>TIGR00499 lysS_bact lysyl-tRNA synthetase; InterPro: IPR002313 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 . Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and some eubacteria . Moreover in some eubacteria there is a gene X, which is similar to a part of lysyl-tRNA synthetase from class II. Lysyl-tRNA synthetase is duplicated in some species with, for example in E. coli, as a constitutive gene (lysS) and an induced one (lysU). No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. Lysine is activated by being attached to the alpha-phosphate of AMP before being transferred to the cognate tRNA. The refined crystal structures give "snapshots" of the active site corresponding to key steps in the aminoacylation reaction and provide the structural framework for understanding the mechanism of lysine activation. The active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding .; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm.

Probab=100.00 E-value=0 Score=447.54 Aligned_cols=345 Identities=31% Similarity=0.514 Sum_probs=298.0 Q ss_pred CCCCCCCCCC--CHHHCCCHHH-----------HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECC Q ss_conf 9988987478--8312615489-----------99999999999999999879889847821056898544541241024 Q gi|254781066|r 1 MHQIPSQPWW--NRDFHYRRRP-----------FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELI 67 (355) Q Consensus 1 ~~~~p~~~~~--~~~~~~r~R~-----------~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~ 67 (355) T Consensus 156 ~~~~p~~~~gl~d~e~~~~~~~~d~~~n~~~~~~~~~~~~~~~~~~~~~~~~g~~e~e~p~~~~~~gg~~-~~pf~~~-- 232 (538) T TIGR00499 156 LRPLPDKWHGLTDQETRYRQRYLDLIVNPDSRDTFLKRSKIIAAIRRFLDDRGFLEVETPLLQVIPGGAN-ARPFITH-- 232 (538) T ss_pred HHCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCHHHCCCCCCC-CCCCEEC-- T ss_conf 4226510046651567777655433105024667788999999999987624842211310101267654-4650100-- Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 78867832000028589999898744688999886424567775448430020001157765787775578887766641 Q gi|254781066|r 68 IQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA 147 (355) Q Consensus 68 ~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~ 147 (355) T Consensus 233 -~n~~~~~~~~~~~~e~~l~~l~~gg~~~~~e~g~~f~neg~~~~hnpef~~~e~y~~~~~~~~~~~~~~~l~~~~~~~~ 311 (538) T TIGR00499 233 -HNALDLDLYLRIAPELYLKRLVVGGLEKVYEIGRNFRNEGVDTTHNPEFTSLEFYQAYADYEDLLDLTENLFKFLAKEL 311 (538) T ss_pred -CCCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf -2322442121122577887776401367787643331046654457530245567765108899998999999999875 Q ss_pred C-CCEE------------CCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCC---CC-CC Q ss_conf 8-8300------------022343324677320788886566608765323455562327999999997688---77-87 Q gi|254781066|r 148 N-QKIF------------SFQNVNCNPFSEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGI---RV-AH 210 (355) Q Consensus 148 ~-~~~~------------~~~~~~~~~~~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~---~~-~~ 210 (355) T Consensus 312 ~~~~~~~~~p~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~ 389 (538) T TIGR00499 312 LGTTKITRLPVPKTFPELTYGDLELDLKKPWKRITMLDALKKYDLLETGID--FDDLKDDETAKALAKELGIKYFEVAED 389 (538) T ss_pred HHHHHEEECCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCC--CHHCCHHHHHHHHHHHHHHHHHCCCCC T ss_conf 321100112566543112203210023554002245677765200004654--001002578888888754332022345 Q ss_pred C--CCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHH Q ss_conf 6--53478987664300362237675443257688886413678778363302202236712256402106999999999 Q gi|254781066|r 211 D--DTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESALANIYPADPRFTKRFELYACNIELCNACDELLDPIEQRHRF 288 (355) Q Consensus 211 ~--~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~plak~~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf 288 (355) T Consensus 390 ~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~p~~~~pl~~~~~~~p~~~~~fe~f~~g~e~~n~~~e~~~p~~~~~~~ 469 (538) T TIGR00499 390 SGPLTLGHILNELFEEFLEHTLIQTLPTFITGYPAEISPLAKRNPSNPELTDRFELFIGGKEIANAFSELNDPLDQRERF 469 (538) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCHHCCCCCCCCHHHHHHHEECCHHHHCCHHHHCCHHHHHHHH T ss_conf 77420688999988887755666532143404641222100057777530111110010112201012204627889999 Q ss_pred HHHHHHHHCC----CCCCCHHHHHHHHHHC-CCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCCCCC Q ss_conf 9999999728----8853010189999861-8896324531599998998155971311158564874 Q gi|254781066|r 289 EKEMQEKKKI----YNETYPIDEDFLACLT-EMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFSQSN 351 (355) Q Consensus 289 ~~q~~~k~~~----~~e~~~~D~~fl~al~-G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~r~~ 351 (355) T Consensus 470 ~~~~~~~~~gg~~~~~~~~~~d~~~~~~l~~g~pp~~g~g~g~d~l~~l~~~~~~~~~~~~fp~~~~~ 537 (538) T TIGR00499 470 EAQLAEKEAGGNKTDDEAPLLDEDFVEALEYGLPPTGGLGIGIDRLVMLLTDSPSIRDVLLFPALRPD 537 (538) T ss_pred HHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHCCCCCCC T ss_conf 99888875067754103444336788888716886565443277787766167510133202531357

HHsearch alignment for GI: 254781066 and conserved domain: TIGR00499