EzCatDB: D00169
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DB codeD00169
RLCP classification1.30.36010.970 : Hydrolysis
CATH domainDomain 12.80.10.50 : Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Domain 23.20.20.80 : TIM BarrelCatalytic domain
E.C.3.2.1.8

CATH domainRelated DB codes (homologues)
2.80.10.50 : Trefoil (Acidic Fibroblast Growth Factor, subunit A)D00666,M00185
3.20.20.80 : TIM BarrelS00202,S00210,S00748,S00906,S00907,S00911,S00912,S00915,M00134,M00160,D00479,S00204,S00205,S00206,S00207,S00203,S00208,S00209,S00211,S00213,S00214,M00113,T00307,D00165,D00166,D00176,D00501,D00502,D00503,D00844,D00861,D00864,M00026,M00112,M00193,M00346,T00057,T00062,T00063,T00066,T00067

Enzyme Name
UniProtKBKEGG

P26514Q7SI98
Protein nameEndo-1,4-beta-xylanase A
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
SynonymsXylanase A
EC 3.2.1.8
1,4-beta-D-xylan xylanohydrolase A
Hydrolase
PfamPF00331 (Glyco_hydro_10)
PF00652 (Ricin_B_lectin)
[Graphical view]
PF00331 (Glyco_hydro_10)
PF00652 (Ricin_B_lectin)
[Graphical view]
CAZyGH10 (Glycoside Hydrolase Family)
GH10 (Glycoside Hydrolase Family)


UniProtKB:Accession NumberP26514Q7SI98
Entry nameXYNA_STRLIQ7SI98_STROI
ActivityEndohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.
Subunit

Subcellular locationSecreted.
Cofactor


Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idC00707C00001C00707C00707
CompoundXylanH2OXylanXylan
TypepolysaccharideH2Opolysaccharidepolysaccharide
ChEBI
15377



PubChem
962
22247451



             
1xyfA01Unbound UnboundUnboundUnbound
1xyfB01Unbound UnboundUnboundUnbound
1isvA01Unbound UnboundUnboundUnbound
1isvB01Unbound UnboundUnboundUnbound
1iswA01Unbound UnboundUnboundUnbound
1iswB01Unbound UnboundUnboundUnbound
1isxA01Unbound UnboundUnboundUnbound
1isxB01Unbound UnboundUnboundUnbound
1isyA01Unbound UnboundUnboundUnbound
1isyB01Unbound UnboundUnboundUnbound
1iszA01Unbound UnboundUnboundUnbound
1iszB01Unbound UnboundUnboundUnbound
1it0A01Unbound UnboundUnboundUnbound
1it0B01Unbound UnboundUnboundUnbound
1knlAUnbound UnboundUnboundUnbound
1knmAUnbound UnboundUnboundUnbound
1mc9AUnbound UnboundUnboundUnbound
1xyfA02Unbound UnboundUnboundUnbound
1xyfB02Unbound UnboundUnboundUnbound
1isvA02Unbound UnboundUnboundUnbound
1isvB02Unbound UnboundUnboundUnbound
1iswA02Unbound Bound:XYP-XYP(chain C)Bound:XYP-XYP(chain D)Unbound
1iswB02Unbound Bound:XYP-XYP(chain F)Bound:XYP-XYP(chain G)Unbound
1isxA02Unbound Bound:XYP-XYP-XYP(chain C)Bound:XYP-XYP(chain D)Unbound
1isxB02Unbound Bound:XYP-XYP-XYP(chain F)Bound:XYP-XYP-XYP(chain G)Unbound
1isyA02Unbound UnboundUnboundUnbound
1isyB02Unbound UnboundUnboundUnbound
1iszA02Unbound UnboundUnboundUnbound
1iszB02Unbound UnboundUnboundUnbound
1it0A02Unbound UnboundUnboundUnbound
1it0B02Unbound UnboundUnboundUnbound
1e0vAUnbound UnboundUnboundIntermediate-analogue:FFC
1e0wAUnbound UnboundUnboundUnbound
1e0xAUnbound UnboundUnboundIntermediate-analogue:XYP-X2F
1e0xBUnbound UnboundUnboundIntermediate-analogue:XYP-X2F
1od8AUnbound Analogue:XYP-XDLUnboundUnbound

Active-site residues
resource
PDB;1xyf, Swiss-prot;P26514
pdbCatalytic residues
         
1xyfA01 
1xyfB01 
1isvA01 
1isvB01 
1iswA01 
1iswB01 
1isxA01 
1isxB01 
1isyA01 
1isyB01 
1iszA01 
1iszB01 
1it0A01 
1it0B01 
1knlA 
1knmA 
1mc9A 
1xyfA02GLU 128;HIS 207;GLU 236;ASP 238
1xyfB02GLU 628;HIS 707;GLU 736;ASP 738
1isvA02GLU 128;HIS 207;GLU 236;ASP 238
1isvB02GLU 628;HIS 707;GLU 736;ASP 738
1iswA02GLU 128;HIS 207;GLU 236;ASP 238
1iswB02GLU 628;HIS 707;GLU 736;ASP 738
1isxA02GLU 128;HIS 207;GLU 236;ASP 238
1isxB02GLU 628;HIS 707;GLU 736;ASP 738
1isyA02GLU 128;HIS 207;GLU 236;ASP 238
1isyB02GLU 628;HIS 707;GLU 736;ASP 738
1iszA02GLU 128;HIS 207;GLU 236;ASP 238
1iszB02GLU 628;HIS 707;GLU 736;ASP 738
1it0A02GLU 128;HIS 207;GLU 236;ASP 238
1it0B02GLU 628;HIS 707;GLU 736;ASP 738
1e0vAGLU 128;HIS 207;GLU 236;ASP 238
1e0wAGLU 128;HIS 207;GLU 236;ASP 238
1e0xAGLU 128;HIS 207;GLU 236;ASP 238
1e0xBGLU 128;HIS 207;GLU 236;ASP 238
1od8AGLU 128;HIS 207;GLU 236;ASP 238

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[7]

[11]Fig.4
[12]p.20813
[19]

[20]

[22]Fig.14

references
[1]
PubMed ID3141761
JournalMicrobiol Rev
Year1988
Volume52
Pages305-17
AuthorsWong KK, Tan LU, Saddler JN
TitleMultiplicity of beta-1,4-xylanase in microorganisms: functions and applications.
[2]
PubMed ID1368510
JournalAgric Biol Chem
Year1990
Volume54
Pages449-57
AuthorsYoshida S, Kusakabe I, Matsuo N, Shimizu K, Yasui T, Murakami K
TitleStructure of rice-straw arabinoglucuronoxylan and specificity of Streptomyces xylanase toward the xylan.
[3]
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.
[4]
PubMed ID1886523
JournalMicrobiol Rev
Year1991
Volume55
Pages303-15
AuthorsGilkes NR, Henrissat B, Kilburn DG, Miller RC Jr, Warren RA
TitleDomains in microbial beta-1, 4-glycanases: sequence conservation, function, and enzyme families.
[5]
PubMed ID8457588
JournalBiochim Biophys Acta
Year1993
Volume1162
Pages246-54
AuthorsBiely P, Kluepfel D, Morosoli R, Shareck F
TitleMode of action of three endo-beta-1,4-xylanases of Streptomyces lividans.
[6]
PubMed ID8471845
JournalProtein Expr Purif
Year1993
Volume4
Pages120-9
AuthorsGrabski AC, Forrester IT, Patel R, Jeffries TW
TitleCharacterization and N-terminal amino acid sequences of beta-(1-4)endoxylanases from Streptomyces roseiscleroticus: purification incorporating a bioprocessing agent.
[7]
PubMed ID7915112
JournalBiochem J
Year1994
Volume302
Pages291-5
AuthorsMoreau A, Roberge M, Manin C, Shareck F, Kluepfel D, Morosoli R
TitleIdentification of two acidic residues involved in the catalysis of xylanase A from Streptomyces lividans.
[8]
PubMed ID7765032
JournalBiosci Biotechnol Biochem
Year1994
Volume58
Pages1041-4
AuthorsYoshida S, Satoh T, Shimokawa S, Oku T, Ito T, Kusakabe I
TitleSubstrate specificity of Streptomyces beta-xylanase toward glucoxylan.
[9]
PubMed ID8000329
JournalBraz J Med Biol Res
Year1994
Volume27
Pages1093-109
AuthorsFerreira-Filho EX
TitleThe xylan-degrading enzyme system.
[10]
PubMed ID7764794
JournalEnzyme Microb Technol
Year1994
Volume16
Pages420-4
AuthorsMoreau A, Shareck F, Kluepfel D, Morosoli R
TitleIncrease in catalytic activity and thermostability of the xylanase A of Streptomyces lividans 1326 by site-specific mutagenesis.
[11]
PubMed ID8306993
JournalEur J Biochem
Year1994
Volume219
Pages261-6
AuthorsMoreau A, Shareck F, Kluepfel D, Morosoli R
TitleAlteration of the cleavage mode and of the transglycosylation reactions of the xylanase A of Streptomyces lividans 1326 by site-directed mutagenesis of the Asn173 residue.
[12]
PubMed ID8063693
JournalJ Biol Chem
Year1994
Volume269
Pages20811-4
AuthorsDerewenda U, Swenson L, Green R, Wei Y, Morosoli R, Shareck F, Kluepfel D, Derewenda ZS
TitleCrystal structure, at 2.6-A resolution, of the Streptomyces lividans xylanase A, a member of the F family of beta-1,4-D-glycanases.
[13]
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.
[14]
PubMed ID9201919
JournalBiochemistry
Year1997
Volume36
Pages7769-75
AuthorsRoberge M, Shareck F, Morosoli R, Kluepfel D, Dupont C
TitleCharacterization of two important histidine residues in the active site of xylanase A from Streptomyces lividans, a family 10 glycanase.
[15]
PubMed ID9118232
JournalCrit Rev Biotechnol
Year1997
Volume17
Pages39-67
AuthorsSunna A, Antranikian G
TitleXylanolytic enzymes from fungi and bacteria.
[16]
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.
[17]
PubMed ID9211898
JournalJ Biol Chem
Year1997
Volume272
Pages17523-30
AuthorsSpurway TD, Morland C, Cooper A, Sumner I, Hazlewood GP, O'Donnell AG, Pickersgill RW, Gilbert HJ
TitleCalcium protects a mesophilic xylanase from proteinase inactivation and thermal unfolding.
[18]
PubMed ID9335171
JournalJ Biotechnol
Year1997
Volume57
Pages151-66
AuthorsBiely P, Vrsanska M, Tenkanen M, Kluepfel D
TitleEndo-beta-1,4-xylanase families: differences in catalytic properties.
[19]
PubMed ID9194164
JournalProtein Eng
Year1997
Volume10
Pages399-403
AuthorsRoberge M, Dupont C, Morosoli R, Shareck F, Kluepfel D
TitleAsparagine-127 of xylanase A from Streptomyces lividans, a key residue in glycosyl hydrolases of superfamily 4/7: kinetic evidence for its involvement in stabilization of the catalytic intermediate.
[20]
PubMed ID9681873
JournalProtein Eng
Year1998
Volume11
Pages399-404
AuthorsRoberge M, Shareck F, Morosoli R, Kluepfel D, Dupont C
TitleSite-directed mutagenesis study of a conserved residue in family 10 glycanases: histidine 86 of xylanase A from Streptomyces lividans.
[21]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
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.
Related PDB1xyf
Related UniProtKBQ7SI98
[22]
PubMed ID10359093
JournalFEBS Lett
Year1999
Volume450
Pages299-305
AuthorsKuno A, Shimizu D, Kaneko S, Hasegawa T, Gama Y, Hayashi K, Kusakabe I, Taira K
TitleSignificant enhancement in the binding of p-nitrophenyl-beta-D-xylobioside by the E128H mutant F/10 xylanase from Streptomyces olivaceoviridis E-86.
[23]
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.
[24]
PubMed ID10235626
JournalProtein Eng
Year1999
Volume12
Pages251-7
AuthorsRoberge M, Shareck F, Morosoli R, Kluepfel D, Dupont C
TitleCharacterization of active-site aromatic residues in xylanase A from Streptomyces lividans.
[25]
PubMed ID10884353
JournalJ Mol Biol
Year2000
Volume300
Pages575-85
AuthorsFujimoto Z, Kuno A, Kaneko S, Yoshida S, Kobayashi H, Kusakabe I, Mizuno H
TitleCrystal structure of Streptomyces olivaceoviridis E-86 beta-xylanase containing xylan-binding domain.
[26]
PubMed ID10767281
JournalJ Biol Chem
Year2000
Volume275
Pages23027-33
AuthorsAndrews SR, Charnock SJ, Lakey JH, Davies GJ, Claeyssens M, Nerinckx W, Underwood M, Sinnott ML, Warren RA, Gilbert HJ
TitleSubstrate specificity in glycoside hydrolase family 10. Tyrosine 87 and leucine 314 play a pivotal role in discriminating between glucose and xylose binding in the proximal active site of Pseudomonas cellulosa xylanase 10A.
Related PDB1e0v,1e0w,1e0x
[27]
CommentsX-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
PubMed ID11829503
JournalJ Mol Biol
Year2002
Volume316
Pages65-78
AuthorsFujimoto Z, Kuno A, Kaneko S, Kobayashi H, Kusakabe I, Mizuno H
TitleCrystal structures of the sugar complexes of Streptomyces olivaceoviridis E-86 xylanase: sugar binding structure of the family 13 carbohydrate binding module.
Related PDB1isv,1isw,1isx,1isy,1isz,1it0
Related UniProtKBQ7SI98
[28]
PubMed ID11914070
JournalBiochemistry
Year2002
Volume41
Pages4246-54
AuthorsNotenboom V, Boraston AB, Williams SJ, Kilburn DG, Rose DR
TitleHigh-resolution crystal structures of the lectin-like xylan binding domain from Streptomyces lividans xylanase 10A with bound substrates reveal a novel mode of xylan binding.
Related PDB1knl,1knm,1mc9
[29]
PubMed ID12744311
JournalChem Commun (Camb)
Year2003
Volume
Pages944-5
AuthorsGloster T, Williams SJ, Tarling CA, Roberts S, Dupont C, Jodoin P, Shareck F, Withers SG, Davies GJ
TitleA xylobiose-derived isofagomine lactam glycosidase inhibitor binds as its amide tautomer.
Related PDB1od8
[30]
PubMed ID15078885
JournalJ Biol Chem
Year2004
Volume279
Pages26619-26
AuthorsKaneko S, Ichinose H, Fujimoto Z, Kuno A, Yura K, Go M, Mizuno H, Kusakabe I, Kobayashi H
TitleStructure and function of a family 10 beta-xylanase chimera of Streptomyces olivaceoviridis E-86 FXYN and Cellulomonas fimi Cex.

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.
According to the literature [22], Glu236 and Glu128 (of 1ece) 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, Glu236 approaches the C1 atom of xylan substrate, whilst Glu128 protonates the leaving sugar group.
At the second stage, or during the deglycosylation, a water molecule can be activated by a general base, Glu128. This deglycosylation also goes through the dissociative-type reaction with an oxocarbonium ion in the transition state, in which water replaced the xylan leaving group in the first step.
According to the paper [19], the conserved residue at active site, Asn127, may stabilize the intermediate or transition state. Meanwhile, the paper [20] mentioned that His86 might modulate the acid-base catalyst (Glu128), by maintaining the elevated pKa of the catalytic residue.
Moreover, comparing the structural data with that of the other family-10 enzyme, xylanase (E.C. 3.2.1.8) (D00479 in EzCatDB), His207-Asp238 dyad seems to stabilize the leaving nucleophile, Glu236, during the deglycosylation.

createdupdated
2004-08-192009-02-26


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 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)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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