1XYM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

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: 1488-1494

  • DOI: 10.1021/bi00172a027
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The distinct roles of the two magnesium ions essential to the activity of D-xylose isomerase from Streptomyces olivochromogenes were examined. The enzyme-magnesium complex was isolated, and the stoichiometry of cation binding determined by neutron ac ...

    The distinct roles of the two magnesium ions essential to the activity of D-xylose isomerase from Streptomyces olivochromogenes were examined. The enzyme-magnesium complex was isolated, and the stoichiometry of cation binding determined by neutron activation analysis to be 2 mol of magnesium per mole of enzyme. A plot of Mg2+ added versus Mg2+ bound to enzyme is consistent with apparent KD values of < or = 0.5-1.0 mM for one Mg2+ and < or = 2-5 mM for the second. A site-directed mutant of D-xylose isomerase was designed to remove the tighter, tetracoordinated magnesium binding site (site 1, Mg-1); Glu180 was replaced with Lys180. The stoichiometry of metal binding to this mutant, E180K, is 1 mol of magnesium per mole of enzyme. Ring-opening assays with 1-thioglucose (H2S released upon ring opening) show E180K catalyzes the opening of the sugar ring at 20% the rate of the wild-type, but E180K does not catalyze isomerization of glucose to fructose. Thus, the magnesium bound to Glu180 is essential for isomerization but not essential for ring opening. The X-ray crystallographic structures of E180K in the absence of magnesium and in the presence and absence of 250 mM glucose were obtained to 1.8-A resolution and refined to R factors of 17.7% and 19.7%, respectively. The wild-type and both E180K structures show no significant structural differences, except the epsilon-amino group of Lys180, which occupies the position usually occupied by the Mg-1.(ABSTRACT TRUNCATED AT 250 WORDS)


    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
    • 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.
      () To be published --: --

    Organizational Affiliation

    Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02254-9110.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
XYLOSE ISOMERASEA, B386Streptomyces olivochromogenesMutation(s): 0 
Gene Names: xylA
EC: 5.3.1.5
Find proteins for P15587 (Streptomyces olivochromogenes)
Explore P15587 
Go to UniProtKB:  P15587
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLO
Query on GLO

Download CCD File 
A, B
D-glucose
C6 H12 O6
GZCGUPFRVQAUEE-SLPGGIOYSA-N
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
OH
Query on OH

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A, B
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.12α = 90
b = 99.53β = 90
c = 94.79γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-05-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 1.4: 2020-07-08
    Changes: Database references
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary