8XIA

X-RAY ANALYSIS OF D-XYLOSE ISOMERASE AT 1.9 ANGSTROMS: NATIVE ENZYME IN COMPLEX WITH SUBSTRATE AND WITH A MECHANISM-DESIGNED INACTIVATOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.140 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

X-ray analysis of D-xylose isomerase at 1.9 A: native enzyme in complex with substrate and with a mechanism-designed inactivator.

Carrell, H.L.Glusker, J.P.Burger, V.Manfre, F.Tritsch, D.Biellmann, J.F.

(1989) Proc Natl Acad Sci U S A 86: 4440-4444

  • DOI: https://doi.org/10.1073/pnas.86.12.4440
  • Primary Citation of Related Structures:  
    8XIA, 9XIA

  • PubMed Abstract: 

    The structures of crystalline D-xylose isomerase (D-xylose ketol-isomerase; EC 5.3.1.5) from Streptomyces rubiginosus and of its complexes with substrate and with an active-site-directed inhibitor have been determined by x-ray diffraction techniques and refined to 1.9-A resolution. This study identifies the active site, as well as two metal-binding sites. The metal ions are important in maintaining the structure of the active-site region and one of them binds C3-O and C5-O of the substrate forming a six-membered ring. This study has revealed a very close contact between histidine and C1 of a substrate, suggesting that this is the active-site base that abstracts a proton from substrate. The mechanism-based inhibitor is a substrate analog and is turned over by the enzyme to give a product that alkylates this same histidine, reinforcing our interpretation. The changes in structure of the native enzyme, the enzyme with bound substrate, and the alkylated enzyme indicate that the mechanism involves an "open-chain" conformation of substrate and that the intermediate in the isomerization reaction is probably a cis-ene diol because the active-site histidine is correctly placed to abstract a proton from C1 or C2 of the substrate. A water molecule binds to C1O and C2O of the substrate and so may act as a proton donor or acceptor in the enolization of a ring-opened substrate.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
XYLOSE ISOMERASE388Streptomyces rubiginosusMutation(s): 0 
EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces rubiginosus)
Explore P24300 
Go to UniProtKB:  P24300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24300
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XLS
Query on XLS

Download Ideal Coordinates CCD File 
B [auth A]D-xylose
C5 H10 O5
PYMYPHUHKUWMLA-VPENINKCSA-N
MN
Query on MN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.140 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.2α = 90
b = 100.2β = 90
c = 103.2γ = 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: 1991-10-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Database references, Derived calculations, Other, Structure summary
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Structure summary