DB code: D00479

RLCP classification 1.30.36010.970 : Hydrolysis
CATH domain 3.20.20.80 : TIM Barrel Catalytic domain
2.60.40.290 : Immunoglobulin-like
E.C. 3.2.1.8 3.2.1.91
CSA 2his 1exp
M-CSA 2his 1exp
MACiE

CATH domain Related DB codes (homologues)
2.60.40.290 : Immunoglobulin-like M00219 D00502 D00504 M00026 M00192
3.20.20.80 : TIM Barrel S00202 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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Includes CAZy Pfam
P07986 Exoglucanase/xylanase
None Exoglucanase
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
CBM2 (Carbohydrate-Binding Module Family 2)
GH10 (Glycoside Hydrolase Family 10)
PF00553 (CBM_2)
PF00331 (Glyco_hydro_10)
[Graphical View]

KEGG enzyme name
endo-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 )

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P07986 GUX_CELFI Hydrolysis 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.

KEGG Pathways
Map code Pathways E.C.
MAP00500 Starch and sucrose metabolism 3.2.1.91

Compound table
Substrates Products Intermediates
KEGG-id C00707 C00760 C02013 C00001 C00707 C00185 C00760
E.C. 3.2.1.8
3.2.1.91
3.2.1.91
3.2.1.8
3.2.1.91
3.2.1.8
3.2.1.91
3.2.1.91
Compound Xylan Cellulose Cellotetraose H2O Xylan Cellobiose Cellulose Transition-state in glycosylation Enzyme-Substrate intermediate Transition-state in deglycosylation
Type polysaccharide polysaccharide polysaccharide H2O polysaccharide polysaccharide polysaccharide
ChEBI 62974
15377
17057
PubChem 439626
22247451
962
439178
1expA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Intermediate-analogue:GLC-G2F Unbound
1fh7A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Transition-state-analogue:XYP-XDN
1fh8A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Transition-state-analogue:XYP-XIF
1fh9A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:XYP-LOX Unbound Unbound Unbound Unbound Unbound
1fhdA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:XYP-XIM Unbound Unbound Unbound Unbound Unbound
1j01A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:XIL Unbound Unbound Unbound Unbound Unbound
2exoA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2hisA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Intermediate-bound:GLC-GLC Unbound
2xylA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Intermediate-analogue:XYP-X2F Unbound
1exgA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1exhA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P07986 &literature [5], [9]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1expA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 127;HIS 205;GLU 233;ASP 235
1fh7A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 127;HIS 205;GLU 233;ASP 235
1fh8A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 127;HIS 205;GLU 233;ASP 235
1fh9A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 127;HIS 205;GLU 233;ASP 235
1fhdA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 127;HIS 205;GLU 233;ASP 235
1j01A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 127;HIS 205;GLU 233;ASP 235
2exoA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 127;HIS 205;GLU 233;ASP 235
2hisA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ; ;GLU 233;ASP 235 mutant E127A, H205N
2xylA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 127;HIS 205;GLU 233;ASP 235
1exgA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1exhA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
p.6372
[5]
p.12549-12552
[8]
Scheme 1 4
[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]
Resource
Comments DISULFIDE BONDS.
Medline ID 92104156
PubMed ID 1761039
Journal Eur J Biochem
Year 1991
Volume 202
Pages 367-77
Authors Gilkes NR, Claeyssens M, Aebersold R, Henrissat B, Meinke A, Morrison HD, Kilburn DG, Warren RA, Miller RC Jr
Title Structural and functional relationships in two families of beta-1,4-glycanases.
Related PDB
Related UniProtKB P07986
[2]
Resource
Comments ACTIVE SITE GLU-274.
Medline ID 91340691
PubMed ID 1678739
Journal J Biol Chem
Year 1991
Volume 266
Pages 15621-5
Authors Tull D, Withers SG, Gilkes NR, Kilburn DG, Warren RA, Aebersold R
Title Glutamic acid 274 is the nucleophile in the active site of a "retaining" exoglucanase from Cellulomonas fimi.
Related PDB
Related UniProtKB P07986
[3]
Resource
Comments
Medline ID
PubMed ID 1453471
Journal J Mol Biol
Year 1992
Volume 228
Pages 693-5
Authors Bedarkar S, Gilkes NR, Kilburn DG, Kwan E, Rose DR, Miller RC Jr, Warren RA, Withers SG
Title Crystallization 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.
Related PDB
Related UniProtKB
[4]
Resource
Comments MUTAGENESIS OF GLU-168.
Medline ID 94250681
PubMed ID 7910761
Journal Biochemistry
Year 1994
Volume 33
Pages 6371-6
Authors MacLeod AM, Lindhorst T, Withers SG, Warren RA
Title The acid/base catalyst in the exoglucanase/xylanase from Cellulomonas fimi is glutamic acid 127: evidence from detailed kinetic studies of mutants.
Related PDB
Related UniProtKB P07986
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID 95001978
PubMed ID 7918478
Journal Biochemistry
Year 1994
Volume 33
Pages 12546-52
Authors White A, Withers SG, Gilkes NR, Rose DR
Title Crystal structure of the catalytic domain of the beta-1,4-glycanase cex from Cellulomonas fimi.
Related PDB 2exo
Related UniProtKB P07986
[6]
Resource
Comments STRUCTURE BY NMR OF 377-484.
Medline ID 95284032
PubMed ID 7766609
Journal Biochemistry
Year 1995
Volume 34
Pages 6993-7009
Authors Xu GY, Ong E, Gilkes NR, Kilburn DG, Muhandiram DR, Harris-Brandts M, Carver JP, Kay LE, Harvey TS
Title Solution structure of a cellulose-binding domain from Cellulomonas fimi by nuclear magnetic resonance spectroscopy.
Related PDB 1exg 1exh
Related UniProtKB P07986
[7]
Resource
Comments
Medline ID
PubMed ID 8714589
Journal Anal Biochem
Year 1996
Volume 234
Pages 119-25
Authors Tull D, Burgoyne DL, Chow DT, Withers SG, Aebersold R
Title A 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.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 8855954
Journal Biochemistry
Year 1996
Volume 35
Pages 13165-72
Authors MacLeod AM, Tull D, Rupitz K, Warren RA, Withers SG
Title Mechanistic consequences of mutation of active site carboxylates in a retaining beta-1,4-glycanase from Cellulomonas fimi.
Related PDB
Related UniProtKB
[9]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID 96163434
PubMed ID 8564541
Journal Nat Struct Biol
Year 1996
Volume 3
Pages 149-54
Authors White A, Tull D, Johns K, Withers SG, Rose DR
Title Crystallographic observation of a covalent catalytic intermediate in a beta-glycosidase.
Related PDB 1exp
Related UniProtKB P07986
[10]
Resource
Comments
Medline ID
PubMed ID 8901562
Journal Proc Natl Acad Sci U S A
Year 1996
Volume 93
Pages 12229-34
Authors Creagh AL, Ong E, Jervis E, Kilburn DG, Haynes CA
Title Binding of the cellulose-binding domain of exoglucanase Cex from Cellulomonas fimi to insoluble microcrystalline cellulose is entropically driven.
Related PDB
Related UniProtKB
[11]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 42-353.
Medline ID 98206890
PubMed ID 9537990
Journal Biochemistry
Year 1998
Volume 37
Pages 4751-8
Authors Notenboom V, Birsan C, Warren RA, Withers SG, Rose DR
Title Exploring the cellulose/xylan specificity of the beta-1,4-glycanase cex from Cellulomonas fimi through crystallography and mutation.
Related PDB 2xyl
Related UniProtKB P07986
[12]
Resource
Comments
Medline ID
PubMed ID 9822697
Journal J Biol Chem
Year 1998
Volume 273
Pages 32187-99
Authors Charnock SJ, Spurway TD, Xie H, Beylot MH, Virden R, Warren RA, Hazlewood GP, Gilbert HJ
Title The topology of the substrate binding clefts of glycosyl hydrolase family 10 xylanases are not conserved.
Related PDB
Related UniProtKB
[13]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 42-353.
Medline ID 98400502
PubMed ID 9731776
Journal Nat Struct Biol
Year 1998
Volume 5
Pages 812-8
Authors Notenboom V, Birsan C, Nitz M, Rose DR, Warren RA, Withers SG
Title Insights into transition state stabilization of the beta-1,4-glycosidase Cex by covalent intermediate accumulation in active site mutants.
Related PDB 2his
Related UniProtKB P07986
[14]
Resource
Comments
Medline ID
PubMed ID 10571062
Journal FEBS Lett
Year 1999
Volume 460
Pages 61-6
Authors Kaneko S, Kuno A, Fujimoto Z, Shimizu D, Machida S, Sato Y, Yura K, Go M, Mizuno H, Taira K, Kusakabe I, Hayashi K
Title An 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.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 10570988
Journal Gene
Year 1999
Volume 238
Pages 93-101
Authors Sato Y, Niimura Y, Yura K, Go M
Title Module-intron correlation and intron sliding in family F/10 xylanase genes.
Related PDB
Related UniProtKB
[16]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10995222
Journal Biochemistry
Year 2000
Volume 39
Pages 11553-63
Authors Notenboom V, Williams SJ, Hoos R, Withers SG, Rose DR
Title Detailed structural analysis of glycosidase/inhibitor interactions: complexes of Cex from Cellulomonas fimi with xylobiose-derived aza-sugars.
Related PDB 1fh7 1fh8 1fh9 1fhd
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 11239087
Journal Protein Eng
Year 2000
Volume 13
Pages 873-9
Authors Kaneko S, Iwamatsu S, Kuno A, Fujimoto Z, Sato Y, Yura K, Go M, Mizuno H, Taira K, Hasegawa T, Kusakabe I, Hayashi K
Title Module 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.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 11025547
Journal Proteins
Year 2000
Volume 41
Pages 362-73
Authors Leggio LL, Jenkins J, Harris GW, Pickersgill RW
Title X-ray crystallographic study of xylopentaose binding to Pseudomonas fluorescens xylanase A.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 11963886
Journal Appl Biochem Biotechnol
Year 2001
Volume 91-93
Pages 575-92
Authors Esteghlalian AR, Srivastava V, Gilkes NR, Kilburn DG, Warren RA, Saddle JN
Title Do cellulose binding domains increase substrate accessibility?
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 12418218
Journal Methods Enzymol
Year 2002
Volume 354
Pages 84-105
Authors Wicki J, Rose DR, Withers SG
Title Trapping covalent intermediates on beta-glycosidases.
Related PDB
Related UniProtKB

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.

Created Updated
2005-03-14 2009-02-26