EzCatDB: M00160
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DB codeM00160
RLCP classification1.30.36010.970 : Hydrolysis
CATH domainDomain 1-.-.-.-
Domain 2-.-.-.-
Domain 32.30.32.30 : Xylanase; Chain A
Domain 4-.-.-.-
Domain 53.20.20.80 : TIM BarrelCatalytic domain
E.C.3.2.1.8

CATH domainRelated DB codes (homologues)
3.20.20.80 : TIM BarrelS00202,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

Enzyme Name
UniProtKBKEGG

P14768
Protein nameEndo-1,4-beta-xylanase Aendo-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
SynonymsXylanase A
EC 3.2.1.8
1,4-beta-D-xylan xylanohydrolase A
XYLA
RefSeqYP_001982932.1 (Protein)
NC_010995.1 (DNA/RNA sequence)
PfamPF02013 (CBM_10)
PF00553 (CBM_2)
PF00331 (Glyco_hydro_10)
[Graphical view]
CAZyGH10 (Glycoside Hydrolase Family)


UniProtKB:Accession NumberP14768
Entry nameXYNA_PSEFL
ActivityEndohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.
Subunit
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC00707C00001C00707
CompoundXylanH2OXylan
TypepolysaccharideH2Opolysaccharide
ChEBI
15377

PubChem
962
22247451

           
1ct7AUnbound Unbound
1e8rAUnbound Unbound
1qldAUnbound Unbound
1clxAUnbound Unbound
1clxBUnbound Unbound
1clxCUnbound Unbound
1clxDUnbound Unbound
1e5nABound:XYP-XYP-XYP-XYP-XYP Unbound
1e5nBBound:XYP-XYP-XYP-XYP-XYP Unbound

Active-site residues
pdbCatalytic residuescomment
          
1ct7A 
 
1e8rA 
 
1qldA 
 
1clxAGLU 127;HIS 215;GLU 246;ASP 248
 
1clxBGLU 127;HIS 215;GLU 246;ASP 248
 
1clxCGLU 127;HIS 215;GLU 246;ASP 248
 
1clxDGLU 127;HIS 215;GLU 246;ASP 248
 
1e5nAGLU 127;HIS 215;       ;ASP 248
mutant E246C
1e5nBGLU 127;HIS 215;       ;ASP 248
mutant E246C

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]Fig. 3, p.1108-1109
[10]p.32194-32196

references
[1]
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.
[2]
CommentsX-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 265-611, AND REVISIONS.
Medline ID95187712
PubMed ID7881909
JournalStructure
Year1994
Volume2
Pages1107-16
AuthorsHarris GW, Jenkins JA, Connerton I, Cummings N, Lo Leggio L, Scott M, Hazlewood GP, Laurie JI, Gilbert HJ, Pickersgill RW
TitleStructure of the catalytic core of the family F xylanase from Pseudomonas fluorescens and identification of the xylopentaose-binding sites.
Related UniProtKBP14768
[3]
PubMed ID7729513
JournalFEBS Lett
Year1995
Volume362
Pages281-5
AuthorsJenkins J, Lo Leggio L, Harris G, Pickersgill R
TitleBeta-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.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 265-611.
JournalActa Crystallogr D Biol Crystallogr
Year1996
Volume52
Pages393-401
AuthorsHarris GW, Jenkins JA, Connerton I, Pickersgill RW
TitleRefined crystal structure of the catalytic domain of xylanase A from Pseudomonas fluorescens at 1.8-A resolution.
Related PDB1clx
Related UniProtKBP14768
[5]
PubMed ID8912689
JournalBiochem J
Year1996
Volume319
Pages515-20
AuthorsBlack GW, Rixon JE, Clarke JH, Hazlewood GP, Theodorou MK, Morris P, Gilbert HJ
TitleEvidence that linker sequences and cellulose-binding domains enhance the activity of hemicellulases against complex substrates.
[6]
PubMed ID9006940
JournalJ Biol Chem
Year1997
Volume272
Pages2942-51
AuthorsCharnock SJ, Lakey JH, Virden R, Hughes N, Sinnott ML, Hazlewood GP, Pickersgill R, Gilbert HJ
TitleKey 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.
[7]
PubMed ID9560304
JournalBiochem J
Year1998
Volume331
Pages775-81
AuthorsBolam DN, Ciruela A, McQueen-Mason S, Simpson P, Williamson MP, Rixon JE, Boraston A, Hazlewood GP, Gilbert HJ
TitlePseudomonas cellulose-binding domains mediate their effects by increasing enzyme substrate proximity.
[8]
PubMed ID9662439
JournalFEBS Lett
Year1998
Volume429
Pages312-6
AuthorsNagy T, Simpson P, Williamson MP, Hazlewood GP, Gilbert HJ, Orosz L
TitleAll three surface tryptophans in Type IIa cellulose binding domains play a pivotal role in binding both soluble and insoluble ligands.
[9]
PubMed ID9812357
JournalFEMS Microbiol Lett
Year1998
Volume168
Pages1-7
AuthorsKarlsson EN, Bartonek-Roxa E, Holst O
TitleEvidence for substrate binding of a recombinant thermostable xylanase originating from Rhodothermus marinus.
[10]
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.
[11]
PubMed ID10455036
JournalBiochem J
Year1999
Volume342
Pages473-80
AuthorsGill J, Rixon JE, Bolam DN, McQueen-Mason S, Simpson PJ, Williamson MP, Hazlewood GP, Gilbert HJ
TitleThe type II and X cellulose-binding domains of Pseudomonas xylanase A potentiate catalytic activity against complex substrates by a common mechanism.
[12]
PubMed ID10653642
JournalBiochemistry
Year2000
Volume39
Pages985-91
AuthorsPonyi T, Szabo L, Nagy T, Orosz L, Simpson PJ, Williamson MP, Gilbert HJ
TitleTrp22, Trp24, and Tyr8 play a pivotal role in the binding of the family 10 cellulose-binding module from Pseudomonas xylanase A to insoluble ligands.
[13]
CommentsNMR Structure
PubMed ID10653641
JournalBiochemistry
Year2000
Volume39
Pages978-84
AuthorsRaghothama S, Simpson PJ, Szabo L, Nagy T, Gilbert HJ, Williamson MP
TitleSolution structure of the CBM10 cellulose binding module from Pseudomonas xylanase A.
Related PDB1ct7,1e8r,1qld
[14]
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.
Related PDB1e5n
[15]
PubMed ID11281716
JournalProtein Expr Purif
Year2001
Volume21
Pages417-23
AuthorsBoraston AB, McLean BW, Guarna MM, Amandaron-Akow E, Kilburn DG
TitleA family 2a carbohydrate-binding module suitable as an affinity tag for proteins produced in Pichia pastoris.

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.

createdupdated
2003-08-282009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
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Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
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)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
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