EzCatDB: D00538
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DB codeD00538
RLCP classification1.30.36211.974 : Hydrolysis
CATH domainDomain 12.60.120.180 : Jelly RollsCatalytic domain
Domain 22.60.120.- : Jelly Rolls
E.C.3.2.1.8

CATH domainRelated DB codes (homologues)
2.60.120.180 : Jelly RollsS00533,S00150,S00151,D00504

Enzyme Name
UniProtKBKEGG

P77853
Protein nameEndo-1,4-beta-xylanaseendo-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
SynonymsEC 3.2.1.8
PfamPF03422 (CBM_6)
PF00457 (Glyco_hydro_11)
[Graphical view]
CAZyGH11 (Glycoside Hydrolase Family)


UniProtKB:Accession NumberP77853
Entry nameP77853_DICTH
ActivityEndohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.
Subunit
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idC00707C00001C00707
CompoundXylanH2OXylan
TypepolysaccharideH2Opolysaccharide
ChEBI
15377


PubChem
962
22247451


            
1f5jAUnbound UnboundUnbound
1f5jBUnbound UnboundUnbound

Active-site residues
resource
see S00151
pdbCatalytic residues
         
1f5jATYR  81;GLU  90;TYR  92;GLU 180
1f5jBTYR  81;GLU  90;TYR  92;GLU 180

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]p.68
[3]p.2499-2500
[7]Fig.1, p.471-473
[8]p.851-853
[10]p.9624
[11]Scheme 1
[12]Fig.1, Fig.3, p.9964-9965
[13]p.74-76
[18]Fig.4, p.143-145
[21]Fig.1, Fig.2
[23]

[26]Fig.1, Fig.6
[28]p.486-487
[32]Fig.10, p.268-271
[37]Fig.1, p.1012410-10128
[43]Scheme 1, Scheme 3, p.525
[44]Fig. 1, p.3539

references
[1]
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.
[2]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) (ISBN: 9518913625)
JournalTRICEL Symposium on Trichoderma Reesei Cellulases and Other Hydrolases
Year1993
Volume
Pages63-72
AuthorsCampbell RL, Rose DR, Wakarchuk WW, To RJ, Sung W, Yaguchi M
TitleHigh-resolution structures of xylanases from B.circulans and T.harzianum identify a new folding pattern and implications for the atomic basis of the catalysis.
Related UniProtKBP48793
[3]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID94283373
PubMed ID8013449
JournalEMBO J
Year1994
Volume13
Pages2493-501
AuthorsTorronen A, Harkki A, Rouvinen J
TitleThree-dimensional structure of endo-1,4-beta-xylanase II from Trichoderma reesei: two conformational states in the active site.
Related UniProtKBP36217
[4]
PubMed ID7988708
JournalFEBS Lett
Year1994
Volume356
Pages137-40
AuthorsBiely P, Kremnicky L, Alfoldi J, Tenkanen M
TitleStereochemistry of the hydrolysis of glycosidic linkage by endo-beta-1,4-xylanases of Trichoderma reesei.
[5]
CommentsX-ray crystallography
PubMed ID7966300
JournalJ Mol Biol
Year1994
Volume243
Pages806-8
AuthorsEswaramoorthy S, Vithayathil PJ, Viswamitra MA
TitleCrystallization and preliminary X-ray crystallographic studies of thermostable xylanase crystals isolated from Paecilomyces varioti.
Related PDB1pvx
[6]
PubMed ID7700870
JournalProtein Eng
Year1994
Volume7
Pages1379-86
AuthorsWakarchuk WW, Sung WL, Campbell RL, Cunningham A, Watson DC, Yaguchi M
TitleThermostabilization of the Bacillus circulans xylanase by the introduction of disulfide bonds.
[7]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS), AND MUTAGENESIS.
Medline ID94290322
PubMed ID8019418
JournalProtein Sci
Year1994
Volume3
Pages467-75
AuthorsWakarchuk WW, Campbell RL, Sung WL, Davoodi J, Yaguchi M
TitleMutational and crystallographic analyses of the active site residues of the Bacillus circulans xylanase.
Related PDB1bcx
Related UniProtKBP09850
[8]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID95127663
PubMed ID7827044
JournalBiochemistry
Year1995
Volume34
Pages847-56
AuthorsTorronen A, Rouvinen J
TitleStructural comparison of two major endo-1,4-xylanases from Trichoderma reesei.
Related PDB1enx,1xyn,1xyo,1xyp
Related UniProtKBP36218,P36217
[9]
PubMed ID7648585
JournalCarbohydr Res
Year1995
Volume272
Pages55-71
AuthorsTeleman A, Harjunpaa V, Tenkanen M, Buchert J, Hausalo T, Drakenberg T, Vuorinen T
TitleCharacterisation of 4-deoxy-beta-L-threo-hex-4-enopyranosyluronic acid attached to xylan in pine kraft pulp and pulping liquor by 1H and 13C NMR spectroscopy.
[10]
CommentsX-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
Medline ID96302263
PubMed ID8755744
JournalBiochemistry
Year1996
Volume35
Pages9617-24
AuthorsHavukainen R, Torronen A, Laitinen T, Rouvinen J
TitleCovalent binding of three epoxyalkyl xylosides to the active site of endo-1,4-xylanase II from Trichoderma reesei.
Related PDB1red,1ree,1ref
Related UniProtKBP36217
[11]
PubMed ID8756474
JournalBiochemistry
Year1996
Volume35
Pages10110-8
AuthorsLawson SL, Wakarchuk WW, Withers SG
TitleEffects of both shortening and lengthening the active site nucleophile of Bacillus circulans xylanase on catalytic activity.
[12]
CommentsSTRUCTURE BY NMR.
Medline ID96322313
PubMed ID8756457
JournalBiochemistry
Year1996
Volume35
Pages9958-66
AuthorsMcIntosh LP, Hand G, Johnson PE, Joshi MD, Korner M, Plesniak LA, Ziser L, Wakarchuk WW, Withers SG
TitleThe pKa of the general acid/base carboxyl group of a glycosidase cycles during catalysis: a 13C-NMR study of bacillus circulans xylanase.
Related UniProtKBP09850
[13]
CommentsX-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
Medline ID97045991
PubMed ID8890913
JournalJ Mol Biol
Year1996
Volume263
Pages70-8
AuthorsKrengel U, Dijkstra BW
TitleThree-dimensional structure of Endo-1,4-beta-xylanase I from Aspergillus niger: molecular basis for its low pH optimum.
Related PDB1ukr
Related UniProtKBP55329
[14]
PubMed ID8845760
JournalProtein Sci
Year1996
Volume5
Pages705-8
AuthorsChen X, Whitmire D, Bowen JP
TitleXylanase homology modeling using the inverse protein folding approach.
[15]
PubMed ID8931150
JournalProtein Sci
Year1996
Volume5
Pages2319-28
AuthorsPlesniak LA, Connelly GP, Wakarchuk WW, McIntosh LP
TitleCharacterization of a buried neutral histidine residue in Bacillus circulans xylanase: NMR assignments, pH titration, and hydrogen exchange.
[16]
PubMed ID8762143
JournalProtein Sci
Year1996
Volume5
Pages1118-35
AuthorsPlesniak LA, Wakarchuk WW, McIntosh LP
TitleSecondary structure and NMR assignments of Bacillus circulans xylanase.
[17]
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.
[18]
PubMed ID9335170
JournalJ Biotechnol
Year1997
Volume57
Pages137-49
AuthorsTorronen A, Rouvinen J
TitleStructural and functional properties of low molecular weight endo-1,4-beta-xylanases.
[19]
PubMed ID9416621
JournalProtein Sci
Year1997
Volume6
Pages2667-70
AuthorsJoshi MD, Hedberg A, McIntosh LP
TitleComplete measurement of the pKa values of the carboxyl and imidazole groups in Bacillus circulans xylanase.
[20]
PubMed ID9675021
JournalArch Biochem Biophys
Year1998
Volume355
Pages153-9
AuthorsSubray SH, Ameeta RK, Krishna NG, Khan IM
TitleCatalytic thiol and carboxylate: role of cysteine and glutamic acid in the xylosidic activity of endoxylanase from Chainia sp. (NCL 82-5-1).
[21]
PubMed ID9649739
JournalBiochem Soc Trans
Year1998
Volume26
Pages156-60
AuthorsBirsan C, Johnson P, Joshi M, MacLeod A, McIntosh L, Monem V, Nitz M, Rose DR, Tull D, Wakarchuck WW, Wang Q, Warren RA, White A, Withers SG
TitleMechanisms of cellulases and xylanases.
[22]
PubMed ID9485306
JournalBiochemistry
Year1998
Volume37
Pages1810-8
AuthorsConnelly GP, McIntosh LP
TitleCharacterization of a buried neutral histidine in Bacillus circulans xylanase: internal dynamics and interaction with a bound water molecule.
[23]
CommentsX-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS).
Medline ID98426042
PubMed ID9753433
JournalBiochemistry
Year1998
Volume37
Pages13475-85
AuthorsGruber K, Klintschar G, Hayn M, Schlacher A, Steiner W, Kratky C
TitleThermophilic xylanase from Thermomyces lanuginosus: high-resolution X-ray structure and modeling studies.
Related PDB1yna
Related UniProtKBO43097
[24]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 29-210.
Medline ID99127851
PubMed ID9930661
JournalProtein Eng
Year1998
Volume11
Pages1121-8
AuthorsFushinobu S, Ito K, Konno M, Wakagi T, Matsuzawa H
TitleCrystallographic and mutational analyses of an extremely acidophilic and acid-stable xylanase: biased distribution of acidic residues and importance of Asp37 for catalysis at low pH.
Related PDB1bk1
Related UniProtKBP33557
[25]
PubMed ID9626702
JournalProteins
Year1998
Volume31
Pages434-44
AuthorsMuilu J, Torronen A, Perakyla M, Rouvinen J
TitleFunctional conformational changes of endo-1,4-xylanase II from Trichoderma reesei: a molecular dynamics study.
[26]
CommentsX-ray crystallography
PubMed ID10220321
JournalBiochemistry
Year1999
Volume38
Pages5346-54
AuthorsSidhu G, Withers SG, Nguyen NT, McIntosh LP, Ziser L, Brayer GD
TitleSugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase.
Related PDB1bvv,2bvv
[27]
PubMed ID10467122
JournalBiotechnol Appl Biochem
Year1999
Volume30
Pages73-9
AuthorsLin J, Ndlovu LM, Singh S, Pillay B
TitlePurification and biochemical characteristics of beta-D-xylanase from a thermophilic fungus, Thermomyces lanuginosus-SSBP.
[28]
CommentsX-ray crystallography
PubMed ID10381409
JournalChem Biol
Year1999
Volume6
Pages483-92
AuthorsSabini E, Sulzenbacher G, Dauter M, Dauter Z, Jorgensen PL, Schulein M, Dupont C, Davies GJ, Wilson KS
TitleCatalysis and specificity in enzymatic glycoside hydrolysis: a 2,5B conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase.
Related PDB1qh6,1qh7
[29]
PubMed ID10356996
JournalExtremophiles
Year1999
Volume3
Pages103-11
AuthorsMorris DD, Gibbs MD, Ford M, Thomas J, Bergquist PL
TitleFamily 10 and 11 xylanase genes from Caldicellulosiruptor sp. strain Rt69B.1.
[30]
CommentsX-ray crystallography
PubMed ID11053833
JournalActa Crystallogr D Biol Crystallogr
Year2000
Volume56
Pages1367-75
AuthorsMcCarthy AA, Morris DD, Bergquist PL, Baker EN
TitleStructure of XynB, a highly thermostable beta-1,4-xylanase from Dictyoglomus thermophilum Rt46B.1, at 1.8 A resolution.
Related PDB1f5j
[31]
PubMed ID10981683
JournalFEMS Microbiol Lett
Year2000
Volume190
Pages13-9
AuthorsTe'o VS, Cziferszky AE, Bergquist PL, Nevalainen KM
TitleCodon optimization of xylanase gene xynB from the thermophilic bacterium Dictyoglomus thermophilum for expression in the filamentous fungus Trichoderma reesei.
[32]
CommentsX-ray crystallography
PubMed ID10860737
JournalJ Mol Biol
Year2000
Volume299
Pages255-79
AuthorsJoshi MD, Sidhu G, Pot I, Brayer GD, Withers SG, McIntosh LP
TitleHydrogen bonding and catalysis: a novel explanation for how a single amino acid substitution can change the pH optimum of a glycosidase.
Related PDB1c5h,1c5i,1hv0,1hv1
[33]
PubMed ID10623548
JournalJ Mol Biol
Year2000
Volume295
Pages581-93
AuthorsKumar PR, Eswaramoorthy S, Vithayathil PJ, Viswamitra MA
TitleThe tertiary structure at 1.59 A resolution and the proposed amino acid sequence of a family-11 xylanase from the thermophilic fungus Paecilomyces varioti bainier.
[34]
PubMed ID10752613
JournalProtein Sci
Year2000
Volume9
Pages512-24
AuthorsConnelly GP, Withers SG, McIntosh LP
TitleAnalysis of the dynamic properties of Bacillus circulans xylanase upon formation of a covalent glycosyl-enzyme intermediate.
[35]
PubMed ID11526340
JournalActa Crystallogr D Biol Crystallogr
Year2001
Volume57
Pages1344-7
AuthorsSabini E, Wilson KS, Danielsen S, Schulein M, Davies GJ
TitleOligosaccharide binding to family 11 xylanases: both covalent intermediate and mutant product complexes display (2,5)B conformations at the active centre.
[36]
PubMed ID11717493
JournalActa Crystallogr D Biol Crystallogr
Year2001
Volume57
Pages1813-9
AuthorsWouters J, Georis J, Engher D, Vandenhaute J, Dusart J, Frere JM, Depiereux E, Charlier P
TitleCrystallographic analysis of family 11 endo-beta-1,4-xylanase Xyl1 from Streptomyces sp. S38.
[37]
PubMed ID11513590
JournalBiochemistry
Year2001
Volume40
Pages10115-39
AuthorsJoshi MD, Sidhu G, Nielsen JE, Brayer GD, Withers SG, McIntosh LP
TitleDissecting the electrostatic interactions and pH-dependent activity of a family 11 glycosidase.
[38]
PubMed ID11180071
JournalBiotechnol Bioeng
Year2001
Volume72
Pages501-5
AuthorsLeisola M, Jokela J, Finell J, Pastinen O
TitleSimultaneous catalysis and product separation by cross-linked enzyme crystals.
[39]
PubMed ID11304525
JournalJ Biol Chem
Year2001
Volume276
Pages24309-14
AuthorsAro N, Saloheimo A, Ilmen M, Penttila M
TitleACEII, a novel transcriptional activator involved in regulation of cellulase and xylanase genes of Trichoderma reesei.
[40]
PubMed ID11377763
JournalJ Biotechnol
Year2001
Volume88
Pages37-46
AuthorsTurunen O, Etuaho K, Fenel F, Vehmaanpera J, Wu X, Rouvinen J, Leisola M
TitleA combination of weakly stabilizing mutations with a disulfide bridge in the alpha-helix region of Trichoderma reesei endo-1,4-beta-xylanase II increases the thermal stability through synergism.
[41]
PubMed ID12207016
JournalJ Biol Chem
Year2002
Volume277
Pages44035-43
AuthorsTahir TA, Berrin JG, Flatman R, Roussel A, Roepstorff P, Williamson G, Juge N
TitleSpecific characterization of substrate and inhibitor binding sites of a glycosyl hydrolase family 11 xylanase from Aspergillus niger.
[42]
PubMed ID11917150
JournalProtein Eng
Year2002
Volume15
Pages141-5
AuthorsTurunen O, Vuorio M, Fenel F, Leisola M
TitleEngineering of multiple arginines into the Ser/Thr surface of Trichoderma reesei endo-1,4-beta-xylanase II increases the thermotolerance and shifts the pH optimum towards alkaline pH.
[43]
PubMed ID12773149
JournalBiochem Soc Trans
Year2003
Volume31
Pages523-7
AuthorsDavies GJ, Ducros VM, Varrot A, Zechel DL
TitleMapping the conformational itinerary of beta-glycosidases by X-ray crystallography.
[44]
PubMed ID14599014
JournalOrg Biomol Chem
Year2003
Volume1
Pages3535-40
AuthorsLaitinen T, Rouvinen J, Perakyla M
TitleMM-PBSA free energy analysis of endo-1,4-xylanase II (XynII)-substrate complexes: binding of the reactive sugar in a skew boat and chair conformation.
[45]
PubMed ID15134456
JournalBiochemistry
Year2004
Volume43
Pages5820-31
AuthorsBetz M, Lohr F, Wienk H, Ruterjans H
TitleLong-range nature of the interactions between titratable groups in Bacillus agaradhaerens family 11 xylanase: pH titration of B. agaradhaerens xylanase.
[46]
PubMed ID15166216
JournalJ Biol Chem
Year2004
Volume279
Pages36022-8
AuthorsSansen S, De Ranter CJ, Gebruers K, Brijs K, Courtin CM, Delcour JA, Rabijns A
TitleStructural basis for inhibition of Aspergillus niger xylanase by triticum aestivum xylanase inhibitor-I.
Related PDB1t6g

comments
There are many kinds of xylanases, family-2b, family-10, & family-11.
This enzyme belongs to the glycosidase family-11 along with the homologous enzyme (S00151 in EzCatDB), while the entries D00169, D00479 & M00160 belong to family-10.
According to the literature [7], [18], [26] & [28], the catalytic reaction proceeds as follows:
(1) Glu180 acts as a general acid to protonate the leaving oxygen atom, leading to a oxocarbenium-like transtion state from xylan substrate.
(2) pKa of Glu90, which acts as a nucleophile, is modulated by Tyr81 and Tyr92. Glu90 makes a nucleophilic attack on C1 atom of the transition state, forming a glycosyl-enzyme intermediate.
(2') As the glycosyl-enzyme intermediate is formed, Tyr81 switched from Glu90 to Glu180. Tyr92 may modulate the activity of Glu180 as a general base.
(3) Glu170 acts as a general base to activate a water molecule.
(4) The activated water makes a nucleophilic attack on the C1 atom of the intermediate. This reaction proceeds through an oxocarbenium-like transition state to complete the hydrolysis.
###
According to the literature [26] & [28], the homologous enzyme of this enzyme (S00151 in EzCatDB) adopts 2,5B (or Boat) conformation, which places C5, O5, C1 and C2 in a planar arrangement, for the intermediate.
Moreover, at the position of 37 of 1bk1 (see S00151), the family-11 has an aspartic acid or an aspargine residue. For high pH optimum, aspartic acid residue is used at the position, whilst an aspargine residue is adopted for lower pH optimum, according to the literature [13]. This residue makes a hydrogen bond with the acid-base, Glu170, modulating its pKa.

createdupdated
2005-04-212009-03-27


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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