Crystal structure of dephospho-coenzyme A kinase

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.197 

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Crystal structure of GTP-dependent dephospho-coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis.

Kita, A.Ishida, Y.Shimosaka, T.Michimori, Y.Makarova, K.Koonin, E.Atomi, H.Miki, K.

(2024) Proteins 92: 768-775

  • DOI: https://doi.org/10.1002/prot.26666
  • Primary Citation of Related Structures:  
    8JVC, 8JVF, 8JVG

  • PubMed Abstract: 

    The biosynthesis pathways of coenzyme A (CoA) in most archaea involve several unique enzymes including dephospho-CoA kinase (DPCK) that converts dephospho-CoA to CoA in the final step of CoA biosynthesis in all domains of life. The archaeal DPCK is unrelated to the analogous bacterial and eukaryotic enzymes and shows no significant sequence similarity to any proteins with known structures. Unusually, the archaeal DPCK utilizes GTP as the phosphate donor although the analogous bacterial and eukaryotic enzymes are ATP-dependent kinases. Here, we report the crystal structure of DPCK and its complex with GTP and a magnesium ion from the archaeal hyperthermophile Thermococcus kodakarensis. The crystal structure demonstrates why GTP is the preferred substrate of this kinase. We also report the activity analyses of site-directed mutants of crucial residues determined based on sequence conservation and the crystal structure. From these results, the key residues involved in the reaction of phosphoryl transfer and the possible dephospho-CoA binding site are inferred.

  • Organizational Affiliation

    Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-dependent dephospho-CoA kinase177Thermococcus kodakarensisMutation(s): 0 
Gene Names: TK1697
Find proteins for Q5JIY7 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JIY7 
Go to UniProtKB:  Q5JIY7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JIY7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.197 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.246α = 90
b = 58.246β = 90
c = 105.137γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release