1GMM

Carbohydrate binding module CBM6 from xylanase U Clostridium thermocellum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Location of the Ligand-Binding Site of Carbohydrate-Binding Modules that Have Evolved from a Common Sequence is not Conserved.

Czjzek, M.Bolam, D.Mosbah, A.Allouch, J.Fontes, C.M.Ferreira, L.M.Bornet, O.Zamboni, V.Darbon, H.Smith, N.L.Black, G.W.Henrissat, B.Gilbert, H.J.

(2001) J.Biol.Chem. 276: 48580

  • DOI: 10.1074/jbc.M109142200

  • PubMed Abstract: 
  • Polysaccharide-degrading enzymes are generally modular proteins that contain non-catalytic carbohydrate-binding modules (CBMs), which potentiate the activity of the catalytic module. CBMs have been grouped into sequence-based families, and three-dime ...

    Polysaccharide-degrading enzymes are generally modular proteins that contain non-catalytic carbohydrate-binding modules (CBMs), which potentiate the activity of the catalytic module. CBMs have been grouped into sequence-based families, and three-dimensional structural data are available for half of these families. Clostridium thermocellum xylanase 11A is a modular enzyme that contains a CBM from family 6 (CBM6), for which no structural data are available. We have determined the crystal structure of this module to a resolution of 2.1 A. The protein is a beta-sandwich that contains two potential ligand-binding clefts designated cleft A and B. The CBM interacts primarily with xylan, and NMR spectroscopy coupled with site-directed mutagenesis identified cleft A, containing Trp-92, Tyr-34, and Asn-120, as the ligand-binding site. The overall fold of CBM6 is similar to proteins in CBM families 4 and 22, although surprisingly the ligand-binding site in CBM4 and CBM22 is equivalent to cleft B in CBM6. These structural data define a superfamily of CBMs, comprising CBM4, CBM6, and CBM22, and demonstrate that, although CBMs have evolved from a relatively small number of ancestors, the structural elements involved in ligand recognition have been assembled at different locations on the ancestral scaffold.


    Related Citations: 
    • Homologous Xylanases from Clostridium Thermocellum: Evidence for Bi-Functional Activity, Synergism between Xylanase Catalytic Modules and the Presence of Xylan-Binding Domains in Enzyme Complexes
      Fernandes, A.,Fontes, C.M.G.A.,Gilbert, H.J.,Hazelwood, G.P.,Fernandes, T.H.,Ferreira, L.M.A.,Gilbert, H.J.
      (1999) Biochem.J. 342: 105


    Organizational Affiliation

    Laboratoire d'Architecture et de Fonction des Macromolécules Biologiques, IBSM, CNRS Marseille and University Aix-Marseille I & II, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France. czjzek@afmb.cnrs-mrs.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CBM6
A
133Clostridium thermocellumMutation(s): 0 
Gene Names: xynU
EC: 3.2.1.8
Find proteins for O52780 (Clostridium thermocellum)
Go to UniProtKB:  O52780
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.208 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 59.650α = 90.00
b = 59.650β = 90.00
c = 157.450γ = 120.00
Software Package:
Software NamePurpose
SHARPphasing
SCALAdata scaling
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-28
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance