2H92 | pdb_00002h92

Crystal Structure of Staphylococcus aureus Cytidine Monophosphate Kinase in complex with cytidine-5'-monophosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.257 (Depositor) 
  • R-Value Work: 
    0.211 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structure of Staphylococcus aureus cytidine monophosphate kinase in complex with cytidine 5'-monophosphate.

Dhaliwal, B.Ren, J.Lockyer, M.Charles, I.Hawkins, A.R.Stammers, D.K.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 710-715

  • DOI: https://doi.org/10.1107/S174430910602447X
  • Primary Citation Related Structures: 
    2H92

  • PubMed Abstract: 

    The crystal structure of Staphylococcus aureus cytidine monophosphate kinase (CMK) in complex with cytidine 5'-monophosphate (CMP) has been determined at 2.3 angstroms resolution. The active site reveals novel features when compared with two orthologues of known structure. Compared with the Streptococcus pneumoniae CMK solution structure of the enzyme alone, S. aureus CMK adopts a more closed conformation, with the NMP-binding domain rotating by approximately 16 degrees towards the central pocket of the molecule, thereby assembling the active site. Comparing Escherichia coli and S. aureus CMK-CMP complex structures reveals differences within the active site, including a previously unreported indirect interaction of CMP with Asp33, the replacement of a serine residue involved in the binding of CDP by Ala12 in S. aureus CMK and an additional sulfate ion in the E. coli CMK active site. The detailed understanding of the stereochemistry of CMP binding to CMK will assist in the design of novel inhibitors of the enzyme. Inhibitors are required to treat the widespread hospital infection methicillin-resistant S. aureus (MRSA), currently a major public health concern.


  • Organizational Affiliation
    • Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England.

Macromolecule Content 

  • Total Structure Weight: 75.34 kDa 
  • Atom Count: 5,512 
  • Modeled Residue Count: 648 
  • Deposited Residue Count: 657 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytidylate kinase
A, B, C
219Staphylococcus aureusMutation(s): 0 
Gene Names: cmk
EC: 2.7.4.14 (PDB Primary Data), 2.7.4.25 (UniProt)
UniProt
Find proteins for P63807 (Staphylococcus aureus (strain MW2))
Explore P63807 
Go to UniProtKB:  P63807
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63807
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C5P

Query on C5P



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
J [auth C]
CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
H [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A],
F [auth B],
I [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.257 (Depositor) 
  • R-Value Work:  0.211 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.89α = 90
b = 157.89β = 90
c = 76.23γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2006-08-08 
  • Deposition Author(s): Dhaliwal, B.

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-08
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description