EzCatDB: D00479

DB codeD00479
RLCP classification1.30.36010.970
CATH domainDomain 13.20.20.80Catalytic domain
Domain 22.60.40.290
E.C.3.2.1.8,3.2.1.91
CSA1exp,2his

CATH domainRelated DB codes (homologues)
2.60.40.290M00219,D00502,D00504,M00026,M00192
3.20.20.80S00202,S00210,S00748,S00906,S00907,S00911,S00912,S00915,M00134,M00160,S00204,S00205,S00206,S00207,S00203,S00208,S00209,S00211,S00213,S00214,M00113,T00307,D00165,D00166,D00169,D00176,D00501,D00502,D00503,D00844,D00861,D00864,M00026,M00112,M00193,M00346,T00057,T00062,T00063,T00066,T00067

Enzyme Name
Swiss-protKEGG

P07986
Protein nameExoglucanase/xylanaseendo-1,4-beta-xylanase
   (EC 3.2.1.8)
endo-(1->4)-beta-xylan 4-xylanohydrolase
   (EC 3.2.1.8)
endo-1,4-xylanase
   (EC 3.2.1.8)
xylanase
   (EC 3.2.1.8)
beta-1,4-xylanase
   (EC 3.2.1.8)
endo-1,4-xylanase
   (EC 3.2.1.8)
endo-beta-1,4-xylanase
   (EC 3.2.1.8)
endo-1,4-beta-D-xylanase
   (EC 3.2.1.8)
1,4-beta-xylan xylanohydrolase
   (EC 3.2.1.8)
beta-xylanase
   (EC 3.2.1.8)
beta-1,4-xylan xylanohydrolase
   (EC 3.2.1.8)
endo-1,4-beta-xylanase
   (EC 3.2.1.8)
beta-D-xylanase
   (EC 3.2.1.8)
cellulose 1,4-beta-cellobiosidase
   (EC 3.2.1.91)
exo-cellobiohydrolase
   (EC 3.2.1.91)
beta-1,4-glucan cellobiohydrolase
   (EC 3.2.1.91)
beta-1,4-glucan cellobiosylhydrolase
   (EC 3.2.1.91)
1,4-beta-glucan cellobiosidase
   (EC 3.2.1.91)
exoglucanase
   (EC 3.2.1.91)
avicelase
   (EC 3.2.1.91)
CBH 1
   (EC 3.2.1.91)
C1 cellulase
   (EC 3.2.1.91)
cellobiohydrolase I
   (EC 3.2.1.91)
cellobiohydrolase
   (EC 3.2.1.91)
exo-beta-1,4-glucan cellobiohydrolase
   (EC 3.2.1.91)
1,4-beta-D-glucan cellobiohydrolase
   (EC 3.2.1.91)
cellobiosidase
   (EC 3.2.1.91)
SynonymsNone
IncludesExoglucanase
   EC 3.2.1.91
Exocellobiohydrolase 1,4-beta-cellobiohydrolase Beta-1,4-glycanase CEX
Endo-1,4-beta-xylanase B
(Xylanase B)
   EC 3.2.1.8

KEGG pathways
MAP codePathwaysE.C.
MAP00500Starch and sucrose metabolism3.2.1.91

Swiss-prot:Accession NumberP07986
Entry nameGUX_CELFI
ActivityHydrolysis of 1,4-beta-D-glucosidic linkages in cellulose and cellotetraose, releasing cellobiose from the non- reducing ends of the chains.,Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.
Subunit
Subcellular location
Cofactor


SubstratesProductsintermediates
KEGG-idC00707C00760C02013C00001C00707C00185C00760


E.C.3.2.1.83.2.1.913.2.1.913.2.1.8,3.2.1.913.2.1.83.2.1.913.2.1.91


CompoundXylanCelluloseCellotetraoseH2OXylanCellobioseCelluloseTransition-state in glycosylationEnzyme-Substrate intermediateTransition-state in deglycosylation
TypepolysaccharidepolysaccharidepolysaccharideH2Opolysaccharidepolysaccharidepolysaccharide


1expAUnboundUnboundUnbound
UnboundUnboundUnboundUnboundIntermediate-analogue:GLC-G2FUnbound
1fh7AUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundTransition-state-analogue:XYP-XDN
1fh8AUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundTransition-state-analogue:XYP-XIF
1fh9AUnboundUnboundUnbound
Analogue:XYP-LOXUnboundUnboundUnboundUnboundUnbound
1fhdAUnboundUnboundUnbound
Analogue:XYP-XIMUnboundUnboundUnboundUnboundUnbound
1j01AUnboundUnboundUnbound
Analogue:XILUnboundUnboundUnboundUnboundUnbound
2exoAUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
2hisAUnboundUnboundUnbound
UnboundUnboundUnboundUnboundIntermediate-bound:GLC-GLCUnbound
2xylAUnboundUnboundUnbound
UnboundUnboundUnboundUnboundIntermediate-analogue:XYP-X2FUnbound
1exgAUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1exhAUnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P07986 &literature [5], [9]
pdbCatalytic residuescomment
1expAGLU 127;HIS 205;GLU 233;ASP 235

1fh7AGLU 127;HIS 205;GLU 233;ASP 235

1fh8AGLU 127;HIS 205;GLU 233;ASP 235

1fh9AGLU 127;HIS 205;GLU 233;ASP 235

1fhdAGLU 127;HIS 205;GLU 233;ASP 235

1j01AGLU 127;HIS 205;GLU 233;ASP 235

2exoAGLU 127;HIS 205;GLU 233;ASP 235

2hisA       ;       ;GLU 233;ASP 235
mutant E127A, H205N
2xylAGLU 127;HIS 205;GLU 233;ASP 235

1exgA               

1exhA               


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]p.6372
[5]p.12549-12552
[8]Scheme 14
[9]Fig. 1, p.150-151
[11]Scheme 1, Scheme 2
[13]Fig.1, Fig.5, p.813-817
[16]Fig.2, p.11560-11561
[20]FIG. 1, p.86

references
[1]
CommentsDISULFIDE BONDS.
Medline ID92104156
PubMed ID1761039
JournalEur J Biochem
Year1991
Volume202
Pages367-77
AuthorsGilkes NR, Claeyssens M, Aebersold R, Henrissat B, Meinke A, Morrison HD, Kilburn DG, Warren RA, Miller RC Jr
TitleStructural and functional relationships in two families of beta-1,4-glycanases.
Related Swiss-protP07986
[2]
CommentsACTIVE SITE GLU-274.
Medline ID91340691
PubMed ID1678739
JournalJ Biol Chem
Year1991
Volume266
Pages15621-5
AuthorsTull D, Withers SG, Gilkes NR, Kilburn DG, Warren RA, Aebersold R
TitleGlutamic acid 274 is the nucleophile in the active site of a "retaining" exoglucanase from Cellulomonas fimi.
Related Swiss-protP07986
[3]
PubMed ID1453471
JournalJ Mol Biol
Year1992
Volume228
Pages693-5
AuthorsBedarkar S, Gilkes NR, Kilburn DG, Kwan E, Rose DR, Miller RC Jr, Warren RA, Withers SG
TitleCrystallization and preliminary X-ray diffraction analysis of the catalytic domain of Cex, an exo-beta-1,4-glucanase and beta-1,4-xylanase from the bacterium Cellulomonas fimi.
[4]
CommentsMUTAGENESIS OF GLU-168.
Medline ID94250681
PubMed ID7910761
JournalBiochemistry
Year1994
Volume33
Pages6371-6
AuthorsMacLeod AM, Lindhorst T, Withers SG, Warren RA
TitleThe acid/base catalyst in the exoglucanase/xylanase from Cellulomonas fimi is glutamic acid 127: evidence from detailed kinetic studies of mutants.
Related Swiss-protP07986
[5]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID95001978
PubMed ID7918478
JournalBiochemistry
Year1994
Volume33
Pages12546-52
AuthorsWhite A, Withers SG, Gilkes NR, Rose DR
TitleCrystal structure of the catalytic domain of the beta-1,4-glycanase cex from Cellulomonas fimi.
Related PDB2exo
Related Swiss-protP07986
[6]
CommentsSTRUCTURE BY NMR OF 377-484.
Medline ID95284032
PubMed ID7766609
JournalBiochemistry
Year1995
Volume34
Pages6993-7009
AuthorsXu GY, Ong E, Gilkes NR, Kilburn DG, Muhandiram DR, Harris-Brandts M, Carver JP, Kay LE, Harvey TS
TitleSolution structure of a cellulose-binding domain from Cellulomonas fimi by nuclear magnetic resonance spectroscopy.
Related PDB1exg,1exh
Related Swiss-protP07986
[7]
PubMed ID8714589
JournalAnal Biochem
Year1996
Volume234
Pages119-25
AuthorsTull D, Burgoyne DL, Chow DT, Withers SG, Aebersold R
TitleA mass spectrometry-based approach for probing enzyme active sites: identification of Glu 127 in Cellulomonas fimi exoglycanase as the residue modified by N-bromoacetyl cellobiosylamine.
[8]
PubMed ID8855954
JournalBiochemistry
Year1996
Volume35
Pages13165-72
AuthorsMacLeod AM, Tull D, Rupitz K, Warren RA, Withers SG
TitleMechanistic consequences of mutation of active site carboxylates in a retaining beta-1,4-glycanase from Cellulomonas fimi.
[9]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID96163434
PubMed ID8564541
JournalNat Struct Biol
Year1996
Volume3
Pages149-54
AuthorsWhite A, Tull D, Johns K, Withers SG, Rose DR
TitleCrystallographic observation of a covalent catalytic intermediate in a beta-glycosidase.
Related PDB1exp
Related Swiss-protP07986
[10]
PubMed ID8901562
JournalProc Natl Acad Sci U S A
Year1996
Volume93
Pages12229-34
AuthorsCreagh AL, Ong E, Jervis E, Kilburn DG, Haynes CA
TitleBinding of the cellulose-binding domain of exoglucanase Cex from Cellulomonas fimi to insoluble microcrystalline cellulose is entropically driven.
[11]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 42-353.
Medline ID98206890
PubMed ID9537990
JournalBiochemistry
Year1998
Volume37
Pages4751-8
AuthorsNotenboom V, Birsan C, Warren RA, Withers SG, Rose DR
TitleExploring the cellulose/xylan specificity of the beta-1,4-glycanase cex from Cellulomonas fimi through crystallography and mutation.
Related PDB2xyl
Related Swiss-protP07986
[12]
PubMed ID9822697
JournalJ Biol Chem
Year1998
Volume273
Pages32187-99
AuthorsCharnock SJ, Spurway TD, Xie H, Beylot MH, Virden R, Warren RA, Hazlewood GP, Gilbert HJ
TitleThe topology of the substrate binding clefts of glycosyl hydrolase family 10 xylanases are not conserved.
[13]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 42-353.
Medline ID98400502
PubMed ID9731776
JournalNat Struct Biol
Year1998
Volume5
Pages812-8
AuthorsNotenboom V, Birsan C, Nitz M, Rose DR, Warren RA, Withers SG
TitleInsights into transition state stabilization of the beta-1,4-glycosidase Cex by covalent intermediate accumulation in active site mutants.
Related PDB2his
Related Swiss-protP07986
[14]
PubMed ID10571062
JournalFEBS Lett
Year1999
Volume460
Pages61-6
AuthorsKaneko S, Kuno A, Fujimoto Z, Shimizu D, Machida S, Sato Y, Yura K, Go M, Mizuno H, Taira K, Kusakabe I, Hayashi K
TitleAn investigation of the nature and function of module 10 in a family F/10 xylanase FXYN of Streptomyces olivaceoviridis E-86 by module shuffling with the Cex of Cellulomonas fimi and by site-directed mutagenesis.
[15]
PubMed ID10570988
JournalGene
Year1999
Volume238
Pages93-101
AuthorsSato Y, Niimura Y, Yura K, Go M
TitleModule-intron correlation and intron sliding in family F/10 xylanase genes.
[16]
CommentsX-ray crystallography
PubMed ID10995222
JournalBiochemistry
Year2000
Volume39
Pages11553-63
AuthorsNotenboom V, Williams SJ, Hoos R, Withers SG, Rose DR
TitleDetailed structural analysis of glycosidase/inhibitor interactions: complexes of Cex from Cellulomonas fimi with xylobiose-derived aza-sugars.
Related PDB1fh7,1fh8,1fh9,1fhd
[17]
PubMed ID11239087
JournalProtein Eng
Year2000
Volume13
Pages873-9
AuthorsKaneko S, Iwamatsu S, Kuno A, Fujimoto Z, Sato Y, Yura K, Go M, Mizuno H, Taira K, Hasegawa T, Kusakabe I, Hayashi K
TitleModule shuffling of a family F/10 xylanase: replacement of modules M4 and M5 of the FXYN of Streptomyces olivaceoviridis E-86 with those of the Cex of Cellulomonas fimi.
[18]
PubMed ID11025547
JournalProteins
Year2000
Volume41
Pages362-73
AuthorsLeggio LL, Jenkins J, Harris GW, Pickersgill RW
TitleX-ray crystallographic study of xylopentaose binding to Pseudomonas fluorescens xylanase A.
[19]
PubMed ID11963886
JournalAppl Biochem Biotechnol
Year2001
Volume91-93
Pages575-92
AuthorsEsteghlalian AR, Srivastava V, Gilkes NR, Kilburn DG, Warren RA, Saddle JN
TitleDo cellulose binding domains increase substrate accessibility?
[20]
PubMed ID12418218
JournalMethods Enzymol
Year2002
Volume354
Pages84-105
AuthorsWicki J, Rose DR, Withers SG
TitleTrapping covalent intermediates on beta-glycosidases.

comments
This family belongs to the glycosidase family-10, which has a retaining mechanism (equatorial to equatorial conformation), and also a family of 4/7 superfamily, which has got catalytic residues at the C-terminal ends of beta-4 and beta-7 on the (alpha/beta)8 barrel fold. The catalytic mechanism must be similar to those of 4/7 superfamily enzymes (such as S00203 in EzCatDB).
According to the literature [4], [5] & [8], Glu233 and Glu127 act as a nucleophile and acid-base, respectively. The catalytic reaction is initiated by the protonation of Glu127 to the O1 atom of Xylan/Cellurose substrate. This suggests that the reaction proceeds through a dissociative-type (or SN1-like) mechanism, with a formation of oxocarbonium ion in the transition state, during the glycosylation of the active site. During the glycosylation, Glu233 makes a covalent bond with the C1 atom of the substrate.
At the second stage, or during the deglycosylation, a water molecule can be activated by a general base, Glu127.
According to the literature [9] & [13], His205-Asp235 dyad seems to stabilize the leaving nucleophile, Glu233, during the deglycosylation.

createdupdated
2005-03-142009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
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)

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