PDBsum entry 1nof

Hydrolase

PDB id

1nof

Loading ...

Contents

			Protein chain

					383 a.a. *

			Ligands

					ACT

			Waters ×522

* Residue conservation analysis

PDB id:

1nof

Links

Name:

Hydrolase

Title:

The first crystallographic structure of a xylanase from glycosyl hydrolase family 5: implications for catalysis

Structure:

Xylanase. Chain: a. Engineered: yes

Source:

Erwinia chrysanthemi. Organism_taxid: 556. Gene: xyna. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.42Å

R-factor:

0.108

R-free:

0.161

Authors:

S.B.Larson,J.Day,A.Mcpherson,A.P.Barba De La Rosa,N.T.Keen

Key ref:

S.B.Larson et al. (2003). First crystallographic structure of a xylanase from glycoside hydrolase family 5: implications for catalysis. Biochemistry, 42, 8411-8422. PubMed id: 12859186 DOI: 10.1021/bi034144c

Date:

16-Jan-03

Release date:

16-Sep-03

PROCHECK

	Headers

	References

Protein chain

Q46961 (Q46961_DICCH) - Xylanase from Dickeya chrysanthemi

Seq: Struc:					413 a.a. 383 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.3.2.1.8 - endo-1,4-beta-xylanase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

Endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.

DOI no: 10.1021/bi034144c	Biochemistry 42:8411-8422 (2003)
PubMed id: 12859186

First crystallographic structure of a xylanase from glycoside hydrolase family 5: implications for catalysis.
S.B.Larson, J.Day, A.P.Barba de la Rosa, N.T.Keen, A.McPherson.

ABSTRACT

The room-temperature structure of xylanase (EC 3.2.1.8) from the bacterial plant pathogen Erwinia chrysanthemi expressed in Escherichia coli, a 45 kDa, 413-amino acid protein belonging to glycoside hydrolase family 5, has been determined by multiple isomorphous replacement and refined to a resolution of 1.42 A. This represents the first structure of a xylanase not belonging to either glycoside hydrolase family 10 or family 11. The enzyme is composed of two domains similar to most family 10 xylanases and the alpha-amylases. The catalytic domain (residues 46-315) has a (beta/alpha)(8)-barrel motif with a binding cleft along the C-terminal side of the beta-barrel. The catalytic residues, Glu165 and Glu253, determined by correspondence to other family 5 and family 10 glycoside hydrolases, lie inside this cleft on the C-terminal ends of beta-strands 4 and 7, respectively, with an O(epsilon)2...O(epsilon)1 distance of 4.22 A. The smaller domain (residues 31-43 and 323-413) has a beta(9)-barrel motif with five of the strands interfacing with alpha-helices 7 and 8 of the catalytic domain. The first 13 N-terminal residues form one beta-strand of this domain. Residues 44, 45, and 316-322 form the linkers between this domain and the catalytic domain.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21234787

J.Wang, H.Zhang, M.Wu, and C.Tang (2011).
Cloning and sequence analysis of a novel xylanase gene, Auxyn10A, from Aspergillus usamii.

Biotechnol Lett, 33, 1029-1038.

20225927

A.Pollet, J.A.Delcour, and C.M.Courtin (2010).
Structural determinants of the substrate specificities of xylanases from different glycoside hydrolase families.

Crit Rev Biotechnol, 30, 176-191.

19940147

O.Gallardo, F.I.Pastor, J.Polaina, P.Diaz, R.Łysek, P.Vogel, P.Isorna, B.González, and J.Sanz-Aparicio (2010).
Structural insights into the specificity of Xyn10B from Paenibacillus barcinonensis and its improved stability by forced protein evolution.

J Biol Chem, 285, 2721-2733.

PDB codes:

3emc 3emq 3emz

20656870

O.Gallardo, M.Fernández-Fernández, C.Valls, S.V.Valenzuela, M.B.Roncero, T.Vidal, P.Díaz, and F.I.Pastor (2010).
Characterization of a family GH5 xylanase with activity on neutral oligosaccharides and evaluation as a pulp bleaching aid.

Appl Environ Microbiol, 76, 6290-6294.

19400841

A.Haegeman, B.Vanholme, and G.Gheysen (2009).
Characterization of a putative endoxylanase in the migratory plant-parasitic nematode Radopholus similis.

Mol Plant Pathol, 10, 389-401.

19407387

F.J.St John, D.K.Godwin, J.F.Preston, E.Pozharski, and J.C.Hurlbert (2009).
Crystallization and crystallographic analysis of Bacillus subtilis xylanase C.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 499-503.

PDB code:

3gtn

18320143

J.G.Berrin, and N.Juge (2008).
Factors affecting xylanase functionality in the degradation of arabinoxylans.

Biotechnol Lett, 30, 1139-1150.

18783340

Y.Kacher, B.Brumshtein, S.Boldin-Adamsky, L.Toker, A.Shainskaya, I.Silman, J.L.Sussman, and A.H.Futerman (2008).
Acid beta-glucosidase: insights from structural analysis and relevance to Gaucher disease therapy.

Biol Chem, 389, 1361-1369.

PDB code:

2vt0

17666401

B.Brumshtein, H.M.Greenblatt, T.D.Butters, Y.Shaaltiel, D.Aviezer, I.Silman, A.H.Futerman, and J.L.Sussman (2007).
Crystal structures of complexes of N-butyl- and N-nonyl-deoxynojirimycin bound to acid beta-glucosidase: insights into the mechanism of chemical chaperone action in Gaucher disease.

J Biol Chem, 282, 29052-29058.

PDB codes:

2v3d 2v3e

17329247

M.E.Caines, M.D.Vaughan, C.A.Tarling, S.M.Hancock, R.A.Warren, S.G.Withers, and N.C.Strynadka (2007).
Structural and mechanistic analyses of endo-glycoceramidase II, a membrane-associated family 5 glycosidase in the Apo and GM3 ganglioside-bound forms.

J Biol Chem, 282, 14300-14308.

PDB codes:

2osw 2osx 2osy

17381510

M.Vrsanská, K.Kolenová, V.Puchart, and P.Biely (2007).
Mode of action of glycoside hydrolase family 5 glucuronoxylan xylanohydrolase from Erwinia chrysanthemi.

FEBS J, 274, 1666-1677.

17646981

Y.Cao, J.Qiao, Y.Li, and W.Lu (2007).
De novo synthesis, constitutive expression of Aspergillus sulphureus beta-xylanase gene in Pichia pastoris and partial enzymic characterization.

Appl Microbiol Biotechnol, 76, 579-585.

17905739

Y.Kitago, S.Karita, N.Watanabe, M.Kamiya, T.Aizawa, K.Sakka, and I.Tanaka (2007).
Crystal structure of Cel44A, a glycoside hydrolase family 44 endoglucanase from Clostridium thermocellum.

J Biol Chem, 282, 35703-35711.

PDB codes:

2e0p 2e4t 2eex 2ej1 2eo7 2eqd

17139081

B.Brumshtein, M.R.Wormald, I.Silman, A.H.Futerman, and J.L.Sussman (2006).
Structural comparison of differently glycosylated forms of acid-beta-glucosidase, the defective enzyme in Gaucher disease.

Acta Crystallogr D Biol Crystallogr, 62, 1458-1465.

PDB code:

2j25

17028274

F.J.St John, J.D.Rice, and J.F.Preston (2006).
Characterization of XynC from Bacillus subtilis subsp. subtilis strain 168 and analysis of its role in depolymerization of glucuronoxylan.

J Bacteriol, 188, 8617-8626.

16673939

M.Mitreva-Dautova, E.Roze, H.Overmars, L.de Graaff, A.Schots, J.Helder, A.Goverse, J.Bakker, and G.Smant (2006).
A symbiont-independent endo-1,4-beta-xylanase from the plant-parasitic nematode Meloidogyne incognita.

Mol Plant Microbe Interact, 19, 521-529.

15853815

J.Jänis, J.Hakanpää, N.Hakulinen, F.M.Ibatullin, A.Hoxha, P.J.Derrick, J.Rouvinen, and P.Vainiotalo (2005).
Determination of thioxylo-oligosaccharide binding to family 11 xylanases using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and X-ray crystallography.

FEBS J, 272, 2317-2333.

PDB code:

1xnk

15652973

T.Collins, C.Gerday, and G.Feller (2005).
Xylanases, xylanase families and extremophilic xylanases.

FEMS Microbiol Rev, 29, 3.

14993687

T.Parkkinen, N.Hakulinen, M.Tenkanen, M.Siika-aho, and J.Rouvinen (2004).
Crystallization and preliminary X-ray analysis of a novel Trichoderma reesei xylanase IV belonging to glycoside hydrolase family 5.

Acta Crystallogr D Biol Crystallogr, 60, 542-544.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.