2J4H

Crystal structure of a H121A Escherichia coli dCTP deaminase mutant enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Regulation of Dctp Deaminase from Escherichia Coli by Nonallosteric Dttp Binding to an Inactive Form of the Enzyme

Johansson, E.Thymark, M.Bynck, J.H.Fanoe, M.Larsen, S.Willemoes, M.

(2007) FEBS J. 274: 4188

  • DOI: 10.1111/j.1742-4658.2007.05945.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The trimeric dCTP deaminase produces dUTP that is hydrolysed to dUMP by the structurally closely related dUTPase. This pathway provides 70-80% of the total dUMP as a precursor for dTTP. Accordingly, dCTP deaminase is regulated by dTTP, which increase ...

    The trimeric dCTP deaminase produces dUTP that is hydrolysed to dUMP by the structurally closely related dUTPase. This pathway provides 70-80% of the total dUMP as a precursor for dTTP. Accordingly, dCTP deaminase is regulated by dTTP, which increases the substrate concentration for half-maximal activity and the cooperativity of dCTP saturation. Likewise, increasing concentrations of dCTP increase the cooperativity of dTTP inhibition. Previous structural studies showed that the complexes of inactive mutant protein, E138A, with dUTP or dCTP bound, and wild-type enzyme with dUTP bound were all highly similar and characterized by having an ordered C-terminal. When comparing with a new structure in which dTTP is bound to the active site of E138A, the region between Val120 and His125 was found to be in a new conformation. This and the previous conformation were mutually exclusive within the trimer. Also, the dCTP complex of the inactive H121A was found to have residues 120-125 in this new conformation, indicating that it renders the enzyme inactive. The C-terminal fold was found to be disordered for both new complexes. We suggest that the cooperative kinetics are imposed by a dTTP-dependent lag of product formation observed in presteady-state kinetics. This lag may be derived from a slow equilibration between an inactive and an active conformation of dCTP deaminase represented by the dTTP complex and the dUTP/dCTP complex, respectively. The dCTP deaminase then resembles a simple concerted system subjected to effector binding, but without the use of an allosteric site.


    Organizational Affiliation

    Centre for Crystallographic Studies, Department of Chemistry, University of Copenhagen, Denmark. evjh@novonordisk.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
A, B
193Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: dcd (dus, paxA)
EC: 3.5.4.13
Find proteins for P28248 (Escherichia coli (strain K12))
Go to UniProtKB:  P28248
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YYY
Query on YYY

Download SDF File 
Download CCD File 
A, B
DEOXYCYTIDINE DIPHOSPHATE
C9 H15 N3 O10 P2
FTDHDKPUHBLBTL-SHYZEUOFSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.225 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 62.545α = 90.00
b = 62.545β = 90.00
c = 342.444γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-07
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-17
    Type: Data collection
  • Version 1.4: 2019-03-06
    Type: Data collection, Experimental preparation