1XYB

X-RAY CRYSTALLOGRAPHIC STRUCTURES OF D-XYLOSE ISOMERASE-SUBSTRATE COMPLEXES POSITION THE SUBSTRATE AND PROVIDE EVIDENCE FOR METAL MOVEMENT DURING CATALYSIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Work: 0.166 

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This is version 1.3 of the entry. See complete history

Literature

X-ray crystallographic structures of D-xylose isomerase-substrate complexes position the substrate and provide evidence for metal movement during catalysis.

Lavie, A.Allen, K.N.Petsko, G.A.Ringe, D.

(1994) Biochemistry 33: 5469-5480

  • Primary Citation of Related Structures:  1XYA, 1XYC

  • PubMed Abstract: 
  • The X-ray crystallographic structures of the metal-activated enzyme xylose isomerase from Streptomyces olivochromogenes with the substrates D-glucose, 3-O-methyl-D-glucose and in the absence of substrate were determined to 1.96-, 2.19-, and 1.81-A re ...

    The X-ray crystallographic structures of the metal-activated enzyme xylose isomerase from Streptomyces olivochromogenes with the substrates D-glucose, 3-O-methyl-D-glucose and in the absence of substrate were determined to 1.96-, 2.19-, and 1.81-A resolution and refined to R-factors of 16.6%, 15.9%, and 16.1%, respectively. Xylose isomerase catalyzes the interconversion between glucose and fructose (xylose and xylulose under physiological conditions) by utilizing two metal cofactors to promote a hydride shift; the metals are bridged by a glutamate residue. This puts xylose isomerase in the small but rapidly growing family of enzymes with a bridged bimetallic active site, in which both metals are involved in the chemical transformation. The substrate 3-O-methylglucose was chosen in order to position the glucose molecule in the observed electron density unambiguously. Of the two essential magnesium ions per active site, Mg-2 was observed to occupy two alternate positions, separated by 1.8 A, in the substrate-soaked structures. The deduced movement was not observed in the structure without substrate present and is attributed to a step following substrate binding but prior to isomerization. The substrates glucose and 3-O-methylglucose are observed in their linear extended forms and make identical interactions with the enzyme by forming ligands to Mg-1 through O2 and O4 and by forming hydrogen bonds with His53 through O5 and Lys182 through O1. Mg-2 has a water ligand that is interpreted in the crystal structure in the absence of substrate as a hydroxide ion and in the presence of substrate as a water molecule. This hydroxide ion may act as a base to deprotonate the glucose O2 and subsequently protonate the product fructose O1 concomitant with hydride transfer. Calculations of the solvent-accessible surface of possible dimers, with and without the alpha-helical C-terminal domain, suggest that the tetramer is the active form of this xylose isomerase.


    Related Citations: 
    • Isotopic Exchange Plus Substrate and Inhibition Kinetics of D-Xylose Isomerase Do not Support a Proton-Transfer Mechanism
      Allen, K.N.,Lavie, A.,Farber, G.K.,Glasfeld, A.,Petsko, G.A.,Ringe, D.
      (1994) Biochemistry 33: 1481
    • The Role of the Divalent Metal Ion in Sugar Binding, Ring Opening, and Isomerization by D-Xylose Isomerase: Replacement of a Catalytic Metal by an Amino-Acid
      Allen, K.N.,Lavie, A.,Glasfeld, A.,Tanada, T.N.,Gerrity, D.P.,Carlson, S.C.,Farber, G.K.,Petsko, G.A.,Ringe, D.
      (1994) Biochemistry 33: 1488


    Organizational Affiliation

    Department of Biochemistry, Brandeis University, Massachusetts 02254-9110.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
XYLOSE ISOMERASE
A, B
386Streptomyces olivochromogenesGene Names: xylA
EC: 5.3.1.5
Find proteins for P15587 (Streptomyces olivochromogenes)
Go to UniProtKB:  P15587
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLO
Query on GLO

Download SDF File 
Download CCD File 
A, B
D-GLUCOSE IN LINEAR FORM
C6 H12 O6
GZCGUPFRVQAUEE-SLPGGIOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Work: 0.166 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 87.700α = 90.00
b = 99.400β = 90.00
c = 94.200γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-05-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other