2GVE

Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.268 

wwPDB Validation

Currently 2GVE does not have a wwPDB validation report.


This is version 1.3 of the entry. See complete history

Literature

Locating active-site hydrogen atoms in D-xylose isomerase: Time-of-flight neutron diffraction.

Katz, A.K.Li, X.Carrell, H.L.Hanson, B.L.Langan, P.Coates, L.Schoenborn, B.P.Glusker, J.P.Bunick, G.J.

(2006) Proc.Natl.Acad.Sci.Usa 103: 8342-8347

  • DOI: 10.1073/pnas.0602598103
  • Primary Citation of Related Structures:  2GLK, 2GUB

  • PubMed Abstract: 
  • Time-of-flight neutron diffraction has been used to locate hydrogen atoms that define the ionization states of amino acids in crystals of D-xylose isomerase. This enzyme, from Streptomyces rubiginosus, is one of the largest enzymes studied to date at ...

    Time-of-flight neutron diffraction has been used to locate hydrogen atoms that define the ionization states of amino acids in crystals of D-xylose isomerase. This enzyme, from Streptomyces rubiginosus, is one of the largest enzymes studied to date at high resolution (1.8 A) by this method. We have determined the position and orientation of a metal ion-bound water molecule that is located in the active site of the enzyme; this water has been thought to be involved in the isomerization step in which D-xylose is converted to D-xylulose or D-glucose to D-fructose. It is shown to be water (rather than a hydroxyl group) under the conditions of measurement (pH 8.0). Our analyses also reveal that one lysine probably has an -NH(2)-terminal group (rather than NH(3)(+)). The ionization state of each histidine residue also was determined. High-resolution x-ray studies (at 0.94 A) indicate disorder in some side chains when a truncated substrate is bound and suggest how some side chains might move during catalysis. This combination of time-of-flight neutron diffraction and x-ray diffraction can contribute greatly to the elucidation of enzyme mechanisms.


    Related Citations: 
    • Modes of binding substrates and their analogs to the enzyme D-xylose isomerase
      Carrell, H.L.,Hoier, H.,Glusker, J.P.
      (1994) ACTA CRYSTALLOGR.,SECT.D 50: 113


    Organizational Affiliation

    Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Xylose isomerase
A
388Streptomyces rubiginosusGene Names: xylA
EC: 5.3.1.5
Find proteins for P24300 (Streptomyces rubiginosus)
Go to UniProtKB:  P24300
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CO
Query on CO

Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
DOD
Query on DOD

Download SDF File 
Download CCD File 
A
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.268 
Software Package:
Software NamePurpose
SHELXL-97phasing
d*TREKdata scaling
SHELXL-97model building
SHELXL-97refinement
d*TREKdata reduction

Structure Validation

Currently 2GVE does not have a wwPDB validation report.



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-16
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description