>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=100.00 E-value=0 Score=427.98 Aligned_cols=238 Identities=34% Similarity=0.673 Sum_probs=207.9 Q ss_pred CCCCCHHHHHHHHHHHHHHHCC--------CEEECC--CEEECHHHHHHHHCCCCCCCCCCCCCEEEEECCCCCCCCCCC Q ss_conf 6742389999999999998739--------876237--234158898886189887733163312775056665563224 Q gi|254780317|r 112 RGRIHPVTQVIDEVTCIFMDMG--------FALEEG--SDIETDYYNFAALNFPDDHPARQMHDTFFVPGIAGGKHKLLR 181 (366) Q Consensus 112 ~G~~HPItqvi~eI~~IF~~lG--------F~v~eG--PEIEtd~~NFdaLNiP~~HPARdmqDTFyl~~~~~~~~~lLR 181 (366) T Consensus 38 L~~~HP~~I~R~~I~~~l~~~~~nqrGnP~F~~y~~~~P-VVT~~~NFD~L~~P~DH~~R~KSD~YYI-----N~~HLLR 111 (460) T TIGR00469 38 LKEDHPLSILRDLIVKKLYSVDRNQRGNPLFKVYDNFKP-VVTVQENFDSLLIPKDHVSRSKSDTYYI-----NETHLLR 111 (460) T ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEHCCCCCC-EEEECCCCCCCCCCCCCCCCCCCCEEEE-----CCCHHHH T ss_conf 123576467788999876322103568851111005797-4732013311278887788754541330-----3300333 Q ss_pred CCCCCHHHHHHHHC---CCEE--EEEECCCCCCCCC-CCCCCCCCCCCCEEEE--------------------------- Q ss_conf 46763055554303---6312--2541057647454-4213781002005786--------------------------- Q gi|254780317|r 182 THTSPVQIRVMESQ---DLPI--KVIVPGKTYRRDS-DSTHSPMFHQIEGLVV--------------------------- 228 (366) Q Consensus 182 thTS~vQiR~m~~~---~pP~--~~~~~GrvyR~d~-D~tH~~~FhQ~egl~v--------------------------- 228 (366) T Consensus 112 ~HT~AH~~E~~~~~~~~sdniksGFL~~~~VYRRDEID~THYPVFHQ~~Ga~~~~~TK~~~~~~~P~y~E~~~E~~~~~~ 191 (460) T TIGR00469 112 AHTSAHELELISKILDDSDNIKSGFLVVADVYRRDEIDKTHYPVFHQADGAAVRKVTKDDLFVKEPGYLEKIREDIRQVL 191 (460) T ss_pred HCCCHHHHHHHHCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEECCCCCEEHHHHHHHHCCCCCCHHHHHHHHHHHHH T ss_conf 30213454544222353211121206874344123456878870142676212100234430468740124566678885 Q ss_pred ------------CCC------------------C--CHHHHHHHHHHHHHHHCCC--------------CCCEEEEEECC Q ss_conf ------------178------------------6--6899988999999997088--------------86626454238 Q gi|254780317|r 229 ------------SDS------------------A--TIANLRWVLESFCKSFFEV--------------SSLQMRFRPSF 262 (366) Q Consensus 229 ------------~~~------------------i--~~~~lk~~l~~~~~~~fg~--------------~~~~~r~rp~~ 262 (366) T Consensus 192 ~~~nkenvK~~~~~~~~~~K~N~Pkqey~~~~~V~L~~~~lK~~~~~~~~~~F~~~IssmiknkanntPkelK~RW~~~Y 271 (460) T TIGR00469 192 ALLNKENVKLILDDDSIPLKENSPKQEYASDLEVDLMEQELKRVLVLLVKDLFNKKISSMIKNKANNTPKELKVRWVDAY 271 (460) T ss_pred HCCCCCCEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCEEEEEECC T ss_conf 10032640588468875688888514455578899888777899998888641603467764320377420015575033 Q ss_pred CCCCCCCCEEEEEEECCCCEEEECCCCCEEEEECCCCCCHHHHHHCCCCCCCEEEEEEECCHHHHHHHHCCCCCHHHHHH Q ss_conf 89852661036787505880422468834898457563888998569880003799631344699799738970587663 Q gi|254780317|r 263 FPFTEPSFEVDVRCSFSDGIIKFDEGTEWMEILGCGMVDPRVLRGVGIDPDIYQGFAWGMGLDRIAMLKYGMPDVREFFG 342 (366) Q Consensus 263 fPftePs~Evdv~~~~~~~~~~~~~~~~WiEi~g~Gm~~p~vl~~~g~d~~~~~g~AfG~G~eRlaml~~gi~diR~~~~ 342 (366) T Consensus 272 FP~T~PSWE~E~y~-----------~~~WLE~~GCG~~R~~~L~R~G~~~SetIGyAFG~GL~R~AM~LF~IPDIRLlWS 340 (460) T TIGR00469 272 FPFTAPSWELEVYF-----------KDEWLELLGCGLIRQDVLLRAGVKQSETIGYAFGLGLDRLAMLLFDIPDIRLLWS 340 (460) T ss_pred CCCCCCCCEEEEEE-----------CCCEEEEECCCHHHHHHHHHCCCCCCCCCCEEECCCHHHHHHHHHCCCCEEEEEE T ss_conf 88988840589888-----------3765565155146778988458973332200001008899988734886156620 Q ss_pred CCHHHHHHCC---------CCCC-CCCCCCCCCC Q ss_conf 5888887448---------9844-6884145889 Q gi|254780317|r 343 ADVRWIEHYG---------FSPL-DIPPLFSRLA 366 (366) Q Consensus 343 ~d~rfl~qf~---------~~~~-~~~~~~~~~~ 366 (366) T Consensus 341 ~D~~F~~QFS~~dlh~~~~yKP~S~~P~~~~D~~ 374 (460) T TIGR00469 341 RDERFLRQFSKKDLHLLTKYKPISKYPQSFRDLA 374 (460) T ss_pred CCCCHHHHHCCHHHHCCCCCCCCCCCCCCCCHHH T ss_conf 4530233311102321567686457887402053

HHsearch alignment for GI: 254780317 and conserved domain: TIGR00469