1I82

FAMILY 9 CARBOHYDRATE-BINDING MODULE FROM THERMOTOGA MARITIMA XYLANASE 10A WITH CELLOBIOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal structures of the family 9 carbohydrate-binding module from Thermotoga maritima xylanase 10A in native and ligand-bound forms.

Notenboom, V.Boraston, A.B.Kilburn, D.G.Rose, D.R.

(2001) Biochemistry 40: 6248-6256

  • DOI: 10.1021/bi0101704
  • Primary Citation of Related Structures:  
    1I82, 1I8A, 1I8U

  • PubMed Abstract: 
  • The C-terminal module of the thermostable Thermotoga maritima xylanase 10A (CBM9-2) is a family 9 carbohydrate-binding module that binds to amorphous and crystalline cellulose and a range of soluble di- and monosaccharides as well as to cello and xylo oligomers of different degrees of polymerization [Boraston, A ...

    The C-terminal module of the thermostable Thermotoga maritima xylanase 10A (CBM9-2) is a family 9 carbohydrate-binding module that binds to amorphous and crystalline cellulose and a range of soluble di- and monosaccharides as well as to cello and xylo oligomers of different degrees of polymerization [Boraston, A. B., Creagh, A. L., Alam, Md. M., Kormos, J. M., Tomme, P., Haynes, C. A., Warren, R. A. J., and Kilburn, D. G. (2001) Biochemistry 40, 6240-6247]. The crystal structure of CBM9-2 has been determined by the multiwavelength anomalous dispersion method to 1.9 A resolution. CBM9-2 assumes a beta-sandwich fold and contains three metal binding sites. The bound metal atoms, which are most likely calcium cations, are in an octahedral coordination. The crystal structures of CBM9-2 in complex with glucose and cellobiose were also determined in order to identify the sugar-binding site and provide insight into the structural basis for sugar binding by CBM9-2. The sugar-binding site is a solvent-exposed slot sufficient in depth, width, and length to accommodate a disaccharide. Two tryptophan residues are stacked together on the surface of the protein forming the sugar-binding site. From the complex structures with glucose and cellobiose, it was inferred that CBM9-2 binds exclusively to the reducing end of mono-, di-, and oligosaccharides with an intricate hydrogen-bonding network involving mainly charged residues, as well as stacking interactions by Trp175 and Trp71. The binding interactions are limited to disaccharides as was expected from calorimetric data. Comparison of the glucose and cellobiose complexes revealed surprising differences in binding of these two substrates by CBM9-2. Cellobiose was found to bind in a distinct orientation from glucose, while still maintaining optimal stacking and electrostatic interactions with the reducing end sugar.


    Organizational Affiliation

    Protein Engineering Network of Centres of Excellence, Ontario Cancer Institute, University of Toronto, Toronto, Ontario, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENDO-1,4-BETA-XYLANASE AA189Thermotoga maritimaMutation(s): 0 
EC: 3.2.1.8
UniProt
Find proteins for Q60037 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q60037 
Go to UniProtKB:  Q60037
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ60037
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranoseB 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G84824ZO
GlyCosmos:  G84824ZO
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900005
Query on PRD_900005
Bbeta-cellobioseOligosaccharide / Metabolism Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.67α = 90
b = 56.67β = 90
c = 122.97γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    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, Structure summary