2V4V

Crystal Structure of a Family 6 Carbohydrate-Binding Module from Clostridium cellulolyticum in complex with xylose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report



Literature

Analysis of the Structural and Functional Diversity of Plant Cell Wall Specific Family 6 Carbohydrate Binding Modules.

Abbott, D.W.Ficko-Blean, E.Van Bueren, A.L.Rogowski, A.Cartmell, A.Coutinho, P.M.Henrissat, B.Gilbert, H.J.Boraston, A.B.

(2009) Biochemistry 48: 10395

  • DOI: 10.1021/bi9013424
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Carbohydrate binding modules (CBMs) play important biological roles in targeting appended catalytic modules to their dedicated substrate(s) within complex macromolecular structures such as the plant cell wall. Because of the large potential in ligand ...

    Carbohydrate binding modules (CBMs) play important biological roles in targeting appended catalytic modules to their dedicated substrate(s) within complex macromolecular structures such as the plant cell wall. Because of the large potential in ligand diversity within nature and our continually expanding knowledge of sequence-based information of carbohydrate-modifying enzymes, empirical determination of CBM binding specificity and identification of novel mechanisms in carbohydrate recognition by these proteins have become time-consuming and complicated processes. To help overcome these experimental hurdles, we present here a predictive model for family 6 CBMs (CBM6) that is based upon several factors, including phylogenetic relatedness, and structural and functional evidence. This analysis has determined that five regions within the binding site, termed A-E, play key roles in ligand selection and affinity. Regions A-C are located in a primary subsite and contribute mainly to binding energy and selection for O2, O3, and O4 equatorial hydroxyls. Region D appears to determine whether the CBM will interact with internal or terminal structures of the carbohydrate ligand. Region E displays the largest degree of variation and is thus predicted to make the most significant contribution to specificity. This model is supported by the biochemical properties and structure of a CBM6 from Clostridium cellulolyticum (CcCBM6), which we also report here. The protein bound specifically to xylose and the nonreducing of end of polymers containing this pentose sugar. The crystal structure of CcCBM6 in complex with xylose showed that a tyrosine residue made hydrophobic contacts with the unsubstituted C5 atom of xylose and sterically hindered decorations at this sugar ring position. The mechanism, by which the CBM recognizes xylose but not glucose, a specificity not previously observed in this family, supports our predictive model that holds that variation in region E plays a key role in the diverse ligand selection evident in CBM6.


    Organizational Affiliation

    Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 3055 STN CSC, Victoria, British Columbia V8W 3P6, Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GH59 GALACTOSIDASEA129Ruminiclostridium cellulolyticumMutation(s): 0 
Find proteins for Q0PRN1 (Ruminiclostridium cellulolyticum (strain ATCC 35319 / DSM 5812 / JCM 6584 / H10))
Explore Q0PRN1 
Go to UniProtKB:  Q0PRN1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XYP
Query on XYP

Download CCD File 
A
beta-D-xylopyranose
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
XYPKa:  1700   M^-1  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.026α = 90
b = 43.598β = 90
c = 93.323γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-13
    Type: Initial release
  • Version 1.1: 2011-06-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary