>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=96.81  E-value=0.00073  Score=47.13  Aligned_cols=67  Identities=30%  Similarity=0.441  Sum_probs=44.1

Q ss_pred             CCCHHHCCCCCCCCCHHHHHCCCHHHHHHHCCCEEECCEEECC-CCEECCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHH
Q ss_conf             0002110024766430655418877741313677775677212-512315699999999985999899986677899998
Q gi|254780419|r  451 KIDFAHNPFTMPQGGMESLKGNDLLSIKAFQYDLVCNGFEIAS-GGIRNHMSEVMLQAFSNVGISKEVVENRFGGLYRAF  529 (622)
Q Consensus       451 r~~s~HHPFTaP~~~~~~l~~~dp~~v~a~~YDLVlNG~Eigg-GSiRIHd~~iQ~~~f~~lgl~~ee~~~~Fg~lL~Al  529 (622)
T Consensus       266 RW~~~YFP~T~PSWE~E~y~~~~WL--------------E~~GCG~~R-------~~~L~--------------------  304 (460)
T TIGR00469       266 RWVDAYFPFTAPSWELEVYFKDEWL--------------ELLGCGLIR-------QDVLL--------------------  304 (460)
T ss_pred             EEEECCCCCCCCCCEEEEEECCCEE--------------EEECCCHHH-------HHHHH--------------------
T ss_conf             5750338898884058988837655--------------651551467-------78988--------------------


Q ss_pred             HCCCCCC--CC--EECCHHHHHHHHCCCCCCEE
Q ss_conf             6084973--42--22468999999837398403
Q gi|254780419|r  530 QCGMPPH--GG--IAAGIDRIVMLLLGAKNVRE  558 (622)
Q Consensus       530 ~yG~PPH--gG--~alGlDRlvmll~g~~sIRd  558 (622)
T Consensus       305 R~G~~~SetIGyAFG~GL~R~AM~LF~IPDIRL  337 (460)
T TIGR00469       305 RAGVKQSETIGYAFGLGLDRLAMLLFDIPDIRL  337 (460)
T ss_pred             HCCCCCCCCCCEEECCCHHHHHHHHHCCCCEEE
T ss_conf             458973332200001008899988734886156