DB code: S00151

RLCP classification	1.30.36211.974 : Hydrolysis
CATH domain	2.60.120.180 : Jelly Rolls	Catalytic domain
E.C.	3.2.1.8
CSA	1bvv
M-CSA	1bvv
MACiE

CATH domain	Related DB codes (homologues)
2.60.120.180 : Jelly Rolls	S00533 S00150 D00504 D00538

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	CAZy	Pfam	RefSeq
P09850	Endo-1,4-beta-xylanase	Xylanase EC 3.2.1.8 1,4-beta-D-xylan xylanohydrolase	GH11 (Glycoside Hydrolase Family 11)	PF00457 (Glyco_hydro_11) [Graphical View]
Q7SIE3	Endo-1,4-beta-xylanase	EC 3.2.1.8		PF00457 (Glyco_hydro_11) [Graphical View]
P18429	Endo-1,4-beta-xylanase A	Xylanase A EC 3.2.1.8 1,4-beta-D-xylan xylanohydrolase A	GH11 (Glycoside Hydrolase Family 11)	PF00457 (Glyco_hydro_11) [Graphical View]	NP_389765.1 (Protein) NC_000964.3 (DNA/RNA sequence)
P33557	Endo-1,4-beta-xylanase 3	Xylanase 3 EC 3.2.1.8 1,4-beta-D-xylan xylanohydrolase 3 Xylanase C	GH11 (Glycoside Hydrolase Family 11)	PF00457 (Glyco_hydro_11) [Graphical View]
P81536	Endo-1,4-beta-xylanase	Xylanase EC 3.2.1.8 1,4-beta-D-xylan xylanohydrolase PVX	GH11 (Glycoside Hydrolase Family 11)	PF00457 (Glyco_hydro_11) [Graphical View]
P36217	Endo-1,4-beta-xylanase 2	Xylanase 2 EC 3.2.1.8 1,4-beta-D-xylan xylanohydrolase 2	GH11 (Glycoside Hydrolase Family 11)	PF00457 (Glyco_hydro_11) [Graphical View]
P55329	Endo-1,4-beta-xylanase I	Xylanase I EC 3.2.1.8 1,4-beta-D-xylan xylanohydrolase I	GH11 (Glycoside Hydrolase Family 11)	PF00457 (Glyco_hydro_11) [Graphical View]
P48793	Endo-1,4-beta-xylanase	Xylanase EC 3.2.1.8 1,4-beta-D-xylan xylanohydrolase	GH11 (Glycoside Hydrolase Family 11)	PF00457 (Glyco_hydro_11) [Graphical View]
P36218	Endo-1,4-beta-xylanase 1	Xylanase 1 EC 3.2.1.8 1,4-beta-D-xylan xylanohydrolase 1	GH11 (Glycoside Hydrolase Family 11)	PF00457 (Glyco_hydro_11) [Graphical View]
O43097	Endo-1,4-beta-xylanase	Xylanase EC 3.2.1.8 1,4-beta-D-xylan xylanohydrolase	GH11 (Glycoside Hydrolase Family 11)	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	Subcellular location
P09850	XYNA_BACCI	Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.
Q7SIE3	Q7SIE3_BACAG	Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.
P18429	XYNA_BACSU	Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.
P33557	XYN3_ASPKA	Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.	Secreted.
P81536	XYNA_PAEVA	Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.
P36217	XYN2_TRIRE	Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.
P55329	XYN1_ASPNG	Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.
P48793	XYN_TRIHA	Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.
P36218	XYN1_TRIRE	Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.
O43097	XYNA_THELA	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

1bcxA	Unbound		Bound:XYP-XYP	Unbound
1bvvA	Unbound		Unbound	Intermediate-analogue:XYP-DFX
1c5hA	Unbound		Unbound	Unbound
1c5iA	Unbound		Unbound	Intermediate-analogue:XYP-DFX
1hv0A	Unbound		Unbound	Unbound
1hv1A	Unbound		Unbound	Unbound
1xnbA	Unbound		Unbound	Unbound
1xncA	Unbound		Unbound	Unbound
2bvvA	Unbound		Unbound	Unbound
1qh6A	Unbound		Unbound	Intermediate-analogue:FXP
1qh6B	Unbound		Unbound	Intermediate-analogue:FXP
1qh7A	Unbound		Analogue:XYP	Unbound
1qh7B	Unbound		Analogue:XYP	Unbound
1axkA02	Unbound		Unbound	Unbound
1axkB02	Unbound		Unbound	Unbound
1bk1A	Unbound		Unbound	Unbound
1pvxA	Unbound		Unbound	Unbound
1enxA	Unbound		Unbound	Unbound
1enxB	Unbound		Unbound	Unbound
1redA	Unbound		Unbound	Unbound
1redB	Unbound		Unbound	Intermediate-analogue:C5X
1reeA	Unbound		Unbound	Unbound
1reeB	Unbound		Unbound	Intermediate-analogue:C4X
1refA	Unbound		Unbound	Unbound
1refB	Unbound		Unbound	Intermediate-analogue:C3X
1xyoA	Unbound		Unbound	Unbound
1xyoB	Unbound		Unbound	Unbound
1xypA	Unbound		Unbound	Unbound
1xypB	Unbound		Unbound	Unbound
1t6gC	Unbound		Unbound	Unbound
1t6gD	Unbound		Unbound	Unbound
1ukrA	Unbound		Unbound	Unbound
1ukrB	Unbound		Unbound	Unbound
1ukrC	Unbound		Unbound	Unbound
1ukrD	Unbound		Unbound	Unbound
1xndA	Unbound		Unbound	Unbound
1xynA	Unbound		Unbound	Unbound
1ynaA	Unbound		Unbound	Unbound

Reference for Active-site residues
resource	references	E.C.
Swiss-prot;P55329, P36218, P36217, P33557, P09850, O43097, P48793, P18429

Active-site residues
PDB	Catalytic residues	Cofactor-binding residues	Modified residues	Main-chain involved in catalysis	Comment

1bcxA	TYR 69;GLU 78;TYR 80;				mutant E172C
1bvvA	TYR 69;GLU 78;TYR 80;GLU 172
1c5hA	TYR 69;GLU 78;TYR 80;GLU 172				mutant N35D
1c5iA	TYR 69;GLU 78;TYR 80;GLU 172				mutant N35D
1hv0A	TYR 69;GLU 78; ;GLU 172				mutant Y80F
1hv1A	TYR 69;GLU 78;TYR 80;GLU 172				mutant Q127A
1xnbA	TYR 69;GLU 78;TYR 80;GLU 172
1xncA	TYR 69;GLU 78;TYR 80;GLU 172				mutant S100C, N148C
2bvvA	;GLU 78;TYR 80;GLU 172				mutant Y69F
1qh6A	TYR 85;GLU 94;TYR 96;GLU 184
1qh6B	TYR 85;GLU 94;TYR 96;GLU 184
1qh7A	TYR 85;GLU 94;TYR 96;GLU 184
1qh7B	TYR 85;GLU 94;TYR 96;GLU 184
1axkA02	TYR 225;GLU 234;TYR 236;GLU 328
1axkB02	TYR 225;GLU 234;TYR 236;GLU 328
1bk1A	TYR 70;GLU 79;TYR 81;GLU 170
1pvxA	TYR 77;GLU 86;TYR 88;GLU 178
1enxA	TYR 77;GLU 86;TYR 88;GLU 177
1enxB	TYR 77;GLU 86;TYR 88;GLU 177
1redA	TYR 77;GLU 86;TYR 88;GLU 177
1redB	TYR 77;GLU 86;TYR 88;GLU 177
1reeA	TYR 77;GLU 86;TYR 88;GLU 177
1reeB	TYR 77;GLU 86;TYR 88;GLU 177
1refA	TYR 77;GLU 86;TYR 88;GLU 177
1refB	TYR 77;GLU 86;TYR 88;GLU 177
1xyoA	TYR 77;GLU 86;TYR 88;GLU 177
1xyoB	TYR 77;GLU 86;TYR 88;GLU 177
1xypA	TYR 77;GLU 86;TYR 88;GLU 177
1xypB	TYR 77;GLU 86;TYR 88;GLU 177
1t6gC	TYR 70;GLU 79;TYR 81;GLU 170
1t6gD	TYR 70;GLU 79;TYR 81;GLU 170
1ukrA	TYR 70;GLU 79;TYR 81;GLU 170
1ukrB	TYR 70;GLU 79;TYR 81;GLU 170
1ukrC	TYR 70;GLU 79;TYR 81;GLU 170
1ukrD	TYR 70;GLU 79;TYR 81;GLU 170
1xndA	TYR 77;GLU 86;TYR 88;GLU 177
1xynA	TYR 66;GLU 75;TYR 77;GLU 164
1ynaA	TYR 77;GLU 86;TYR 88;GLU 178

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

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Medline ID
PubMed ID	1886523
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Year	1991
Volume	55
Pages	303-15
Authors	Gilkes NR, Henrissat B, Kilburn DG, Miller RC Jr, Warren RA
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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]
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Comments	X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID	94283373
PubMed ID	8013449
Journal	EMBO J
Year	1994
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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
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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
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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
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Resource
Comments	X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID	95127663
PubMed ID	7827044
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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
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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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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 (D00538), 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) Glu170 (of PDB;1bk1) acts as a general acid to protonate the leaving oxygen atom, leading to a oxocarbenium-like transtion state from xylan substrate. (2) pKa of Glu79 (of PDB;1bk1), which acts as a nucleophile, is modulated by Tyr70 and Tyr81. Glu79 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 Glu79 to Glu170. Tyr81 may modulate the activity of Glu170 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], this enzyme 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, 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.

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 (D00538), 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) Glu170 (of PDB;1bk1) acts as a general acid to protonate the leaving oxygen atom, leading to a oxocarbenium-like transtion state from xylan substrate.
(2) pKa of Glu79 (of PDB;1bk1), which acts as a nucleophile, is modulated by Tyr70 and Tyr81. Glu79 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 Glu79 to Glu170. Tyr81 may modulate the activity of Glu170 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], this enzyme 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, 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	2009-09-30