Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.81 kDa 
• Atom Count: 2140 
• Residue Count: 229 
• Unique protein chains: 1

1JYK

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

• DOI: 10.2210/pdb1JYK/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-09-12 Released: 2002-02-22 
• Deposition Author(s): Kwak, B.-Y., Yun, M., Park, H.-w.

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Experimental Data Snapshot

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

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

• PubMed: 11706035 
• DOI: 10.1074/jbc.M109163200
• Primary Citation of Related Structures:  
  1JYL, 1JYK


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CTP:phosphocholine Cytidylyltransferase	A	254	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: licC
Find proteins for A0A0H2UQB5 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UQB5  Go to UniProtKB:  A0A0H2UQB5

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

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 = 42.62	α = 90
b = 63.59	β = 90
c = 122.38	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
XTALVIEW	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-09-12 
• Released Date: 2002-02-22 
Deposition Author(s): Kwak, B.-Y., Yun, M., Park, H.-w.

Revision History 

• 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