Structure of deoxyadenosine kinase from M. mycoides with bound dCTP

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 

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Structure-Function Analysis of a Bacterial Deoxyadenosine Kinase Reveals the Basis for Substrate Specificity.

Welin, M.Wang, L.Eriksson, S.Eklund, H.

(2007) J Mol Biol 366: 1615

  • DOI: https://doi.org/10.1016/j.jmb.2006.12.010
  • Primary Citation of Related Structures:  
    2JAQ, 2JAS, 2JAT

  • PubMed Abstract: 

    Deoxyribonucleoside kinases (dNKs) catalyze the transfer of a phosphoryl group from ATP to a deoxyribonucleoside (dN), a key step in DNA precursor synthesis. Recently structural information concerning dNKs has been obtained, but no structure of a bacterial dCK/dGK enzyme is known. Here we report the structure of such an enzyme, represented by deoxyadenosine kinase from Mycoplasma mycoides subsp. mycoides small colony type (Mm-dAK). Superposition of Mm-dAK with its human counterpart's deoxyguanosine kinase (dGK) and deoxycytidine kinase (dCK) reveals that the overall structures are very similar with a few amino acid alterations in the proximity of the active site. To investigate the substrate specificity, Mm-dAK has been crystallized in complex with dATP and dCTP, as well as the products dCMP and dCDP. Both dATP and dCTP bind to the enzyme in a feedback-inhibitory manner with the dN part in the deoxyribonucleoside binding site and the triphosphates in the P-loop. Substrate specificity studies with clinically important nucleoside analogs as well as several phosphate donors were performed. Thus, in this study we combine structural and kinetic data to gain a better understanding of the substrate specificity of the dCK/dGK family of enzymes. The structure of Mm-dAK provides a starting point for making new anti bacterial agents against pathogenic bacteria.

  • Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, Biomedical Center, S-751 24 Uppsala, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
205Mycoplasma mycoides subsp. mycoides SCMutation(s): 0 
EC: (PDB Primary Data), (PDB Primary Data)
Find proteins for Q93IG4 (Mycoplasma mycoides subsp. mycoides SC)
Explore Q93IG4 
Go to UniProtKB:  Q93IG4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93IG4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DCP

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C9 H16 N3 O13 P3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.527α = 90
b = 84.527β = 90
c = 53.603γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-01-03
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Other, Refinement description