DB code: D00538

RLCP classification 1.30.36211.974 : Hydrolysis
CATH domain 2.60.120.180 : Jelly Rolls Catalytic domain
2.60.120.- : Jelly Rolls
E.C. 3.2.1.8
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
2.60.120.180 : Jelly Rolls S00533 S00150 S00151 D00504

Uniprot Enzyme Name
UniprotKB Protein name Synonyms CAZy Pfam
P77853 Endo-1,4-beta-xylanase
EC 3.2.1.8
CBM36 (Carbohydrate-Binding Module Family 36)
GH11 (Glycoside Hydrolase Family 11)
PF03422 (CBM_6)
PF00457 (Glyco_hydro_11)
[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
P77853 P77853_DICTH 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
 15377
PubChem 22247451
 962
 22247451
 962
1f5jA Unbound Unbound Unbound
1f5jB Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
see S00151

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1f5jA TYR 81;GLU 90;TYR 92;GLU 180
1f5jB TYR 81;GLU 90;TYR 92;GLU 180

References for Catalytic Mechanism
References Sections No. 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]
Resource
Comments
Medline ID
PubMed ID 1886523
Journal Microbiol Rev
Year 1991
Volume 55
Pages 303-15
Authors Gilkes NR, Henrissat B, Kilburn DG, Miller RC Jr, Warren RA
Title Domains in microbial beta-1, 4-glycanases: sequence conservation, function, and enzyme families.
Related PDB
Related UniProtKB
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) (ISBN: 9518913625)
Medline ID
PubMed ID
Journal TRICEL Symposium on Trichoderma Reesei Cellulases and Other Hydrolases
Year 1993
Volume
Pages 63-72
Authors Campbell RL, Rose DR, Wakarchuk WW, To RJ, Sung W, Yaguchi M
Title High-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 PDB
Related UniProtKB P48793
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID 94283373
PubMed ID 8013449
Journal EMBO J
Year 1994
Volume 13
Pages 2493-501
Authors Torronen A, Harkki A, Rouvinen J
Title Three-dimensional structure of endo-1,4-beta-xylanase II from Trichoderma reesei: two conformational states in the active site.
Related PDB
Related UniProtKB P36217
[4]
Resource
Comments
Medline ID
PubMed ID 7988708
Journal FEBS Lett
Year 1994
Volume 356
Pages 137-40
Authors Biely P, Kremnicky L, Alfoldi J, Tenkanen M
Title Stereochemistry of the hydrolysis of glycosidic linkage by endo-beta-1,4-xylanases of Trichoderma reesei.
Related PDB
Related UniProtKB
[5]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 7966300
Journal J Mol Biol
Year 1994
Volume 243
Pages 806-8
Authors Eswaramoorthy S, Vithayathil PJ, Viswamitra MA
Title Crystallization and preliminary X-ray crystallographic studies of thermostable xylanase crystals isolated from Paecilomyces varioti.
Related PDB 1pvx
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 7700870
Journal Protein Eng
Year 1994
Volume 7
Pages 1379-86
Authors Wakarchuk WW, Sung WL, Campbell RL, Cunningham A, Watson DC, Yaguchi M
Title Thermostabilization of the Bacillus circulans xylanase by the introduction of disulfide bonds.
Related PDB
Related UniProtKB
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS), AND MUTAGENESIS.
Medline ID 94290322
PubMed ID 8019418
Journal Protein Sci
Year 1994
Volume 3
Pages 467-75
Authors Wakarchuk WW, Campbell RL, Sung WL, Davoodi J, Yaguchi M
Title Mutational and crystallographic analyses of the active site residues of the Bacillus circulans xylanase.
Related PDB 1bcx
Related UniProtKB P09850
[8]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID 95127663
PubMed ID 7827044
Journal Biochemistry
Year 1995
Volume 34
Pages 847-56
Authors Torronen A, Rouvinen J
Title Structural comparison of two major endo-1,4-xylanases from Trichoderma reesei.
Related PDB 1enx 1xyn 1xyo 1xyp
Related UniProtKB P36218 P36217
[9]
Resource
Comments
Medline ID
PubMed ID 7648585
Journal Carbohydr Res
Year 1995
Volume 272
Pages 55-71
Authors Teleman A, Harjunpaa V, Tenkanen M, Buchert J, Hausalo T, Drakenberg T, Vuorinen T
Title Characterisation 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.
Related PDB
Related UniProtKB
[10]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
Medline ID 96302263
PubMed ID 8755744
Journal Biochemistry
Year 1996
Volume 35
Pages 9617-24
Authors Havukainen R, Torronen A, Laitinen T, Rouvinen J
Title Covalent binding of three epoxyalkyl xylosides to the active site of endo-1,4-xylanase II from Trichoderma reesei.
Related PDB 1red 1ree 1ref
Related UniProtKB P36217
[11]
Resource
Comments
Medline ID
PubMed ID 8756474
Journal Biochemistry
Year 1996
Volume 35
Pages 10110-8
Authors Lawson SL, Wakarchuk WW, Withers SG
Title Effects of both shortening and lengthening the active site nucleophile of Bacillus circulans xylanase on catalytic activity.
Related PDB
Related UniProtKB
[12]
Resource
Comments STRUCTURE BY NMR.
Medline ID 96322313
PubMed ID 8756457
Journal Biochemistry
Year 1996
Volume 35
Pages 9958-66
Authors McIntosh LP, Hand G, Johnson PE, Joshi MD, Korner M, Plesniak LA, Ziser L, Wakarchuk WW, Withers SG
Title The pKa of the general acid/base carboxyl group of a glycosidase cycles during catalysis: a 13C-NMR study of bacillus circulans xylanase.
Related PDB
Related UniProtKB P09850
[13]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
Medline ID 97045991
PubMed ID 8890913
Journal J Mol Biol
Year 1996
Volume 263
Pages 70-8
Authors Krengel U, Dijkstra BW
Title Three-dimensional structure of Endo-1,4-beta-xylanase I from Aspergillus niger: molecular basis for its low pH optimum.
Related PDB 1ukr
Related UniProtKB P55329
[14]
Resource
Comments
Medline ID
PubMed ID 8845760
Journal Protein Sci
Year 1996
Volume 5
Pages 705-8
Authors Chen X, Whitmire D, Bowen JP
Title Xylanase homology modeling using the inverse protein folding approach.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 8931150
Journal Protein Sci
Year 1996
Volume 5
Pages 2319-28
Authors Plesniak LA, Connelly GP, Wakarchuk WW, McIntosh LP
Title Characterization of a buried neutral histidine residue in Bacillus circulans xylanase: NMR assignments, pH titration, and hydrogen exchange.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 8762143
Journal Protein Sci
Year 1996
Volume 5
Pages 1118-35
Authors Plesniak LA, Wakarchuk WW, McIntosh LP
Title Secondary structure and NMR assignments of Bacillus circulans xylanase.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 9335171
Journal J Biotechnol
Year 1997
Volume 57
Pages 151-66
Authors Biely P, Vrsanska M, Tenkanen M, Kluepfel D
Title Endo-beta-1,4-xylanase families: differences in catalytic properties.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 9335170
Journal J Biotechnol
Year 1997
Volume 57
Pages 137-49
Authors Torronen A, Rouvinen J
Title Structural and functional properties of low molecular weight endo-1,4-beta-xylanases.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 9416621
Journal Protein Sci
Year 1997
Volume 6
Pages 2667-70
Authors Joshi MD, Hedberg A, McIntosh LP
Title Complete measurement of the pKa values of the carboxyl and imidazole groups in Bacillus circulans xylanase.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 9675021
Journal Arch Biochem Biophys
Year 1998
Volume 355
Pages 153-9
Authors Subray SH, Ameeta RK, Krishna NG, Khan IM
Title Catalytic thiol and carboxylate: role of cysteine and glutamic acid in the xylosidic activity of endoxylanase from Chainia sp. (NCL 82-5-1).
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 9649739
Journal Biochem Soc Trans
Year 1998
Volume 26
Pages 156-60
Authors Birsan 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
Title Mechanisms of cellulases and xylanases.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 9485306
Journal Biochemistry
Year 1998
Volume 37
Pages 1810-8
Authors Connelly GP, McIntosh LP
Title Characterization of a buried neutral histidine in Bacillus circulans xylanase: internal dynamics and interaction with a bound water molecule.
Related PDB
Related UniProtKB
[23]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS).
Medline ID 98426042
PubMed ID 9753433
Journal Biochemistry
Year 1998
Volume 37
Pages 13475-85
Authors Gruber K, Klintschar G, Hayn M, Schlacher A, Steiner W, Kratky C
Title Thermophilic xylanase from Thermomyces lanuginosus: high-resolution X-ray structure and modeling studies.
Related PDB 1yna
Related UniProtKB O43097
[24]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 29-210.
Medline ID 99127851
PubMed ID 9930661
Journal Protein Eng
Year 1998
Volume 11
Pages 1121-8
Authors Fushinobu S, Ito K, Konno M, Wakagi T, Matsuzawa H
Title Crystallographic 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 PDB 1bk1
Related UniProtKB P33557
[25]
Resource
Comments
Medline ID
PubMed ID 9626702
Journal Proteins
Year 1998
Volume 31
Pages 434-44
Authors Muilu J, Torronen A, Perakyla M, Rouvinen J
Title Functional conformational changes of endo-1,4-xylanase II from Trichoderma reesei: a molecular dynamics study.
Related PDB
Related UniProtKB
[26]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10220321
Journal Biochemistry
Year 1999
Volume 38
Pages 5346-54
Authors Sidhu G, Withers SG, Nguyen NT, McIntosh LP, Ziser L, Brayer GD
Title Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase.
Related PDB 1bvv 2bvv
Related UniProtKB
[27]
Resource
Comments
Medline ID
PubMed ID 10467122
Journal Biotechnol Appl Biochem
Year 1999
Volume 30
Pages 73-9
Authors Lin J, Ndlovu LM, Singh S, Pillay B
Title Purification and biochemical characteristics of beta-D-xylanase from a thermophilic fungus, Thermomyces lanuginosus-SSBP.
Related PDB
Related UniProtKB
[28]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10381409
Journal Chem Biol
Year 1999
Volume 6
Pages 483-92
Authors Sabini E, Sulzenbacher G, Dauter M, Dauter Z, Jorgensen PL, Schulein M, Dupont C, Davies GJ, Wilson KS
Title Catalysis 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 PDB 1qh6 1qh7
Related UniProtKB
[29]
Resource
Comments
Medline ID
PubMed ID 10356996
Journal Extremophiles
Year 1999
Volume 3
Pages 103-11
Authors Morris DD, Gibbs MD, Ford M, Thomas J, Bergquist PL
Title Family 10 and 11 xylanase genes from Caldicellulosiruptor sp. strain Rt69B.1.
Related PDB
Related UniProtKB
[30]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11053833
Journal Acta Crystallogr D Biol Crystallogr
Year 2000
Volume 56
Pages 1367-75
Authors McCarthy AA, Morris DD, Bergquist PL, Baker EN
Title Structure of XynB, a highly thermostable beta-1,4-xylanase from Dictyoglomus thermophilum Rt46B.1, at 1.8 A resolution.
Related PDB 1f5j
Related UniProtKB
[31]
Resource
Comments
Medline ID
PubMed ID 10981683
Journal FEMS Microbiol Lett
Year 2000
Volume 190
Pages 13-9
Authors Te'o VS, Cziferszky AE, Bergquist PL, Nevalainen KM
Title Codon optimization of xylanase gene xynB from the thermophilic bacterium Dictyoglomus thermophilum for expression in the filamentous fungus Trichoderma reesei.
Related PDB
Related UniProtKB
[32]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10860737
Journal J Mol Biol
Year 2000
Volume 299
Pages 255-79
Authors Joshi MD, Sidhu G, Pot I, Brayer GD, Withers SG, McIntosh LP
Title Hydrogen bonding and catalysis: a novel explanation for how a single amino acid substitution can change the pH optimum of a glycosidase.
Related PDB 1c5h 1c5i 1hv0 1hv1
Related UniProtKB
[33]
Resource
Comments
Medline ID
PubMed ID 10623548
Journal J Mol Biol
Year 2000
Volume 295
Pages 581-93
Authors Kumar PR, Eswaramoorthy S, Vithayathil PJ, Viswamitra MA
Title The 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.
Related PDB
Related UniProtKB
[34]
Resource
Comments
Medline ID
PubMed ID 10752613
Journal Protein Sci
Year 2000
Volume 9
Pages 512-24
Authors Connelly GP, Withers SG, McIntosh LP
Title Analysis of the dynamic properties of Bacillus circulans xylanase upon formation of a covalent glycosyl-enzyme intermediate.
Related PDB
Related UniProtKB
[35]
Resource
Comments
Medline ID
PubMed ID 11526340
Journal Acta Crystallogr D Biol Crystallogr
Year 2001
Volume 57
Pages 1344-7
Authors Sabini E, Wilson KS, Danielsen S, Schulein M, Davies GJ
Title Oligosaccharide binding to family 11 xylanases: both covalent intermediate and mutant product complexes display (2,5)B conformations at the active centre.
Related PDB
Related UniProtKB
[36]
Resource
Comments
Medline ID
PubMed ID 11717493
Journal Acta Crystallogr D Biol Crystallogr
Year 2001
Volume 57
Pages 1813-9
Authors Wouters J, Georis J, Engher D, Vandenhaute J, Dusart J, Frere JM, Depiereux E, Charlier P
Title Crystallographic analysis of family 11 endo-beta-1,4-xylanase Xyl1 from Streptomyces sp. S38.
Related PDB
Related UniProtKB
[37]
Resource
Comments
Medline ID
PubMed ID 11513590
Journal Biochemistry
Year 2001
Volume 40
Pages 10115-39
Authors Joshi MD, Sidhu G, Nielsen JE, Brayer GD, Withers SG, McIntosh LP
Title Dissecting the electrostatic interactions and pH-dependent activity of a family 11 glycosidase.
Related PDB
Related UniProtKB
[38]
Resource
Comments
Medline ID
PubMed ID 11180071
Journal Biotechnol Bioeng
Year 2001
Volume 72
Pages 501-5
Authors Leisola M, Jokela J, Finell J, Pastinen O
Title Simultaneous catalysis and product separation by cross-linked enzyme crystals.
Related PDB
Related UniProtKB
[39]
Resource
Comments
Medline ID
PubMed ID 11304525
Journal J Biol Chem
Year 2001
Volume 276
Pages 24309-14
Authors Aro N, Saloheimo A, Ilmen M, Penttila M
Title ACEII, a novel transcriptional activator involved in regulation of cellulase and xylanase genes of Trichoderma reesei.
Related PDB
Related UniProtKB
[40]
Resource
Comments
Medline ID
PubMed ID 11377763
Journal J Biotechnol
Year 2001
Volume 88
Pages 37-46
Authors Turunen O, Etuaho K, Fenel F, Vehmaanpera J, Wu X, Rouvinen J, Leisola M
Title A 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.
Related PDB
Related UniProtKB
[41]
Resource
Comments
Medline ID
PubMed ID 12207016
Journal J Biol Chem
Year 2002
Volume 277
Pages 44035-43
Authors Tahir TA, Berrin JG, Flatman R, Roussel A, Roepstorff P, Williamson G, Juge N
Title Specific characterization of substrate and inhibitor binding sites of a glycosyl hydrolase family 11 xylanase from Aspergillus niger.
Related PDB
Related UniProtKB
[42]
Resource
Comments
Medline ID
PubMed ID 11917150
Journal Protein Eng
Year 2002
Volume 15
Pages 141-5
Authors Turunen O, Vuorio M, Fenel F, Leisola M
Title Engineering 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.
Related PDB
Related UniProtKB
[43]
Resource
Comments
Medline ID
PubMed ID 12773149
Journal Biochem Soc Trans
Year 2003
Volume 31
Pages 523-7
Authors Davies GJ, Ducros VM, Varrot A, Zechel DL
Title Mapping the conformational itinerary of beta-glycosidases by X-ray crystallography.
Related PDB
Related UniProtKB
[44]
Resource
Comments
Medline ID
PubMed ID 14599014
Journal Org Biomol Chem
Year 2003
Volume 1
Pages 3535-40
Authors Laitinen T, Rouvinen J, Perakyla M
Title MM-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.
Related PDB
Related UniProtKB
[45]
Resource
Comments
Medline ID
PubMed ID 15134456
Journal Biochemistry
Year 2004
Volume 43
Pages 5820-31
Authors Betz M, Lohr F, Wienk H, Ruterjans H
Title Long-range nature of the interactions between titratable groups in Bacillus agaradhaerens family 11 xylanase: pH titration of B. agaradhaerens xylanase.
Related PDB
Related UniProtKB
[46]
Resource
Comments
Medline ID
PubMed ID 15166216
Journal J Biol Chem
Year 2004
Volume 279
Pages 36022-8
Authors Sansen S, De Ranter CJ, Gebruers K, Brijs K, Courtin CM, Delcour JA, Rabijns A
Title Structural basis for inhibition of Aspergillus niger xylanase by triticum aestivum xylanase inhibitor-I.
Related PDB 1t6g
Related UniProtKB

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.

Created Updated
2005-04-21 2009-03-27