1HXQ

THE STRUCTURE OF NUCLEOTIDYLATED GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE FROM ESCHERICHIA COLI AT 1.86 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structure of nucleotidylated histidine-166 of galactose-1-phosphate uridylyltransferase provides insight into phosphoryl group transfer.

Wedekind, J.E.Frey, P.A.Rayment, I.

(1996) Biochemistry 35: 11560-11569

  • DOI: 10.1021/bi9612677
  • Primary Citation of Related Structures:  
    1HXQ

  • PubMed Abstract: 
  • Galactose-1-phosphate uridylyltransferase catalyzes the reaction of UDP-glucose with galactose 1-phosphate to form UDP-galactose and glucose 1-phosphate during normal cellular metabolism. The reaction proceeds through a double displacement mechanism ...

    Galactose-1-phosphate uridylyltransferase catalyzes the reaction of UDP-glucose with galactose 1-phosphate to form UDP-galactose and glucose 1-phosphate during normal cellular metabolism. The reaction proceeds through a double displacement mechanism characterized by the formation of a stable nucleotidylated histidine intermediate. This paper describes the preparation of the uridylyl-enzyme complex on the crystalline enzyme from Escherichia coli and its subsequent structure determination by X-ray crystallography. The refined structure has an R-factor of 19.6% (data between 65 and 1.86 A resolution) and reveals modest conformational changes at the active site compared to the inactive UMP/UDP-enzyme complex reported previously [Wedekind, J.E., Frey, P.A., & Rayment, I. (1995) Biochemistry 34, 11049-11061]. In particular, positions of the respective UMP alpha-phosphoryl groups differ by approximately 4 A. Well-defined electron density for the nucleotidylated imidazole supports the existence of a covalent bond between N epsilon 2 of the nucleophile and the alpha-phosphorus of UMP. A hydrogen bond that is conserved in both complexes between His 166 N delta 1 and the carbonyl O of His 164 serves to properly orient the nucleophile and electrostatically stabilize the positively charged imidazolium that results from nucleotidylation. Hydrogen bonds from side-chain Gln 168 to the nonbridging phosphoryl oxygens of the nucleotidyl intermediate appear crucial for the formation and reaction of the uridylyl-enzyme complex as well. The significance of the latter interaction is underscored by the fact that the predominant cause of the metabolic disease galactosemia is the mutation of the corresponding Gln (Gln 188 in humans) to Arg. A comparison to other phosphohistidyl enzymes is described, as well as a revised model for the mechanism of the uridylyltransferase.


    Related Citations: 
    • Three-Dimensional Structure of Galactose-1-Phosphate Uridylyltransferase from Escherichia Coli at 1.8 A Resolution
      Wedekind, J.E., Frey, P.A., Rayment, I.
      (1995) Biochemistry 34: 11049
    • Galactose-1-Phosphate Uridylyltransferase from Escherichia Coli, a Zinc and Iron Metalloenzyme
      Ruzicka, F.J., Wedekind, J.E., Kim, J., Rayment, I., Frey, P.A.
      (1995) Biochemistry 34: 5610
    • Crystallization and Preliminary Crystallographic Analysis of Galactose-1-Phosphate Uridylyltransferase from Escherichia Coli
      Wedekind, J.E., Frey, P.A., Rayment, I.
      (1994) Acta Crystallogr D Biol Crystallogr 50: 329
    • The Nucleotide Sequence of the Gal T Gene of Escherichia Coli
      Cornwell, T.L., Adhya, S.L., Reznikoff, W.S., Frey, P.A.
      (1987) Nucleic Acids Res 15: 8116

    Organizational Affiliation

    Institute for Enzyme Research, Graduate School, College of Agricultural and Life Sciences, University of Wisconsin, Madison 53705, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HEXOSE-1-PHOSPHATE URIDYLYLTRANSFERASEA, B348Escherichia coliMutation(s): 0 
EC: 2.7.7.12
Find proteins for P09148 (Escherichia coli (strain K12))
Explore P09148 
Go to UniProtKB:  P09148
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U5P
Query on U5P

Download CCD File 
A, B
URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N
 Ligand Interaction
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Work: 0.196 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.2α = 90
b = 215.4β = 90
c = 68.9γ = 90
Software Package:
Software NamePurpose
TNTrefinement
SAINTdata reduction
XSCALIBREdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-10-22
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other