PDBsum entry 2d59

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protein links
Structural genomics, unknown function PDB id
Protein chain
141 a.a. *
Waters ×123
* Residue conservation analysis
PDB id:
Name: Structural genomics, unknown function
Title: Hypothetical protein from pyrococcus horikoshii ot3
Structure: Hypothetical protein ph1109. Chain: a. Engineered: yes
Source: Pyrococcus horikoshii. Organism_taxid: 70601. Strain: ot3. Gene: ph1109. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
1.65Å     R-factor:   0.212     R-free:   0.239
Authors: T.B.Hiyama,S.Sekine,S.Yokoyama,Riken Structural Genomics/pro Initiative (Rsgi)
Key ref: T.B.Hiyama et al. (2006). Structural basis of CoA recognition by the Pyrococcus single-domain CoA-binding proteins. J Struct Funct Genomics, 7, 119-129. PubMed id: 17342453
31-Oct-05     Release date:   31-Oct-06    
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Protein chain
Pfam   ArchSchema ?
O58836  (O58836_PYRHO) -  Putative uncharacterized protein PH1109
144 a.a.
141 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     cofactor binding     2 terms  


J Struct Funct Genomics 7:119-129 (2006)
PubMed id: 17342453  
Structural basis of CoA recognition by the Pyrococcus single-domain CoA-binding proteins.
T.B.Hiyama, M.Zhao, Y.Kitago, M.Yao, S.Sekine, T.Terada, C.Kuroishi, Z.J.Liu, J.P.Rose, S.Kuramitsu, M.Shirouzu, N.Watanabe, S.Yokoyama, I.Tanaka, B.C.Wang.
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.