1NOF

THE FIRST CRYSTALLOGRAPHIC STRUCTURE OF A XYLANASE FROM GLYCOSYL HYDROLASE FAMILY 5: IMPLICATIONS FOR CATALYSIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.102 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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

Larson, S.B.Day, J.Barba de la Rosa, A.P.Keen, N.T.McPherson, A.

(2003) Biochemistry 42: 8411-8422

  • DOI: 10.1021/bi034144c

  • PubMed 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 ...

    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.


    Related Citations: 
    • Cloning and Characterization of a Xylanase Gene from Corn Strains of Erwinia chrysanthemi
      Keen, N.T.,Boyd, C.,Henrissat, B.
      (1996) Mol.Plant Microbe Interact. 9: 651
    • Crystallization of Xylanase from Erwinia chrysanthemi: Influence of Heat and Polymeric Substrate
      Barba De La Rosa, A.P.,Day, J.,Larson, S.B.,Keen, N.T.,McPherson, A.
      (1997) Acta Crystallogr.,Sect.D 53: 256


    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
xylanase
A
383Dickeya chrysanthemiN/A
Find proteins for Q46961 (Dickeya chrysanthemi)
Go to UniProtKB:  Q46961
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.102 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.368α = 90.00
b = 49.580β = 101.66
c = 91.009γ = 90.00
Software Package:
Software NamePurpose
PHASESphasing
X-PLORmodel building
X-PLORphasing
SDMSdata scaling
SOLVEphasing
SHELXL-97refinement
SDMSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-16
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-02-08
    Type: Derived calculations
  • Version 1.4: 2017-10-11
    Type: Refinement description