ATP-induced structural change of dephosphocoenzyme A kinase from Thermus thermophilus HB8.
Dephosphocoenzyme A kinase (DCK) catalyzes phosphorylation in the final step of coenzyme A (CoA) biosynthesis. In this phosphorylation process, domain movements play a very important role. To reveal the structural changes induced by ligand binding, we determined the crystal structure of DCK from Thermus thermophilus HB8 by the multiwavelength anomalous dispersion method at 2.8 A. The crystal structure includes three independent protein molecules in the asymmetric unit: One is a liganded form and the others are unliganded. The topology shows a canonical nucleotide-binding protein possessing the P-loop motif. A structure homology search by DALI revealed the similarity of the DCKs from T. thermophilus HB8, Haemophilus influenzae, and Escherichia coli. Structural comparisons between the liganded and unliganded forms of DCK from T. thermophilus HB8 indicated domain movements induced by adenosine triphosphate (ATP) binding. For the domain movements, proline residues confer flexibility at the domain linkages. In particular, Pro91 plays an important role in moving the CoA domain.
Seto
Azusa
A
RIKEN Genomic Sciences Center, Yokohama, Japan.
Murayama
Kazutaka
K
Toyama
Mitsutoshi
M
Ebihara
Akio
A
Nakagawa
Noriko
N
Kuramitsu
Seiki
S
Shirouzu
Mikako
M
Yokoyama
Shigeyuki
S
D000255:Adenosine Triphosphate / Q000737:chemistry*; D000595:Amino Acid Sequence / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites / Q000502:physiology; D018360:Crystallography, X-Ray / Q000379:methods; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017853:Phosphotransferases (Alcohol Group Acceptor) / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D017433:Protein Structure, Secondary / Q000235:genetics; D016963:Thermus thermophilus / Q000737:chemistry / Q000201:enzymology* / Q000235:genetics
D001426:Bacterial Proteins; D008024:Ligands; D000255:Adenosine Triphosphate; D017853:Phosphotransferases (Alcohol Group Acceptor); C020021:dephospho-CoA kinase