2e7j
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Crystal Structure of Sep-tRNA:Cys-tRNA Synthase from Archaeoglobus fulgidus
OverviewOverview
In the ancient organisms, methanogenic archaea, lacking the canonical, cysteinyl-tRNA synthetase, Cys-tRNA(Cys) is produced by an indirect, pathway, in which O-phosphoseryl-tRNA synthetase ligates O-phosphoserine, (Sep) to tRNA(Cys) and Sep-tRNA:Cys-tRNA synthase (SepCysS) converts, Sep-tRNA(Cys) to Cys-tRNA(Cys). In this study, the crystal structure of, SepCysS from Archaeoglobus fulgidus has been determined at 2.4 A, resolution. SepCysS forms a dimer, composed of monomers bearing large and, small domains. The large domain harbors the seven-stranded beta-sheet, which is typical of the pyridoxal 5'-phosphate (PLP)-dependent enzymes. In, the active site, which is located near the dimer interface, PLP is, covalently bound to the side-chain of the conserved Lys209. In the, proximity of PLP, a sulfate ion is bound by the side-chains of the, conserved Arg79, His103, and Tyr104 residues. The active site is located, deep within the large, basic cleft to accommodate Sep-tRNA(Cys). On the, basis of the surface electrostatic potential, the amino acid residue, conservation mapping, the position of the bound sulfate ion, and the, substrate amino acid binding manner in other PLP-dependent enzymes, a, binding model of Sep-tRNA(Cys) to SepCysS was constructed. One of the, three strictly conserved Cys residues (Cys39, Cys42, or Cys247), of one, subunit may play a crucial role in the catalysis in the active site of the, other subunit.
About this StructureAbout this Structure
2E7J is a Single protein structure of sequence from Archaeoglobus fulgidus with and as ligands. Full crystallographic information is available from OCA.
ReferenceReference
Structural insights into the second step of RNA-dependent cysteine biosynthesis in archaea: crystal structure of Sep-tRNA:Cys-tRNA synthase from Archaeoglobus fulgidus., Fukunaga R, Yokoyama S, J Mol Biol. 2007 Jun 29;370(1):128-41. Epub 2007 May 4. PMID:17512006
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- Archaeoglobus fulgidus
- Single protein
- Fukunaga, R.
- RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.
- Yokoyama, S.
- PLP
- SO4
- Lyase
- National project on protein structural and functional analyses
- Nppsfa
- Riken structural genomics/proteomics initiative
- Rsgi
- Seven-stranded bete-strand
- Structural genomics