PDBsum entry 1nof

Hydrolase

PDB id: 1nof

Contents

Protein chain

383 a.a. *

Ligands

ACT

Waters ×522

* Residue conservation analysis

References listed in PDB file

Key reference

• Title: First crystallographic structure of a xylanase from glycoside hydrolase family 5: implications for catalysis.
• Authors: S.B.Larson, J.Day, A.P.Barba de la rosa, N.T.Keen, A.Mcpherson.
• Ref.: Biochemistry, 2003, 42, 8411-8422. [DOI no: 10.1021/bi034144c]
• PubMed id: 12859186

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.

Secondary reference #1

• Title: Crystallization of xylanase from erwinia chrysanthemi: influence of heat and polymeric substrate.
• Authors: A.P.De la rosa, J.Day, S.B.Larson, N.Keene, A.Mcpherson.
• Ref.: Acta Crystallogr D Biol Crystallogr, 1997, 53, 256-261. [DOI no: 10.1107/S0907444996014734]
• PubMed id: 15299927

Figure 3.
Fig. 3. (a) The xylan substrate dissolved in the crystallization mother liquor to a concentration of 5 % with no heating. Again a substantial phase separation is observed which is only partly eliminated upon heating to 323 K for 15 rain, as shown in (b). The crystals shown in both (c) and (d) were grown from a mixture of the xylanase plus 5% xylan after heating to 323 K for 15 min. The conditions were, otherwise, the same as for crystals not heated.

The above figure is reproduced from the cited reference with permission from the IUCr

Secondary reference #2

• Title: Cloning and characterization of a xylanase gene from corn strains of erwinia chrysanthemi.
• Authors: N.T.Keen, C.Boyd, B.Henrissat.
• Ref.: Mol Plant Microbe Interact, 1996, 9, 651-657.
• PubMed id: 8810080