2D59

hypothetical protein from Pyrococcus horikoshii OT3

Summary for 2D59

• Entry DOI: 10.2210/pdb2d59/pdb
• Related: 2D5A
• Descriptor: hypothetical protein PH1109 (2 entities in total)
• Functional Keywords: coa binding, hypothetical protein, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, unknown function
• Biological source: Pyrococcus horikoshii
• Total number of polymer chains: 1
• Total formula weight: 16747.43

Authors

Hiyama, T.B.,Sekine, S.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2005-10-31, release date: 2006-10-31, Last modification date: 2024-03-13)

Primary citation

Hiyama, T.B.,Zhao, M.,Kitago, Y.,Yao, M.,Sekine, S.,Terada, T.,Kuroishi, C.,Liu, Z.J.,Rose, J.P.,Kuramitsu, S.,Shirouzu, M.,Watanabe, N.,Yokoyama, S.,Tanaka, I.,Wang, B.C.
Structural basis of CoA recognition by the Pyrococcus single-domain CoA-binding proteins.
J.STRUCT.FUNCT.GENOM., 7:119-129, 2006

PubMed Abstract: 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.

PubMed: 17342453
DOI: 10.1007/s10969-007-9015-6

Experimental method

X-RAY DIFFRACTION (1.65 Å)