4TTP

Crystal structure of Legionella pneumophila dephospho-CoA kinase in apo-form

Summary for 4TTP

• Entry DOI: 10.2210/pdb4ttp/pdb
• Related: 4TTQ 4TTR
• Descriptor: Dephospho-CoA kinase (2 entities in total)
• Functional Keywords: kinase, p-loop, coenzyme metabolism, transferase
• Biological source: Legionella pneumophila subsp. pneumophila
• Total number of polymer chains: 1
• Total formula weight: 24633.60

Authors

Gong, X.,Ge, H. (deposition date: 2014-06-22, release date: 2014-12-10, Last modification date: 2023-09-27)

Primary citation

Gong, X.,Chen, X.,Yu, D.,Zhang, N.,Zhu, Z.,Niu, L.,Mao, Y.,Ge, H.
Crystal structure of Legionella pneumophila dephospho-CoA kinase reveals a non-canonical conformation of P-loop.
J.Struct.Biol., 188:233-239, 2014

PubMed Abstract: Dephospho-CoA kinase (DPCK; EC 2.7.1.24) catalyzes the final step in the coenzyme A biosynthetic pathway. DPCK transfers a phosphate group from ATP to the 3-hydroxyl group of the ribose of dephosphocoenzyme A (dCoA) to yield CoA and ADP. Upon the binding of ligands, large conformational changes is induced in DPCKs, as well as in many other kinases, to shield the bound ATP in their catalytic site from the futile hydrolysis by bulk water molecules. To investigate the molecular mechanisms underlying the phosphoryl transfer during DPCK catalytic cycle, we determined the crystal structures of the Legionellapneumophila DPCK (LpDPCK) both in its apo-form and in complex with ATP. The structures reveal that LpDPCK comprises of three domains, the classical core domain, the CoA domain, and the LID domain, which are packed together to create a central cavity for substrate-binding and enzymatic catalysis. The binding of ATP induces large conformational changes, including a hinge-bending motion of the CoA binding domain and the "helix to loop" conformational change of the P-loop. Finally, modeling of a dCoA molecule to the enzyme provides insights into the catalytic mechanism of DPCK.

PubMed: 25449315
DOI: 10.1016/j.jsb.2014.10.008

Experimental method

X-RAY DIFFRACTION (2.2 Å)