2E7J

Crystal Structure of Sep-tRNA:Cys-tRNA Synthase from Archaeoglobus fulgidus

Summary for 2E7J

• Entry DOI: 10.2210/pdb2e7j/pdb
• Related: 2e7i
• Descriptor: Sep-tRNA:Cys-tRNA synthase, SULFATE ION, PYRIDOXAL-5'-PHOSPHATE, ... (4 entities in total)
• Functional Keywords: seven-stranded bete-strand, lyase, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi
• Biological source: Archaeoglobus fulgidus
• Total number of polymer chains: 2
• Total formula weight: 84865.03

Authors

Fukunaga, R.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2007-01-10, release date: 2007-07-17, Last modification date: 2024-04-03)

Primary citation

Fukunaga, R.,Yokoyama, S.
Structural Insights into the Second Step of RNA-dependent Cysteine Biosynthesis in Archaea: Crystal Structure of Sep-tRNA:Cys-tRNA Synthase from Archaeoglobus fulgidus
J.Mol.Biol., 370:128-141, 2007

PubMed Abstract: 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.

PubMed: 17512006
DOI: 10.1016/j.jmb.2007.04.050

Experimental method

X-RAY DIFFRACTION (2.4 Å)