8JVG

Crystal structure of dephospho-coenzyme A kinase

Summary for 8JVG

• Entry DOI: 10.2210/pdb8jvg/pdb
• Descriptor: GTP-dependent dephospho-CoA kinase (2 entities in total)
• Functional Keywords: apo enzyme, transferase
• Biological source: Thermococcus kodakarensis
• Total number of polymer chains: 2
• Total formula weight: 39372.30

Authors

Kita, A.,Ishida, Y.,Shimosaka, T.,Michimori, Y.,Makarova, K.,Koonin, E.,Atomi, H.,Miki, K. (deposition date: 2023-06-28, release date: 2024-06-19)

Primary citation

Kita, A.,Ishida, Y.,Shimosaka, T.,Michimori, Y.,Makarova, K.,Koonin, E.,Atomi, H.,Miki, K.
Crystal structure of GTP-dependent dephospho-coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis.
Proteins, 92:768-775, 2024

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.

PubMed: 38235908
DOI: 10.1002/prot.26666

Experimental method

X-RAY DIFFRACTION (2.5 Å)