1JYK

Catalytic Mechanism of CTP:phosphocholine Cytidylyltransferase from Streptococcus pneumoniae (LicC)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and mechanism of CTP:phosphocholine cytidylyltransferase (LicC) from Streptococcus pneumoniae.

Kwak, B.Y.Zhang, Y.M.Yun, M.Heath, R.J.Rock, C.O.Jackowski, S.Park, H.W.

(2002) J Biol Chem 277: 4343-4350

  • DOI: https://doi.org/10.1074/jbc.M109163200
  • Primary Citation of Related Structures:  
    1JYK, 1JYL

  • PubMed Abstract: 

    Pneumococcal LicC is a member of the nucleoside triphosphate transferase superfamily and catalyzes the transfer of a cytidine monophosphate from CTP to phosphocholine to form CDP-choline. The structures of apo-LicC and the LicC-CDP-choline-Mg(2+) ternary complex were determined, and the comparison of these structures reveals a significant conformational change driven by the multivalent coordination of Mg(2+). The key event is breaking the Glu(216)-Arg(129) salt bridge, which triggers the coalescence of four individual beta-strands into two extended beta-sheets. These movements reorient the side chains of Trp(136) and Tyr(190) for the optimal binding and alignment of the phosphocholine moiety. Consistent with these conformational changes, LicC operates via a compulsory ordered kinetic mechanism. The structures explain the substrate specificity of LicC for CTP and phosphocholine and implicate a direct role for Mg(2+) in aligning phosphocholine for in-line nucleophilic attack and stabilizing the negative charge that develops in the pentacoordinate transition state. These results provide a structural basis for assigning a specific role for magnesium in the catalytic mechanism of pneumococcal LicC.


  • Organizational Affiliation

    Department of Structural Biology and the Protein Science Division, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CTP:phosphocholine Cytidylyltransferase254Streptococcus pneumoniaeMutation(s): 0 
Gene Names: LicC
EC: 2.7.7.15
UniProt
Find proteins for Q8DPI6 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DPI6 
Go to UniProtKB:  Q8DPI6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DPI6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.62α = 90
b = 63.59β = 90
c = 122.38γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
XTALVIEWrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance