2CMK

CYTIDINE MONOPHOSPHATE KINASE IN COMPLEX WITH CYTIDINE-DI-PHOSPHATE

• PDB DOI: https://doi.org/10.2210/pdb2CMK/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-09-19 Released: 1999-09-20 
• Deposition Author(s): Golinelli-Pimpaneau, B., Briozzo, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.220 
• R-Value Work: 0.213 
• R-Value Observed: 0.213 

Literature

Structures of escherichia coli CMP kinase alone and in complex with CDP: a new fold of the nucleoside monophosphate binding domain and insights into cytosine nucleotide specificity.

Briozzo, P., Golinelli-Pimpaneau, B., Gilles, A.M., Gaucher, J.F., Burlacu-Miron, S., Sakamoto, H., Janin, J., Barzu, O.

(1998) Structure 6: 1517-1527

• PubMed: 9862805 
• DOI: https://doi.org/10.1016/s0969-2126(98)00150-6
• Primary Citation of Related Structures:  
  1CKE, 2CMK


• PubMed Abstract: 
  

  . Nucleoside monophosphate kinases (NMP kinases) catalyze the reversible transfer of a phosphoryl group from a nucleoside triphosphate to a nucleoside monophosphate. Among them, cytidine monophosphate kinase from Escherichia coli has a striking particularity: it is specific for CMP, whereas in eukaryotes a unique UMP/CMP kinase phosphorylates both CMP and UMP with similar efficiency.

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Organizational Affiliation: 

Laboratoire de Chimie Biologique Institut National Agronomique Paris-Grignon 78850 Thiverval-Grignon France. Pierre.Briozzo@lebs. cnrs-gif.fr

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.37 kDa 
• Atom Count: 1,839 
• Modelled Residue Count: 221 
• Deposited Residue Count: 227 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (CYTIDINE MONOPHOSPHATE KINASE)	A	227	Escherichia coli	Mutation(s): 0  EC: 2.7.4.14
UniProt
Find proteins for P0A6I0 (Escherichia coli (strain K12)) Explore P0A6I0  Go to UniProtKB:  P0A6I0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CDP	D [auth A]	CYTIDINE-5'-DIPHOSPHATE C9 H15 N3 O11 P2 ZWIADYZPOWUWEW-XVFCMESISA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.220 
• R-Value Work: 0.213 
• R-Value Observed: 0.213 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.268	α = 90
b = 77.268	β = 90
c = 81.232	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-09-20 
Deposition Author(s): Golinelli-Pimpaneau, B., Briozzo, P.

Revision History  

• Version 1.0: 1999-09-20
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations