorsChitarra V, Souchon H, Spinelli S, Juy M, Beguin P, Alzari PM
TitleMultiple crystal forms of endoglucanase CelD: signal peptide residues modulate lattice formation.
Related UniProtKBP04954
[8]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 47-651
Medline ID9334746
PubMed ID9334746
JournalNat Struct Biol
Year1997
Volume4
Pages810-8
AuthorsSakon J, Irwin D, Wilson DB, Karplus PA
TitleStructure and mechanism of endo/exocellulase E4 from Thermomonospora fusca.
[9]
PubMed ID11273698
JournalJ Mol Biol
Year2001
Volume307
Pages745-53
AuthorsLytle BL, Volkman BF, Westler WM, Heckman MP, Wu JH
TitleSolution structure of a type I dockerin domain, a novel prokaryotic, extracellular calcium-binding domain.
[10]
CommentsX-ray crystallography (1.4 Angstroms)
PubMed ID11914490
JournalActa Crystallogr D Biol Crystallogr
Year2002
Volume58
Pages653-659
AuthorsKhademi S, Guarino LA, Watanabe H, Tokuda G, Meyer EF
TitleStructure of an endoglucanase from termite, Nasutitermes takasagoensis.
[11]
PubMed ID11844767
JournalJ Bacteriol
Year2002
Volume184
Pages1378-84
AuthorsBelaich A, Parsiegla G, Gal L, Villard C, Haser R, Belaich JP
TitleCel9M, a new family 9 cellulase of the Clostridium cellulolyticum cellulosome.
[12]
CommentsX-ray crystallography
PubMed ID12837787
JournalJ Bacteriol
Year2003
Volume185
Pages4127-35
AuthorsMandelman D, Belaich A, Belaich JP, Aghajari N, Driguez H, Haser R
TitleX-Ray crystal structure of the multidomain endoglucanase Cel9G from Clostridium cellulolyticum complexed with natural and synthetic cello-oligosaccharides.
[13]
CommentsX-ray crystallography
PubMed ID14756552
JournalBiochemistry
Year2004
Volume43
Pages1163-70
AuthorsSchubot FD, Kataeva IA, Chang J, Shah AK, Ljungdahl LG, Rose JP, Wang BC
TitleStructural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum.
[14]
PubMed ID15274620
JournalBiochemistry
Year2004
Volume43
Pages9655-63
AuthorsZhou W, Irwin DC, Escovar-Kousen J, Wilson DB
TitleKinetic studies of Thermobifida fusca Cel9A active site mutant enzymes.

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.

createdupdated
2004-08-182009-02-26


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