4P9E

Crystal structure of dCMP deaminase from the cyanophage S-TIM5 in apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The First Crystal Structure of a dTTP-bound Deoxycytidylate Deaminase Validates and Details the Allosteric-Inhibitor Binding Site.

Marx, A.Alian, A.

(2015) J.Biol.Chem. 290: 682-690

  • DOI: 10.1074/jbc.M114.617720
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Deoxycytidylate deaminase is unique within the zinc-dependent cytidine deaminase family as being allosterically regulated, activated by dCTP, and inhibited by dTTP. Here we present the first crystal structure of a dTTP-bound deoxycytidylate deaminase ...

    Deoxycytidylate deaminase is unique within the zinc-dependent cytidine deaminase family as being allosterically regulated, activated by dCTP, and inhibited by dTTP. Here we present the first crystal structure of a dTTP-bound deoxycytidylate deaminase from the bacteriophage S-TIM5, confirming that this inhibitor binds to the same site as the dCTP activator. The molecular details of this structure, complemented by structures apo- and dCMP-bound, provide insights into the allosteric mechanism. Although the positioning of the nucleoside moiety of dTTP is almost identical to that previously described for dCTP, protonation of N3 in deoxythymidine and not deoxycytidine would facilitate hydrogen bonding of dTTP but not dCTP and may result in a higher affinity of dTTP to the allosteric site conferring its inhibitory activity. Further the functional group on C4 (O in dTTP and NH2 in dCTP) makes interactions with nonconserved protein residues preceding the allosteric motif, and the relative strength of binding to these residues appears to correspond to the potency of dTTP inhibition. The active sites of these structures are also uniquely occupied by dTMP and dCMP resolving aspects of substrate specificity. The methyl group of dTMP apparently clashes with a highly conserved tyrosine residue, preventing the formation of a correct base stacking shown to be imperative for deamination activity. The relevance of these findings to the wider zinc-dependent cytidine deaminase family is also discussed.


    Organizational Affiliation

    From the Faculty of Biology, Technion-Israel Institute of Technology, Haifa 320003, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deoxycytidylate deaminase
A
138Cyanophage S-TIM5Mutation(s): 0 
Find proteins for H6WFU3 (Cyanophage S-TIM5)
Go to UniProtKB:  H6WFU3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.212 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 78.130α = 90.00
b = 78.130β = 90.00
c = 80.560γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-04-03 
  • Released Date: 2014-11-26 
  • Deposition Author(s): Marx, A., Alian, A.

Revision History 

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2014-12-03
    Type: Database references
  • Version 1.2: 2015-01-14
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Database references, Derived calculations, Other, Refinement description, Source and taxonomy