First crystallographic structure of a xylanase from glycoside hydrolase family 5: implications for catalysis

Biochemistry. 2003 Jul 22;42(28):8411-22. doi: 10.1021/bi034144c.

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.

Publication types

  • Comparative Study
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Catalysis
  • Cloning, Molecular
  • Crystallography, X-Ray / methods
  • Dickeya chrysanthemi / enzymology
  • Escherichia coli / enzymology
  • Escherichia coli / genetics
  • Glycoside Hydrolases / chemistry*
  • Models, Molecular
  • Protein Conformation
  • Protein Structure, Secondary
  • Recombinant Proteins / chemistry
  • Xylan Endo-1,3-beta-Xylosidase
  • Xylosidases / chemistry*
  • Xylosidases / genetics

Substances

  • Recombinant Proteins
  • Glycoside Hydrolases
  • Xylosidases
  • Xylan Endo-1,3-beta-Xylosidase

Associated data

  • PDB/1NOF