1KDR

CYTIDINE MONOPHOSPHATE KINASE FROM E.COLI IN COMPLEX WITH ARA-CYTIDINE MONOPHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Sugar specificity of bacterial CMP kinases as revealed by crystal structures and mutagenesis of Escherichia coli enzyme.

Bertrand, T.Briozzo, P.Assairi, L.Ofiteru, A.Bucurenci, N.Munier-Lehmann, H.Golinelli-Pimpaneau, B.Barzu, O.Gilles, A.M.

(2002) J Mol Biol 315: 1099-1110

  • DOI: 10.1006/jmbi.2001.5286
  • Primary Citation of Related Structures:  
    1KDP, 1KDO, 1KDT, 1KDR

  • PubMed Abstract: 
  • Bacterial cytidine monophosphate (CMP) kinases are characterised by an insert enlarging their CMP binding domain, and by their particular substrate specificity. Thus, both CMP and 2'-deoxy-CMP (dCMP) are good phosphate acceptors for the CMP kinase from Escherichia coli (E ...

    Bacterial cytidine monophosphate (CMP) kinases are characterised by an insert enlarging their CMP binding domain, and by their particular substrate specificity. Thus, both CMP and 2'-deoxy-CMP (dCMP) are good phosphate acceptors for the CMP kinase from Escherichia coli (E. coli CMPK), whereas eukaryotic UMP/CMP kinases phosphorylate the deoxynucleotides with very low efficiency. Four crystal structures of E. coli CMPK complexed with nucleoside monophosphates differing in their sugar moiety were solved. Both structures with CMP or dCMP show interactions with the pentose that were not described so far. These interactions are lost with the poorer substrates AraCMP and 2',3'-dideoxy-CMP. Comparison of all four structures shows that the pentose hydroxyls are involved in ligand-induced movements of enzyme domains. It also gives a structural basis of the mechanism by which either ribose or deoxyribose can be accommodated. In parallel, for the four nucleotides the kinetic results of the wild-type enzyme and of three structure-based variants are presented. The phosphorylation rate is significantly decreased when either of the two pentose interacting residues is mutated. One of these is an arginine that is highly conserved in all known nucleoside monophosphate kinases. In contrast, the other residue, Asp185, is typical of bacterial CMP kinases. It interacts with Ser101, the only residue conserved in all CMP binding domain inserts. Mutating Ser101 reduces CMP phosphorylation only moderately, but dramatically reduces dCMP phosphorylation. This is the first experimental evidence of a catalytic role involving the characteristic insert of bacterial CMP kinases. Furthermore, this role concerns only dCMP phosphorylation, a feature of this family of enzymes.


    Organizational Affiliation

    Laboratoire d'Enzymologie et de Biochimie Structurales, UPR 9063 du CNRS, Gif-sur-Yvette Cedex, 91198, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTIDYLATE KINASEA, B227Escherichia coliMutation(s): 0 
Gene Names: cmk
EC: 2.7.4.14 (PDB Primary Data), 2.7.4.25 (UniProt)
UniProt
Find proteins for P0A6I0 (Escherichia coli (strain K12))
Explore P0A6I0 
Go to UniProtKB:  P0A6I0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAR (Subject of Investigation/LOI)
Query on CAR

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]CYTOSINE ARABINOSE-5'-PHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-CCXZUQQUSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], E [auth B], F [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.585α = 90
b = 73.772β = 90
c = 77.644γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-01-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance