1N1D

Glycerol-3-phosphate cytidylyltransferase complexed with CDP-glycerol

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.246 

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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
  • Primary Citation of Related Structures:  
    1N1D

  • 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 cooperativity in substrate binding and appears to form products only when both active sites are occupied by substrates ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
glycerol-3-phosphate cytidylyltransferaseA, B, C, D129Bacillus subtilisMutation(s): 0 
EC: 2.7.7.39
UniProt
Find proteins for P27623 (Bacillus subtilis (strain 168))
Explore P27623 
Go to UniProtKB:  P27623
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27623
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.246 
  • 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
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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