Crystal structure of the human UMP/CMP kinase in open conformation

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.222 

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Substrate-induced Conformational Changes in Human UMP/CMP Kinase.

Sekulic, N.Ort, S.Konrad, M.Lavie, A.

(2004) J Biol Chem 279: 33882-33889

  • DOI: https://doi.org/10.1074/jbc.M401989200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Human UMP/CMP kinase plays a crucial role in supplying precursors for nucleic acid synthesis by catalyzing the conversion of UMP, CMP, and dCMP into their diphosphate form. In addition, this kinase is an essential component of the activation cascade of medicinally relevant nucleoside analog prodrugs such as AraC, gemcitabine, and ddC. During the catalytic cycle the enzyme undergoes large conformational changes from open in the absence of substrates to closed in the presence of both phosphoryl donor and phosphoryl acceptor. Here we report the crystal structure of the substrate-free, open form of human UMP/CMP kinase. Comparison of the open structure with the closed state previously reported for the similar Dictyostelium discoideum UMP/CMP kinase reveals the conformational changes that occur upon substrate binding. We observe a classic example of induced fit where substrate-induced conformational changes in hinge residues result in rigid body movements of functional domains to form the catalytically competent state. In addition, a homology model of the human enzyme in the closed state based on the structure of D. discoideum UMP/CMP kinase aids to rationalize the substrate specificity of the human enzyme.

  • Organizational Affiliation

    University of Illinois at Chicago, Department of Biochemistry and Molecular Genetics, Chicago, Illinois 60607, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UMP-CMP kinase196Homo sapiensMutation(s): 0 
Gene Names: UCK
UniProt & NIH Common Fund Data Resources
Find proteins for P30085 (Homo sapiens)
Explore P30085 
Go to UniProtKB:  P30085
PHAROS:  P30085
GTEx:  ENSG00000162368 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30085
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.222 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.75α = 90
b = 62.75β = 90
c = 226.31γ = 120
Software Package:
Software NamePurpose
MAR345data collection
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description