4QB2

Structure of CBM35 in complex with glucuronic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Analysis of Glucuronoxylan-specific Xyn30D and Its Attached CBM35 Domain Gives Insights into the Role of Modularity in Specificity.

Sainz-Polo, M.A.Valenzuela, S.V.Gonzalez, B.Pastor, F.I.Sanz-Aparicio, J.

(2014) J.Biol.Chem. 289: 31088-31101

  • DOI: 10.1074/jbc.M114.597732
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glucuronoxylanase Xyn30D is a modular enzyme containing a family 30 glycoside hydrolase catalytic domain and an attached carbohydrate binding module of the CBM35 family. We present here the three-dimensional structure of the full-length Xyn30D at 2.4 ...

    Glucuronoxylanase Xyn30D is a modular enzyme containing a family 30 glycoside hydrolase catalytic domain and an attached carbohydrate binding module of the CBM35 family. We present here the three-dimensional structure of the full-length Xyn30D at 2.4 Å resolution. The catalytic domain folds into an (α/β)8 barrel with an associated β-structure, whereas the attached CBM35 displays a jellyroll β-sandwich including two calcium ions. Although both domains fold in an independent manner, the linker region makes polar interactions with the catalytic domain, allowing a moderate flexibility. The ancillary Xyn30D-CBM35 domain has been expressed and crystallized, and its binding abilities have been investigated by soaking experiments. Only glucuronic acid-containing ligands produced complexes, and their structures have been solved. A calcium-dependent glucuronic acid binding site shows distinctive structural features as compared with other uronic acid-specific CBM35s, because the presence of two aromatic residues delineates a wider pocket. The nonconserved Glu(129) makes a bidentate link to calcium and defines region E, previously identified as specificity hot spot. The molecular surface of Xyn30D-CBM35 shows a unique stretch of negative charge distribution extending from its binding pocket that might indicate some oriented interaction with its target substrate. The binding ability of Xyn30D-CBM35 to different xylans was analyzed by affinity gel electrophoresis. Some binding was observed with rye glucuronoarabinoxylan in presence of calcium chelating EDTA, which would indicate that Xyn30D-CBM35 might establish interaction to other components of xylan, such as arabinose decorations of glucuronoarabinoxylan. A role in depolymerization of highly substituted chemically complex xylans is proposed.


    Organizational Affiliation

    From the Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, 28006 Madrid, Spain and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Xyn30D
A
164Paenibacillus barcinonensisMutation(s): 0 
Gene Names: xyn30d
EC: 3.2.1.8
Find proteins for H6WCZ0 (Paenibacillus barcinonensis)
Go to UniProtKB:  H6WCZ0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
GCU
Query on GCU

Download SDF File 
Download CCD File 
A
D-GLUCURONIC ACID
C6 H10 O7
AEMOLEFTQBMNLQ-WAXACMCWSA-N
 Ligand Interaction
BDP
Query on BDP

Download SDF File 
Download CCD File 
A
BETA-D-GLUCOPYRANURONIC ACID
D-GLUCURONIC ACID
C6 H10 O7
AEMOLEFTQBMNLQ-QIUUJYRFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.891α = 90.00
b = 47.552β = 90.00
c = 102.735γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
MOLREPphasing
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2014-11-26
    Type: Database references
  • Version 1.2: 2018-03-07
    Type: Data collection