1H5S

Thymidylyltransferase complexed with TMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.5 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: 831-843

  • DOI: 10.1006/jmbi.2001.5073
  • Primary Citation of Related Structures:  
    1H5T, 1H5S, 1H5R

  • 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucose-1-phosphate thymidylyltransferase 1A293Escherichia coliMutation(s): 0 
Gene Names: rfbArmlArmlA1b2039JW2024
EC: 2.7.7.24
Find proteins for P37744 (Escherichia coli (strain K12))
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Go to UniProtKB:  P37744
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glucose-1-phosphate thymidylyltransferase 1B293Escherichia coliMutation(s): 0 
Gene Names: rfbArmlArmlA1b2039JW2024
EC: 2.7.7.24
Find proteins for P37744 (Escherichia coli (strain K12))
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Go to UniProtKB:  P37744
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Glucose-1-phosphate thymidylyltransferase 1C293Escherichia coliMutation(s): 0 
Gene Names: rfbArmlArmlA1b2039JW2024
EC: 2.7.7.24
Find proteins for P37744 (Escherichia coli (strain K12))
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Go to UniProtKB:  P37744
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Glucose-1-phosphate thymidylyltransferase 1D293Escherichia coliMutation(s): 0 
Gene Names: rfbArmlArmlA1b2039JW2024
EC: 2.7.7.24
Find proteins for P37744 (Escherichia coli (strain K12))
Explore P37744 
Go to UniProtKB:  P37744
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TMP
Query on TMP

Download CCD File 
A, B, C, D
THYMIDINE-5'-PHOSPHATE
C10 H15 N2 O8 P
GYOZYWVXFNDGLU-XLPZGREQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.1α = 90
b = 119.27β = 112.66
c = 81.11γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-11-28
    Changes: Advisory, Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2019-07-10
    Changes: Data collection
  • Version 1.5: 2019-07-24
    Changes: Data collection