Exploring the binding sites of Staphylococcus aureus phenylalanine tRNA synthetase: A homology model approach

Eriani, 1990, Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs, Nature, 347, 203, 10.1038/347203a0 Cassels, 1995, Occurrence of the regulatory nucleotides ppGpp and pppGpp following induction of the stringent response in staphylococci, J. Bacteriol., 177, 5161, 10.1128/jb.177.17.5161-5165.1995 Cusack, 1991, Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases, Nucleic Acids Res., 19, 3489, 10.1093/nar/19.13.3489 WHO, 2014 Hurdle, 2005, Prospects for aminoacyl-tRNA synthetase inhibitors as new antimicrobial agents, Antimicrob. Agents Chemother., 49, 4821, 10.1128/AAC.49.12.4821-4833.2005 Keller, 1992, Cloning and sequence analysis of the phenylalanyl-tRNA synthetase genes (pheST) from Thermus thermophilus, FEBS Lett., 301, 83, 10.1016/0014-5793(92)80215-3 Kreutzer, 1992, Structure of the phenylalanyl-tRNA synthetase genes from Thermus thermophilus HB8 and their expression in Escherichia coli, Nucleic Acids Res., 20, 4173, 10.1093/nar/20.16.4173 Gasteiger, 2003, ExPASy: the proteomics server for in-depth protein knowledge and analysis, Nucleic Acids Res., 31, 3784, 10.1093/nar/gkg563 Savopoulos, 2001, Identification, cloning, and expression of a functional phenylalanyl-tRNA Synthetase (pheRS) from Staphylococcus aureus, Protein Expres Purif, 21, 470, 10.1006/prep.2001.1407 Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3385, 10.1093/nar/25.17.3389 Schaffer, 2001, Improving the accuracy of PSI-BLAST protein database searches with composition- based statics and other refinements, Nucleic Acids Res., 29, 2994, 10.1093/nar/29.14.2994 RCSB, 2017 Li, 2015, EMBL-EBI bioinformatics web and programmatic tools framework, Nucleic Acids Res., 43, 580, 10.1093/nar/gkv279 Sievers, 2011, Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega, Mol. Syst. Biol., 7, 539, 10.1038/msb.2011.75 Jones, 1999, Protein secondary structure prediction based on position-specific scoring matrices, J. Mol. Biol., 292, 195, 10.1006/jmbi.1999.3091 Molecular Operating Environment, (MOE 2014.0901) Chemical Computing Group Inc, Montreal Quebec Canada http://www.chemcomp.com. 2014.0901. Weiner, 1986, An all atom forcefield for simulations of proteins and nucleic acids, J. Comput. Chem., 7, 230, 10.1002/jcc.540070216 RAMPAGE Server http://ravenbioccam.ac.uk/rampage.php. Bowie, 1991, Method to identify protein sequence that fold into a known three dimensional structure, Science, 253, 164, 10.1126/science.1853201 Weiderstein, 2007, ProSA-web: interactive web service for the recognition of errors in three dimensional structures of proteins, Nucleic Scid Res., 35, 407, 10.1093/nar/gkm290 Moor, 2006, The crystal structure of the ternary complex of phenylalanyl-tRNA synthetase with tRNAPhe and a phenylalanyl-adenylate analogue reveals a conformational switch of the CCA end, Biochemistry, 45, 10572, 10.1021/bi060491l Beyer, 2004, New class of bacterial phenylalanyl-tRNA synthetase inhibitors with high potency and broad-spectrum activity, Antimicrob. Agents Chemother., 48, 525, 10.1128/AAC.48.2.525-532.2004 Jarvest, 2005, Discovery and optimisation of potent, selective, ethanolamine inhibitors of bacterial phenylalanyl tRNA synthetase, Bioorg. Med. Chem. Lett., 15, 2305, 10.1016/j.bmcl.2005.03.003 Evdokimov, 2008, Rational protein engineering in action: the first crystal structure of a phenylalanine tRNA synthetase from Staphylococcus haemolyticus, J. Struct. Biol., 162, 152, 10.1016/j.jsb.2007.11.002 Fishman, 2001, Structure at 2.6 Å resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyladenylate in the presence of manganese, Acta Crystallogr. D Biol. Crystallogr., 57, 1534, 10.1107/S090744490101321X Finarov, 2010, Structure of human cytosolic phenylalanyltRNA synthetase: evidence for kingdom-specific design of the active sites and tRNA binding patterns, Structure, 18, 343, 10.1016/j.str.2010.01.002 Moor, 1999, Crystal structures of phenylalanyl-tRNA synthetase complexed with phenylalanine and phenylalanyl-adenylate analogue, J. Mol. Biol., 287, 555, 10.1006/jmbi.1999.2617 Goldgur, 1997, The crystal structure of phenylalanyl-tRNA synthetase from Thermus thermophilus complexed with cognate tRNAPhe, Structure, 5, 59, 10.1016/S0969-2126(97)00166-4 Mosyak, 1995, Structure of phenylalanyl-tRNA synthetase from Thermus thermophilus, Nat. Struct. Mol. Biol., 2, 537, 10.1038/nsb0795-537 Lechler, 1998, The phenylalanyl-tRNA synthetase specifically binds DNA, J. Mol. Biol., 278, 897, 10.1006/jmbi.1998.1744 Cavarelli, 1993, Yeast aspartyl-tRNA synthetase: a structural view of the aminoacylation reaction, Biochimie, 75, 1117, 10.1016/0300-9084(93)90011-G Nagai, 1990, Crystal structure of the RNA-binding domain of the U1 small nuclear ribonucleoprotein, Nature, 348, 515, 10.1038/348515a0 Lechler, 1997, Domains of phenylalanyl-tRNA synthetase from Thermus thermophilus required for aminoacylation, FEBS Lett., 420, 139, 10.1016/S0014-5793(97)01504-4 Koch, 1991, SH2 and SH3 domains: elements that control interactions of cytoplasmic signaling proteins, Science, 252, 668, 10.1126/science.1708916 Zuker, 1981, Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information, Nucleic Acid Res., 133, 10.1093/nar/9.1.133