1N1D

Glycerol-3-phosphate cytidylyltransferase complexed with CDP-glycerol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Glycerol-3-phosphate cytidylyltransferase. Structural changes induced by binding of CDP-glycerol and the role of lysine residues in catalysis

Pattridge, K.A.Weber, C.H.Friesen, J.A.Sanker, S.Kent, C.Ludwig, M.L.

(2003) J.Biol.Chem. 278: 51863-51871

  • DOI: 10.1074/jbc.M306174200

  • PubMed Abstract: 
  • The bacterial enzyme, glycerol-3-phosphate cytidylyltransferase (GCT), is a model for mammalian cytidylyltransferases and is a member of a large superfamily of nucleotidyltransferases. Dimeric GCT from Bacillus subtilis displays unusual negative coop ...

    The bacterial enzyme, glycerol-3-phosphate cytidylyltransferase (GCT), is a model for mammalian cytidylyltransferases and is a member of a large superfamily of nucleotidyltransferases. Dimeric GCT from Bacillus subtilis displays unusual negative cooperativity in substrate binding and appears to form products only when both active sites are occupied by substrates. Here we describe a complex of GCT with the product, CDP-glycerol, in a crystal structure in which bound sulfate serves as a partial mimic of the second product, pyrophosphate. Binding of sulfate to form a pseudo-ternary complex is observed in three of the four chains constituting the asymmetric unit and is accompanied by a backbone rearrangement at Asp11 and ordering of the C-terminal helix. Comparison with the CTP complex of GCT, determined previously, reveals that in the product complex the active site closes around the glycerol phosphate moiety with a concerted motion of the segment 37-47 that includes helix B. This rearrangement allows lysines 44 and 46 to interact with the glycerol and cytosine phosphates of CDP-glycerol. Binding of CDP-glycerol also induces smaller movements of residues 92-100. Roles of lysines 44 and 46 in catalysis have been confirmed by mutagenesis of these residues to alanine, which decreases Vmax(app) and has profound effects on the Km(app) for glycerol-3-phosphate.


    Related Citations: 
    • A prototypical cytidylyltransferase: CTP:glycerol-3-phosphate cytidylyltransferase from Bacillus subtilis
      Weber, C.H.,Park, Y.S.,Sanker, S.,Kent, C.,Ludwig, M.L.
      (1999) Structure 7: 1113


    Organizational Affiliation

    Biophysics Research Division, University of Michigan, Ann Arbor, Michigan 48109-1055, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
glycerol-3-phosphate cytidylyltransferase
A, B, C, D
129Bacillus subtilis (strain 168)Gene Names: tagD
EC: 2.7.7.39
Find proteins for P27623 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P27623
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
C2G
Query on C2G

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Download CCD File 
A, B, C, D
[CYTIDINE-5'-PHOSPHATE] GLYCERYLPHOSPHORIC ACID ESTER
CYTIDINE 5'-DIPHOSPHOGLYCEROL
C12 H21 N3 O13 P2
HHPOUCCVONEPRK-CNYIRLTGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.241 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 37.795α = 88.99
b = 55.929β = 75.03
c = 63.701γ = 82.54
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance