DB code: M00160

RLCP classification 1.30.36010.970 : Hydrolysis
CATH domain -.-.-.- :
-.-.-.- :
2.30.32.30 : Xylanase; Chain A
-.-.-.- :
3.20.20.80 : TIM Barrel Catalytic domain
E.C. 3.2.1.8
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.20.20.80 : TIM Barrel S00202 S00210 S00748 S00906 S00907 S00911 S00912 S00915 M00134 D00479 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 RefSeq CAZy Pfam
P14768 Endo-1,4-beta-xylanase A
Xylanase A
EC 3.2.1.8
1,4-beta-D-xylan xylanohydrolase A
XYLA
YP_001982932.1 (Protein)
NC_010995.1 (DNA/RNA sequence)
CBM10 (Carbohydrate-Binding Module Family 10)
CBM2 (Carbohydrate-Binding Module Family 2)
GH10 (Glycoside Hydrolase Family 10)
PF02013 (CBM_10)
PF00553 (CBM_2)
PF00331 (Glyco_hydro_10)
[Graphical View]

KEGG enzyme name
endo-1,4-beta-xylanase
endo-(1->4)-beta-xylan 4-xylanohydrolase
endo-1,4-xylanase
xylanase
beta-1,4-xylanase
endo-1,4-xylanase
endo-beta-1,4-xylanase
endo-1,4-beta-D-xylanase
1,4-beta-xylan xylanohydrolase
beta-xylanase
beta-1,4-xylan xylanohydrolase
endo-1,4-beta-xylanase
beta-D-xylanase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P14768 XYNA_PSEFL Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.

KEGG Pathways
Map code Pathways E.C.

Compound table
Substrates Products Intermediates
KEGG-id C00707 C00001 C00707
E.C.
Compound Xylan H2O Xylan
Type polysaccharide H2O polysaccharide
ChEBI 15377
PubChem 22247451
962
1ct7A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1e8rA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1qldA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1clxA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1clxB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1clxC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1clxD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound
1e5nA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:XYP-XYP-XYP-XYP-XYP Unbound
1e5nB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:XYP-XYP-XYP-XYP-XYP Unbound

Reference for Active-site residues
resource references E.C.

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1ct7A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1e8rA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qldA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1clxA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 127;HIS 215;GLU 246;ASP 248
1clxB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 127;HIS 215;GLU 246;ASP 248
1clxC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 127;HIS 215;GLU 246;ASP 248
1clxD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 127;HIS 215;GLU 246;ASP 248
1e5nA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 127;HIS 215;;ASP 248 mutant E246C
1e5nB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 127;HIS 215;;ASP 248 mutant E246C

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
Fig. 3, p.1108-1109
[10]
p.32194-32196

References
[1]
Resource
Comments
Medline ID
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
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 265-611, AND REVISIONS.
Medline ID 95187712
PubMed ID 7881909
Journal Structure
Year 1994
Volume 2
Pages 1107-16
Authors Harris GW, Jenkins JA, Connerton I, Cummings N, Lo Leggio L, Scott M, Hazlewood GP, Laurie JI, Gilbert HJ, Pickersgill RW
Title Structure of the catalytic core of the family F xylanase from Pseudomonas fluorescens and identification of the xylopentaose-binding sites.
Related PDB
Related UniProtKB P14768
[3]
Resource
Comments
Medline ID
PubMed ID 7729513
Journal FEBS Lett
Year 1995
Volume 362
Pages 281-5
Authors Jenkins J, Lo Leggio L, Harris G, Pickersgill R
Title Beta-glucosidase, beta-galactosidase, family A cellulases, family F xylanases and two barley glycanases form a superfamily of enzymes with 8-fold beta/alpha architecture and with two conserved glutamates near the carboxy-terminal ends of beta-strands four and seven.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 265-611.
Medline ID
PubMed ID
Journal Acta Crystallogr D Biol Crystallogr
Year 1996
Volume 52
Pages 393-401
Authors Harris GW, Jenkins JA, Connerton I, Pickersgill RW
Title Refined crystal structure of the catalytic domain of xylanase A from Pseudomonas fluorescens at 1.8-A resolution.
Related PDB 1clx
Related UniProtKB P14768
[5]
Resource
Comments
Medline ID
PubMed ID 8912689
Journal Biochem J
Year 1996
Volume 319
Pages 515-20
Authors Black GW, Rixon JE, Clarke JH, Hazlewood GP, Theodorou MK, Morris P, Gilbert HJ
Title Evidence that linker sequences and cellulose-binding domains enhance the activity of hemicellulases against complex substrates.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 9006940
Journal J Biol Chem
Year 1997
Volume 272
Pages 2942-51
Authors Charnock SJ, Lakey JH, Virden R, Hughes N, Sinnott ML, Hazlewood GP, Pickersgill R, Gilbert HJ
Title Key residues in subsite F play a critical role in the activity of Pseudomonas fluorescens subspecies cellulosa xylanase A against xylooligosaccharides but not against highly polymeric substrates such as xylan.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 9560304
Journal Biochem J
Year 1998
Volume 331
Pages 775-81
Authors Bolam DN, Ciruela A, McQueen-Mason S, Simpson P, Williamson MP, Rixon JE, Boraston A, Hazlewood GP, Gilbert HJ
Title Pseudomonas cellulose-binding domains mediate their effects by increasing enzyme substrate proximity.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 9662439
Journal FEBS Lett
Year 1998
Volume 429
Pages 312-6
Authors Nagy T, Simpson P, Williamson MP, Hazlewood GP, Gilbert HJ, Orosz L
Title All three surface tryptophans in Type IIa cellulose binding domains play a pivotal role in binding both soluble and insoluble ligands.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 9812357
Journal FEMS Microbiol Lett
Year 1998
Volume 168
Pages 1-7
Authors Karlsson EN, Bartonek-Roxa E, Holst O
Title Evidence for substrate binding of a recombinant thermostable xylanase originating from Rhodothermus marinus.
Related PDB
Related UniProtKB
[10]
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
[11]
Resource
Comments
Medline ID
PubMed ID 10455036
Journal Biochem J
Year 1999
Volume 342
Pages 473-80
Authors Gill J, Rixon JE, Bolam DN, McQueen-Mason S, Simpson PJ, Williamson MP, Hazlewood GP, Gilbert HJ
Title The type II and X cellulose-binding domains of Pseudomonas xylanase A potentiate catalytic activity against complex substrates by a common mechanism.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 10653642
Journal Biochemistry
Year 2000
Volume 39
Pages 985-91
Authors Ponyi T, Szabo L, Nagy T, Orosz L, Simpson PJ, Williamson MP, Gilbert HJ
Title Trp22, Trp24, and Tyr8 play a pivotal role in the binding of the family 10 cellulose-binding module from Pseudomonas xylanase A to insoluble ligands.
Related PDB
Related UniProtKB
[13]
Resource
Comments NMR Structure
Medline ID
PubMed ID 10653641
Journal Biochemistry
Year 2000
Volume 39
Pages 978-84
Authors Raghothama S, Simpson PJ, Szabo L, Nagy T, Gilbert HJ, Williamson MP
Title Solution structure of the CBM10 cellulose binding module from Pseudomonas xylanase A.
Related PDB 1ct7 1e8r 1qld
Related UniProtKB
[14]
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 1e5n
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 11281716
Journal Protein Expr Purif
Year 2001
Volume 21
Pages 417-23
Authors Boraston AB, McLean BW, Guarna MM, Amandaron-Akow E, Kilburn DG
Title A family 2a carbohydrate-binding module suitable as an affinity tag for proteins produced in Pichia pastoris.
Related PDB
Related UniProtKB

Comments
This family belongs to Glycosidase family-10, which has an 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.
According to the literature [2] & [4], Glu246 and Glu127 (of 1clx) act as a nucleophile and acid-base, respectively. The catalysis 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, Glu246 approaches the C1 atom of the glcose to form a covalent intermediate, whilst Glu127 protonates the leaving group. (At the second stage, or during the deglycosylation, a water molecule can be activated by a general base, Glu127.)
Moreover, comparing the structural data with that of the other family-10 enzyme, xylanase (E.C. 3.2.1.8) (D00479 in EzCatDB), His215-Asp248 dyad seems to stabilize the leaving nucleophile, Glu246, during the deglycosylation.

Created Updated
2003-08-28 2009-02-26