Structural basis of CoA recognition by the Pyrococcus single-domain CoA-binding proteins.
The single-domain coenzyme A (CoA)-binding protein is conserved in bacteria, archaea, and a few eukaryal taxa. It consists of a Rossmann-fold domain, belonging to the FAD/NAD(P)-binding ;superfamily. The crystal structure of the Thermus thermophilus single-domain CoA-binding protein, TTHA1899, has been determined and it has been demonstrated, by isothermal titration calorimetry, that the protein interacts with CoA [Wada T. et al. Acta Crystallogr D Biol Crystallogr 59 (2003) 1213]. In the present study, we determined the crystal structures of an orthologous protein from the archaeon Pyrococcus horikoshii (PH1109), alone and complexed with CoA, at 1.65 A and 1.70 A resolutions, respectively, and that of P. furiosus protein (PF0725) in the CoA-bound form at 1.70 A. The CoA-bound structures are very similar to each other, revealing that the Pyrococcus proteins bind CoA in a 1:1 stoichiometry. Five loop-containing regions form the CoA-binding groove, to which the CoA molecule is docked. A comparison of the structures and the sequences of the Pyrococcus proteins with those of the T. theromphilus orthologue TTHA1899 indicated that archaeal and bacterial single-domain CoA-binding proteins share the same CoA-binding mode. Nevertheless, many of the peripheral residues involved in the hydrogen-bonding/electrostatic interactions with CoA are not strictly conserved in the family. The CoA interaction of the single-domain CoA-binding proteins is significantly different and much more extensive than that of the multi-subunit/multi-domain CoA-binding protein succinyl-CoA synthetase.
Hiyama
Takuya B
TB
Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
Zhao
Min
M
Kitago
Yu
Y
Yao
Min
M
Sekine
Shun-Ichi
S
Terada
Takaho
T
Kuroishi
Chizu
C
Liu
Zhi-Jie
ZJ
Rose
John P
JP
Kuramitsu
Seiki
S
Shirouzu
Mikako
M
Watanabe
Nobuhisa
N
Yokoyama
Shigeyuki
S
Tanaka
Isao
I
Wang
Bi-Cheng
BC
D000595:Amino Acid Sequence; D002352:Carrier Proteins / Q000737:chemistry / Q000378:metabolism*; D003065:Coenzyme A / Q000737:chemistry / Q000378:metabolism*; D018360:Crystallography, X-Ray; D008969:Molecular Sequence Data; D011485:Protein Binding / Q000502:physiology; D017434:Protein Structure, Tertiary; D043902:Pyrococcus horikoshii / Q000378:metabolism*
D002352:Carrier Proteins; D003065:Coenzyme A