>TIGR00469 pheS_mito phenylalanyl-tRNA synthetase; InterPro: IPR004530 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Phenylalanyl-tRNA synthetase (6.1.1.20 from EC) is an alpha2/beta2 tetramer composed of 2 subunits that belongs to class IIc. In eubacteria, a small subunit (pheS gene) can be designated as beta (E. coli) or alpha subunit (nomenclature adopted in InterPro). Reciprocally the large subunit (pheT gene) can be designated as alpha (E. coli) or beta (see IPR004531 from INTERPRO and IPR004532 from INTERPRO). In all other kingdoms the two subunits have equivalent length in eukaryota, and can be identified by specific signatures. The enzyme from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the synthetase family. Identification of phenylalanyl-tRNA synthetase as a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other synthetases . This family describes the mitochondrial phenylalanyl-tRNA synthetases. Unlike all other known phenylalanyl-tRNA synthetases, the mitochondrial form demonstrated from yeast is monomeric. It is similar to but longer than the alpha subunit (PheS) of the alpha 2 beta 2 form found in bacteria, Archaea, and eukaryotes, and shares the characteristic motifs of class II aminoacyl-tRNA ligases.; GO: 0000166 nucleotide binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006432 phenylalanyl-tRNA aminoacylation, 0005737 cytoplasm.

Probab=99.79  E-value=1.5e-18  Score=150.91  Aligned_cols=163  Identities=22%  Similarity=0.356  Sum_probs=140.0

Q ss_pred             CEEEECCCCCCCCCCCEEEEEECCE--EEEEEEEEECHHHHHHCCCCCC--E-EEEEEEHHHHH----------------
Q ss_conf             3033058865678981699998792--9999985477899996687997--8-99998787623----------------
Q gi|254780316|r  637 SLRFESGAPSWYHPGRSGIIKTSAE--IVLGYFGEFHPNILDFFGLSNP--I-CGFEVYLDSIP----------------  695 (805)
Q Consensus       637 ~~~~~~~~~~~~hPgrsa~I~~~gk--~iiG~iG~ihP~i~~~~~i~~~--v-~~~EI~ld~L~----------------  695 (805)
T Consensus       264 K~RW~~~YFP~T~PSWE~E~y~~~~WLE~~G-CG~~R~~~L~R~G~~~SetIGyAFG~GL~R~AM~LF~IPDIRLlWS~D  342 (460)
T TIGR00469       264 KVRWVDAYFPFTAPSWELEVYFKDEWLELLG-CGLIRQDVLLRAGVKQSETIGYAFGLGLDRLAMLLFDIPDIRLLWSRD  342 (460)
T ss_pred             EEEEEECCCCCCCCCCEEEEEECCCEEEEEC-CCHHHHHHHHHCCCCCCCCCCEEECCCHHHHHHHHHCCCCEEEEEECC
T ss_conf             1557503388988840589888376556515-514677898845897333220000100889998873488615662045


Q ss_pred             ------HHHHCCCCCCCCCCCCCCCCCEEEEEEEECCCC------CHHHHHHHHHH-CCCCEEEEEEEEEEECCCCCCCC
Q ss_conf             ------545202456631368988872001899966887------99999999971-11003576989876367799884
Q gi|254780316|r  696 ------ISQKKRTKTKKVVHLSSLHPVKRDLAFIVDQHI------PAGTLVNIIKN-VDRLIDDVTVFDVFQGKSLGEGK  762 (805)
Q Consensus       696 ------~~~~~~~~~~~~~~~s~fP~v~RDls~iv~~~v------~~~~I~~~i~~-~~~ll~~v~lfDvY~g~~i~~gk  762 (805)
T Consensus       343 ~~F~~QFS~~dlh~~~~yKP~S~~P~~~~D~~FWLP~D~~~~~~~~~NDl~~~~R~~AGDlVE~~~LVD~F~HPK--TG~  420 (460)
T TIGR00469       343 ERFLRQFSKKDLHLLTKYKPISKYPQSFRDLAFWLPEDKEVIAQVSENDLYDLVRSVAGDLVESVKLVDKFKHPK--TGK  420 (460)
T ss_pred             CCHHHHHCCHHHHCCCCCCCCCCCCCCCCHHHHCCCCCCHHHCCCCCCHHHHHHHHHHCCEEEEEEEEECCCCCC--CCC
T ss_conf             302333111023215676864578874020533188985434468833489999875134033567764135888--887


Q ss_pred             EEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCEE
Q ss_conf             2699999984779888999999999999999999951198
Q gi|254780316|r  763 KSVAIQVLIQPLKDTFRDDDIRILMDRIVENVVKKTNAVL  802 (805)
Q Consensus       763 kSla~rl~fqs~~kTLtd~EI~~i~~~ii~~l~~k~ga~L  802 (805)
T Consensus       421 ~S~CyRI~Y~~M~R~LT~AEVN~~~~~~~S~~V~~y~V~~  460 (460)
T TIGR00469       421 KSVCYRIVYRSMDRTLTNAEVNELQDQVASKLVDEYSVEL  460 (460)
T ss_pred             CCEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHEEECC
T ss_conf             3135886310223311056788898888642010101039