1XII

MODES OF BINDING SUBSTRATES AND THEIR ANALOGUES TO THE ENZYME D-XYLOSE ISOMERASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Modes of binding substrates and their analogues to the enzyme D-xylose isomerase.

Carrell, H.L.Hoier, H.Glusker, J.P.

(1994) Acta Crystallogr D Biol Crystallogr 50: 113-123

  • DOI: 10.1107/S0907444993009345
  • Primary Citation of Related Structures:  
    1XII, 1XIH, 1XIG, 1XIF, 1XIE, 1XID, 1XIC, 1XIB, 1XIJ

  • PubMed Abstract: 
  • Studies of binding of substrates and inhibitors of the enzyme D-xylose isomerase show, from X-ray diffraction data at 1.6-1.9 A resolution, that there are a variety of binding modes. These vary in the manner in which the substrate or its analogue extend, on binding, across the carboxy end of the (betaalpha)(8)-barrel structure ...

    Studies of binding of substrates and inhibitors of the enzyme D-xylose isomerase show, from X-ray diffraction data at 1.6-1.9 A resolution, that there are a variety of binding modes. These vary in the manner in which the substrate or its analogue extend, on binding, across the carboxy end of the (betaalpha)(8)-barrel structure. These binding sites are His54 and the metal ion (magnesium or manganese) that is held in place by Glul81, Asp245, Glu217 and Asp287. Possible catalytic groups have been identified in proposed mechanisms and their role in the binding of ligands is illustrated.


    Related Citations: 
    • X-Ray Analysis of D-Xylose Isomerase at 1.9 Angstroms: Native Enzyme in Complex with Substrate and with a Mechanism-Designed Inactivator
      Carrell, H.L., Glusker, J.P., Burger, V., Manfre, F., Biellmann, D.Tritsch J.-F.
      (1989) Proc Natl Acad Sci U S A 86: 4440
    • Comparison of Backbone Structures of Glucose Isomerase from Streptomyces and Arthrobacter
      Henrick, K., Blow, D.M., Carrell, H.L., Glusker, J.P.
      (1987) Protein Eng 1: 467
    • X-Ray Crystal Structure of D-Xylose Isomerase at 4-Angstroms Resolution
      Carrell, H.L., Rubin, B.H., Hurley, T.J., Glusker, J.P.
      (1984) J Biol Chem 259: 3230

    Organizational Affiliation

    The Institute for Cancer Research, The Fox Chase Cancer Center, Philadelphia, PA 19111, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-XYLOSE ISOMERASEA388Streptomyces rubiginosusMutation(s): 0 
Gene Names: xylA
EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces rubiginosus)
Explore P24300 
Go to UniProtKB:  P24300
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XUL (Subject of Investigation/LOI)
Query on XUL

Download Ideal Coordinates CCD File 
B [auth A]D-XYLULOSE
C5 H10 O5
ZAQJHHRNXZUBTE-WUJLRWPWSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Observed: 0.147 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.78α = 90
b = 99.54β = 90
c = 102.9γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-06-22
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance