1GNY

xylan-binding module CBM15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a Family 15 Carbohydrate-Binding Module in Complex with Xylopentaose: Evidence that Xylan Binds in an Approximate Three-Fold Helical Conformation

Szabo, L.Jamal, S.Xie, H.Charnock, S.J.Bolam, D.N.Gilbert, H.J.Davies, G.J.

(2001) J.Biol.Chem. 276: 49061

  • DOI: 10.1074/jbc.M109558200

  • PubMed Abstract: 
  • The recycling of photosynthetically fixed carbon by the action of microbial glycoside hydrolases is a key biological process. The consortium of degradative enzymes involved in this process frequently display catalytic modules appended to one or more ...

    The recycling of photosynthetically fixed carbon by the action of microbial glycoside hydrolases is a key biological process. The consortium of degradative enzymes involved in this process frequently display catalytic modules appended to one or more noncatalytic carbohydrate-binding modules (CBMs). CBMs play a central role in the optimization of the catalytic activity of plant cell wall hydrolases through their binding to specific plant structural polysaccharides. Despite their pivotal role in the biodegradation of plant biomass, the mechanism by which these proteins recognize their target ligands is unclear. This report describes the structure of a xylan-binding CBM (CBM15) in complex with its ligand. This module, derived from Pseudomonas cellulosa xylanase Xyn10C, binds to both soluble xylan and xylooligosaccharides. The three-dimensional crystal structure of CBM15 bound to xylopentaose has been solved by x-ray crystallography to a resolution of 1.6 A. The protein displays a similar beta-jelly roll fold to that observed in many other families of binding-modules. A groove, 20-25 A in length, on the concave surface of one of the beta-sheets presents two tryptophan residues, the faces of which are orientated at approximately 240 degrees to one another. These form-stacking interactions with the n and n+2 sugars of xylopentaose complementing the approximate 3-fold helical structure of this ligand in the binding cleft of CBM15. In four of the five observed binding subsites, the 2' and 3' hydroxyls of the bound ligand are solvent-exposed, providing an explanation for the capacity of this xylan-binding CBM to accommodate the highly decorated xylans found in the plant cell wall.


    Organizational Affiliation

    Department of Biological and Nutritional Sciences, The University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
XYLANASE 10C
A
153Cellvibrio japonicusMutation(s): 0 
Gene Names: xyn10C (xynF)
EC: 3.2.1.8
Find proteins for Q59675 (Cellvibrio japonicus)
Go to UniProtKB:  Q59675
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
XYP
Query on XYP

Download SDF File 
Download CCD File 
A
BETA-D-XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.150 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 92.150α = 90.00
b = 60.122β = 102.78
c = 33.107γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-29
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance