1TZF

X-ray Crystal Structure of alpha-D-glucose-1-phosphate cytidylyltransferase from Salmonella typhi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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This is version 1.3 of the entry. See complete history


Literature

Molecular structure of alpha-D-glucose-1-phosphate cytidylyltransferase from Salmonella typhi

Koropatkin, N.M.Holden, H.M.

(2004) J Biol Chem 279: 44023-44029

  • DOI: https://doi.org/10.1074/jbc.M407755200
  • Primary Citation of Related Structures:  
    1TZF

  • PubMed Abstract: 

    Dideoxysugars, which display biological activities ranging from mediating cell-cell interactions to serving as components in some antibiotics, are synthesized in various organisms via complex biochemical pathways that begin with the attachment of alpha-D-glucose 1-phosphate to either CTP or dTTP. Here we describe the three-dimensional structure of the alpha-D-glucose-1-phosphate cytidylyltransferase from Salmonella typhi, which catalyzes the first step in the production of CDP-tyvelose. For this investigation, the enzyme was crystallized in the presence of its product, CDP-glucose. In contrast to previous reports, the enzyme exists as a fully integrated hexamer with 32-point group symmetry. Each subunit displays a "bird-like" appearance with the "body" composed predominantly of a seven-stranded mixed beta-sheet and the two "wings" formed by beta-hairpin motifs. These two wings mediate subunit-subunit interactions along the 3-fold and 2-fold rotational axes, respectively. The six active sites of the hexamer are situated between the subunits related by the 2-fold rotational axes. CDP-glucose is anchored to the protein primarily by hydrogen bonds with backbone carbonyl oxygens and peptidic NH groups. The side chains of Arg111 and Asn188 from one subunit and Glu178 and Lys179 from the second subunit are also involved in hydrogen bonding with the ligand. The topology of the main core domain bears striking similarity to that observed for glucose-1-phosphate thymidylyltransferase and 4-diphosphocytidyl-2-C-methylerythritol synthetase.


  • Organizational Affiliation

    Department of Biochemistry, University of Wisconsin, Madison 53706, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucose-1-phosphate cytidylyltransferase259Salmonella enterica subsp. enterica serovar Typhi str. CT18Mutation(s): 0 
Gene Names: rfbF
EC: 2.7.7.33
UniProt
Find proteins for Q8Z5I4 (Salmonella typhi)
Explore Q8Z5I4 
Go to UniProtKB:  Q8Z5I4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8Z5I4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C5G
Query on C5G

Download Ideal Coordinates CCD File 
C [auth A][CYTIDINE-5'-PHOSPHATE]-BETA-GLUCOSYL-PHOSPHORIC ACID ESTER
C15 H25 N3 O16 P2
CGPHZDRCVSLMCF-JZMIEXBBSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.5α = 90
b = 88.5β = 90
c = 162.3γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
TNTrefinement
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations