1H5T

Thymidylyltransferase complexed with Thymidylyldiphosphate-glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Kinetic and Crystallographic Analyses Support a Sequential-Ordered Bi Bi Catalytic Mechanism for Escherichia Coli Glucose-1-Phosphate Thymidylyltransferase

Zuccotti, S.Zanardi, D.Rosano, C.Sturla, L.Tonetti, M.Bolognesi, M.

(2001) J.Mol.Biol. 313: 831

  • DOI: 10.1006/jmbi.2001.5073
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glucose-1-phosphate thymidylyltransferase is the first enzyme in the biosynthesis of dTDP-l-rhamnose, the precursor of l-rhamnose, an essential component of surface antigens, such as the O-lipopolysaccharide, mediating virulence and adhesion to host ...

    Glucose-1-phosphate thymidylyltransferase is the first enzyme in the biosynthesis of dTDP-l-rhamnose, the precursor of l-rhamnose, an essential component of surface antigens, such as the O-lipopolysaccharide, mediating virulence and adhesion to host tissues in many microorganisms. The enzyme catalyses the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis. To shed more light on the catalytic properties of glucose-1-phosphate thymidylyltransferase from Escherichia coli, specifically distinguishing between ping pong and sequential ordered bi bi reaction mechanisms, the enzyme kinetic properties have been analysed in the presence of different substrates and inhibitors. Moreover, three different complexes of glucose-1-phosphate thymidylyltransferase (co-crystallized with dTDP, with dTMP and glucose-1-phosphate, with d-thymidine and glucose-1-phosphate) have been analysed by X-ray crystallography, in the 1.9-2.3 A resolution range (R-factors of 17.3-17.5 %). The homotetrameric enzyme shows strongly conserved substrate/inhibitor binding modes in a surface cavity next to the topological switch-point of a quasi-Rossmann fold. Inspection of the subunit tertiary structure reveals relationships to other enzymes involved in the biosynthesis of nucleotide-sugars, including distant proteins such as the molybdenum cofactor biosynthesis protein MobA. The precise location of the substrate relative to putative reactive residues in the catalytic center suggests that, in keeping with the results of the kinetic measurements, both catalysed reactions, i.e. dTDP-glucose biosynthesis and pyrophosphorolysis, follow a sequential ordered bi bi catalytic mechanism.


    Organizational Affiliation

    Giannina Gaslini Institute, Largo G. Gaslini, Genova, I-16148, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
A, C, D
293Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rfbA (rmlA, rmlA1)
EC: 2.7.7.24
Find proteins for P37744 (Escherichia coli (strain K12))
Go to UniProtKB:  P37744
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
B
293Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rfbA (rmlA, rmlA1)
EC: 2.7.7.24
Find proteins for P37744 (Escherichia coli (strain K12))
Go to UniProtKB:  P37744
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
TYD
Query on TYD

Download SDF File 
Download CCD File 
A, B, C, D
THYMIDINE-5'-DIPHOSPHATE
C10 H16 N2 O11 P2
UJLXYODCHAELLY-XLPZGREQSA-N
 Ligand Interaction
DAU
Query on DAU

Download SDF File 
Download CCD File 
A, B, C, D
2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE
C16 H26 N2 O16 P2
YSYKRGRSMLTJNL-URARBOGNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 72.810α = 90.00
b = 119.490β = 112.67
c = 81.170γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
EPMRphasing
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance