TY - JOUR
T1 - Structural Insights into the Second Step of RNA-dependent Cysteine Biosynthesis in Archaea
T2 - Crystal Structure of Sep-tRNA:Cys-tRNA Synthase from Archaeoglobus fulgidus
AU - Fukunaga, Ryuya
AU - Yokoyama, Shigeyuki
N1 - Funding Information:
We thank Drs S. Sekine, T. Ito (University of Tokyo), T. Yanagisawa, T. Sengoku, R. Ishii (RIKEN), M. Kawamoto, N. Shimizu, and H. Sakai (JASRI) for their help in data collection at SPring-8. We also thank Dr R. Akasaka (RIKEN) for his help in the analytical ultracentrifugation analysis. This work was supported by Grants-in-Aid for Scientific Research in Priority Areas, from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan, the RIKEN Structural Genomics/Proteomics Initiative (RSGI) of the National Project on Protein Structural and Functional Analyses, MEXT. R.F. was supported by Research Fellowships of the Japan Society for the Promotion of Science for Young Scientists.
PY - 2007/6/29
Y1 - 2007/6/29
N2 - In the ancient organisms, methanogenic archaea, lacking the canonical cysteinyl-tRNA synthetase, Cys-tRNACys is produced by an indirect pathway, in which O-phosphoseryl-tRNA synthetase ligates O-phosphoserine (Sep) to tRNACys and Sep-tRNA:Cys-tRNA synthase (SepCysS) converts Sep-tRNACys to Cys-tRNACys. In this study, the crystal structure of SepCysS from Archaeoglobus fulgidus has been determined at 2.4 Å resolution. SepCysS forms a dimer, composed of monomers bearing large and small domains. The large domain harbors the seven-stranded β-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-tRNACys. 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-tRNACys 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.
AB - In the ancient organisms, methanogenic archaea, lacking the canonical cysteinyl-tRNA synthetase, Cys-tRNACys is produced by an indirect pathway, in which O-phosphoseryl-tRNA synthetase ligates O-phosphoserine (Sep) to tRNACys and Sep-tRNA:Cys-tRNA synthase (SepCysS) converts Sep-tRNACys to Cys-tRNACys. In this study, the crystal structure of SepCysS from Archaeoglobus fulgidus has been determined at 2.4 Å resolution. SepCysS forms a dimer, composed of monomers bearing large and small domains. The large domain harbors the seven-stranded β-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-tRNACys. 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-tRNACys 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.
KW - PLP
KW - crystal structure
KW - cysteine
KW - phosphoserine
KW - tRNA
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U2 - 10.1016/j.jmb.2007.04.050
DO - 10.1016/j.jmb.2007.04.050
M3 - Article
C2 - 17512006
AN - SCOPUS:34249337418
SN - 0022-2836
VL - 370
SP - 128
EP - 141
JO - Journal of molecular biology
JF - Journal of molecular biology
IS - 1
ER -