1H6X

The role of conserved amino acids in the cleft of the C-terminal family 22 carbohydrate binding module of Clostridium thermocellum Xyn10B in ligand binding


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


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Literature

Clostridium Thermocellum Xyn10B Carbohydrate-Binding Module 22-2: The Role of Conserved Amino Acids in Ligand Binding

Xie, H.Gilbert, H.J.Charnock, S.J.Davies, G.J.Williamson, M.P.Simpson, P.J.Raghothama, S.Fontes, C.M.G.A.Dias, F.M.Ferreira, L.M.A.Bolam, D.N.

(2001) Biochemistry 40: 9167

  • Primary Citation of Related Structures:  1H6Y

  • PubMed Abstract: 
  • The majority of plant cell wall hydrolases are modular enzymes which, in addition to a catalytic module, possess one or more carbohydrate-binding modules (CBMs). These carbohydrate-active enzymes and their constituent modules have been classified int ...

    The majority of plant cell wall hydrolases are modular enzymes which, in addition to a catalytic module, possess one or more carbohydrate-binding modules (CBMs). These carbohydrate-active enzymes and their constituent modules have been classified into a number of families based upon amino acid sequence similarity. The Clostridium thermocellum xylanase, Xyn10B, contains two CBMs that belong to family 22 (CBM22). The crystal structure of the C-terminal CBM22 (CBM22-2) was determined in a previous study [Charnock, S. J., et al. (2000) Biochemistry 39, 5013--5021] and revealed a surface cleft which presents several conserved residues that are implicated in ligand binding. These amino acids have been substituted and the structure and biochemical properties of the mutants analyzed. The data show that R25A, W53A, Y103A, Y136A, and E138A exhibit greatly reduced affinity for xylotetraose relative to that of the wild-type protein. Conversely, mutations Y103F and Y136F have little effect on ligand binding. Using thermodynamic, X-ray, and NMR measurements on the mutants, we show that the cleft of CBM22-2 does indeed form the ligand-binding site. Trp 53 and Tyr 103 most likely participate in hydrophobic stacking interactions with the ligand, while Glu 138 makes one or more important hydrogen bonds with the tetrasaccharide. Although Arg 25 and Tyr 136 are likely to form hydrogen bonds with the ligand, they are also shown to play a critical role in maintaining the structural integrity of the binding cleft.


    Related Citations: 
    • The X6 "Thermostabilizing" Domains of Xylanases are Carbohydrate-Binding Modules:Structure and Biochemistry of the Clostridium Thermocellum X6B Domain
      Charnock, S.J.,Bolam, D.N.,Turkenburg, J.P.,Gilbert, H.J.,Ferreira, L.M.A.,Davies, G.J.,Fontes, C.M.G.A.
      (2000) Biochemistry 39: 5013


    Organizational Affiliation

    Department of Biological and Nutritional Sciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDO-1,4-BETA-XYLANASE Y
A
170Clostridium thermocellumGene Names: xynY
EC: 3.2.1.8
Find proteins for P51584 (Clostridium thermocellum)
Go to UniProtKB:  P51584
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.214 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 38.680α = 90.00
b = 38.680β = 90.00
c = 207.530γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-27
    Type: Initial release
  • Version 1.1: 2011-11-16
    Type: Data collection, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance