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 

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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

  • 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: 
    • 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
    • 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.,Sect.D 50: 329
    • 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


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEXOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
A, B
348Escherichia coli (strain K12)Gene Names: galT (galB)
EC: 2.7.7.12
Find proteins for P09148 (Escherichia coli (strain K12))
Go to UniProtKB:  P09148
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
U5P
Query on U5P

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

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Download CCD File 
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 = 57.200α = 90.00
b = 215.400β = 90.00
c = 68.900γ = 90.00
Software Package:
Software NamePurpose
SAINTdata reduction
TNTrefinement
XSCALIBREdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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