DB code: M00160

RLCP classification	1.30.36010.970 : Hydrolysis
CATH domain	-.-.-.- :
	-.-.-.- :
	2.30.32.30 : Xylanase; Chain A
	-.-.-.- :
	3.20.20.80 : TIM Barrel	Catalytic domain
E.C.	3.2.1.8
CSA
M-CSA
MACiE

CATH domain	Related DB codes (homologues)
3.20.20.80 : TIM Barrel	S00202 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

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	RefSeq	CAZy	Pfam
P14768	Endo-1,4-beta-xylanase A	Xylanase A EC 3.2.1.8 1,4-beta-D-xylan xylanohydrolase A XYLA	YP_001982932.1 (Protein) NC_010995.1 (DNA/RNA sequence)	CBM10 (Carbohydrate-Binding Module Family 10) CBM2 (Carbohydrate-Binding Module Family 2) GH10 (Glycoside Hydrolase Family 10)	PF02013 (CBM_10) PF00553 (CBM_2) PF00331 (Glyco_hydro_10) [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
P14768	XYNA_PSEFL	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

1ct7A	Unbound		Unbound
1e8rA	Unbound		Unbound
1qldA	Unbound		Unbound
1clxA	Unbound		Unbound
1clxB	Unbound		Unbound
1clxC	Unbound		Unbound
1clxD	Unbound		Unbound
1e5nA	Bound:XYP-XYP-XYP-XYP-XYP		Unbound
1e5nB	Bound:XYP-XYP-XYP-XYP-XYP		Unbound

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

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

1ct7A
1e8rA
1qldA
1clxA	GLU 127;HIS 215;GLU 246;ASP 248
1clxB	GLU 127;HIS 215;GLU 246;ASP 248
1clxC	GLU 127;HIS 215;GLU 246;ASP 248
1clxD	GLU 127;HIS 215;GLU 246;ASP 248
1e5nA	GLU 127;HIS 215;;ASP 248				mutant E246C
1e5nB	GLU 127;HIS 215;;ASP 248				mutant E246C

References for Catalytic Mechanism
References	Sections	No. of steps in catalysis
[2]	Fig. 3, p.1108-1109
[10]	p.32194-32196

References
[1]
Resource
Comments
Medline ID
PubMed ID	1761039
Journal	Eur J Biochem
Year	1991
Volume	202
Pages	367-77
Authors	Gilkes NR, Claeyssens M, Aebersold R, Henrissat B, Meinke A, Morrison HD, Kilburn DG, Warren RA, Miller RC Jr
Title	Structural and functional relationships in two families of beta-1,4-glycanases.
Related PDB
Related UniProtKB
[2]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 265-611, AND REVISIONS.
Medline ID	95187712
PubMed ID	7881909
Journal	Structure
Year	1994
Volume	2
Pages	1107-16
Authors	Harris GW, Jenkins JA, Connerton I, Cummings N, Lo Leggio L, Scott M, Hazlewood GP, Laurie JI, Gilbert HJ, Pickersgill RW
Title	Structure of the catalytic core of the family F xylanase from Pseudomonas fluorescens and identification of the xylopentaose-binding sites.
Related PDB
Related UniProtKB	P14768
[3]
Resource
Comments
Medline ID
PubMed ID	7729513
Journal	FEBS Lett
Year	1995
Volume	362
Pages	281-5
Authors	Jenkins J, Lo Leggio L, Harris G, Pickersgill R
Title	Beta-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.
Related PDB
Related UniProtKB
[4]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 265-611.
Medline ID
PubMed ID
Journal	Acta Crystallogr D Biol Crystallogr
Year	1996
Volume	52
Pages	393-401
Authors	Harris GW, Jenkins JA, Connerton I, Pickersgill RW
Title	Refined crystal structure of the catalytic domain of xylanase A from Pseudomonas fluorescens at 1.8-A resolution.
Related PDB	1clx
Related UniProtKB	P14768
[5]
Resource
Comments
Medline ID
PubMed ID	8912689
Journal	Biochem J
Year	1996
Volume	319
Pages	515-20
Authors	Black GW, Rixon JE, Clarke JH, Hazlewood GP, Theodorou MK, Morris P, Gilbert HJ
Title	Evidence that linker sequences and cellulose-binding domains enhance the activity of hemicellulases against complex substrates.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID	9006940
Journal	J Biol Chem
Year	1997
Volume	272
Pages	2942-51
Authors	Charnock SJ, Lakey JH, Virden R, Hughes N, Sinnott ML, Hazlewood GP, Pickersgill R, Gilbert HJ
Title	Key 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.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID	9560304
Journal	Biochem J
Year	1998
Volume	331
Pages	775-81
Authors	Bolam DN, Ciruela A, McQueen-Mason S, Simpson P, Williamson MP, Rixon JE, Boraston A, Hazlewood GP, Gilbert HJ
Title	Pseudomonas cellulose-binding domains mediate their effects by increasing enzyme substrate proximity.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID	9662439
Journal	FEBS Lett
Year	1998
Volume	429
Pages	312-6
Authors	Nagy T, Simpson P, Williamson MP, Hazlewood GP, Gilbert HJ, Orosz L
Title	All three surface tryptophans in Type IIa cellulose binding domains play a pivotal role in binding both soluble and insoluble ligands.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID	9812357
Journal	FEMS Microbiol Lett
Year	1998
Volume	168
Pages	1-7
Authors	Karlsson EN, Bartonek-Roxa E, Holst O
Title	Evidence for substrate binding of a recombinant thermostable xylanase originating from Rhodothermus marinus.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID	9822697
Journal	J Biol Chem
Year	1998
Volume	273
Pages	32187-99
Authors	Charnock SJ, Spurway TD, Xie H, Beylot MH, Virden R, Warren RA, Hazlewood GP, Gilbert HJ
Title	The topology of the substrate binding clefts of glycosyl hydrolase family 10 xylanases are not conserved.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID	10455036
Journal	Biochem J
Year	1999
Volume	342
Pages	473-80
Authors	Gill J, Rixon JE, Bolam DN, McQueen-Mason S, Simpson PJ, Williamson MP, Hazlewood GP, Gilbert HJ
Title	The type II and X cellulose-binding domains of Pseudomonas xylanase A potentiate catalytic activity against complex substrates by a common mechanism.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID	10653642
Journal	Biochemistry
Year	2000
Volume	39
Pages	985-91
Authors	Ponyi T, Szabo L, Nagy T, Orosz L, Simpson PJ, Williamson MP, Gilbert HJ
Title	Trp22, Trp24, and Tyr8 play a pivotal role in the binding of the family 10 cellulose-binding module from Pseudomonas xylanase A to insoluble ligands.
Related PDB
Related UniProtKB
[13]
Resource
Comments	NMR Structure
Medline ID
PubMed ID	10653641
Journal	Biochemistry
Year	2000
Volume	39
Pages	978-84
Authors	Raghothama S, Simpson PJ, Szabo L, Nagy T, Gilbert HJ, Williamson MP
Title	Solution structure of the CBM10 cellulose binding module from Pseudomonas xylanase A.
Related PDB	1ct7 1e8r 1qld
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID	11025547
Journal	Proteins
Year	2000
Volume	41
Pages	362-73
Authors	Leggio LL, Jenkins J, Harris GW, Pickersgill RW
Title	X-ray crystallographic study of xylopentaose binding to Pseudomonas fluorescens xylanase A.
Related PDB	1e5n
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID	11281716
Journal	Protein Expr Purif
Year	2001
Volume	21
Pages	417-23
Authors	Boraston AB, McLean BW, Guarna MM, Amandaron-Akow E, Kilburn DG
Title	A family 2a carbohydrate-binding module suitable as an affinity tag for proteins produced in Pichia pastoris.
Related PDB
Related UniProtKB

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.

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.

Created	Updated
2003-08-28	2009-02-26