>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=623.92 Aligned_cols=484 Identities=47% Similarity=0.832 Sum_probs=455.6 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCC-CCCCCCCHHHHHHHHCCCCCC---CC--C-CCEEEEEEEECCCC-CCC--CEEE Q ss_conf 8799999999999999838887888-767888599999865155556---43--5-98899986881114-877--2189 Q gi|254781118|r 11 SSNSIEVRSQKLNMLRKSLAEVYPA-HFHRDITNAEVREKYSHLQND---EK--S-QDMITVAGRVYSSR-NSG--MFMD 80 (502) Q Consensus 11 ~~~~~~~R~~kl~~l~~~~~~pyP~-~f~~t~~~~e~~~~~~~l~~~---~~--~-~~~V~i~Grv~~~R-~~G--~Fi~ 80 (502) T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~g~~~~~~~~~~~~~f~~ 81 (538) T TIGR00499 2 LNDELQTRLEKLGRLRETGNNPYPNDKFERTHSSAEFLEKYADLSGEATLELEEKPELEVSIAGRILALRFSGGKATFIT 81 (538) T ss_pred CHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCEEEEE T ss_conf 21367889999998874025410000022333356888887522541000211143200012224665554123225788 Q ss_pred EECCC-----CEEEEEEECCCC--CH-HHHHHHHHC---CCCEEEEEEEEE--ECCCCCCCCCCCCEEEEECCCCCCCCC Q ss_conf 97799-----359999805427--96-788887423---743168996576--305665534212201221135554322 Q gi|254781118|r 81 IHDAS-----GKIQIFTHKDTA--DQ-DSQNLLSMI---DIGDIIGITGQV--RRTKRGELTVNAQKIIMLSKALNSIPE 147 (502) Q Consensus 81 LrD~~-----g~iQv~~~~~~~--~~-~~~~~~~~l---~~gd~i~v~G~v--~~~~~gelei~~~~~~~l~~~~~~lP~ 147 (502) T Consensus 82 ~~~~~g~~~d~~~~~~~~~~~~gg~~p~~~~~~~~~~~~~~gd~~~~~g~~g~~~~~~~~l~~~~~~~~~~~~~~~~~p~ 161 (538) T TIGR00499 82 LQDESGLKNDGQLQLYVNKDDLGGPEPDFYEFDEYLNFLDLGDIIGVTGYPGPFKTKTGELSLHVTELQLLTKALRPLPD 161 (538) T ss_pred EECCCCCCCCCEEEEEEECCCCCCCCCCHHHHHHHCCHHHCCCEEEECCCCCCCCCCCCEEEEEEHHHHHHHHHHHCCCC T ss_conf 62566544563378887301147876430233320120102541232034453224441145540134566776422651 Q ss_pred CCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCC Q ss_conf 21253114454201100123444443357889999999987385534543115653235666554203641222225432 Q gi|254781118|r 148 TYYGLSDVEIRYRKRYLDIISNSDSKIRFQQRSLLISQIRHFMEKKGFMEVETPILQPIYGGATADPFKTHHNILKADMY 227 (502) Q Consensus 148 ~~~~~~d~e~rl~~R~LDl~~~~~~~~~l~~Rs~i~~~iR~~l~~~gF~EveTP~L~~~~~g~~~~~F~~~~~~~~~~~y 227 (502) T Consensus 162 ~~~gl~d~e~~~~~~~~d~~~n~~~~~~~~~~~~~~~~~~~~~~~~g~~e~e~p~~~~~~gg~~~~pf~~~~n~~~~~~~ 241 (538) T TIGR00499 162 KWHGLTDQETRYRQRYLDLIVNPDSRDTFLKRSKIIAAIRRFLDDRGFLEVETPLLQVIPGGANARPFITHHNALDLDLY 241 (538) T ss_pred CCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCHHHCCCCCCCCCCCEECCCCCCCCHH T ss_conf 00466515677776554331050246677889999999999876248422113101012676544650100232244212 Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCC--- Q ss_conf 10012234444210243024543453202542344324521000100110001112456789999889987088613--- Q gi|254781118|r 228 LRIAPELYLKRVLISGLTDQVFELNRNFRNEGVSSRHNPEFTMIEAYWAYTDYRDMMKLVEDLCHNLAKTLHGTTDI--- 304 (502) Q Consensus 228 L~qSpql~~k~l~~~G~~drvfeI~~~FR~E~~~~~H~pEFt~lE~e~a~~d~~dim~l~E~li~~i~~~~~~~~~~--- 304 (502) T Consensus 242 ~~~~~e~~l~~l~~gg~-~~~~e~g~~f~neg~~~~hnpef~~~e~y~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 320 (538) T TIGR00499 242 LRIAPELYLKRLVVGGL-EKVYEIGRNFRNEGVDTTHNPEFTSLEFYQAYADYEDLLDLTENLFKFLAKELLGTTKITRL 320 (538) T ss_pred HHHHHHHHHHHHHHCCH-HHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEC T ss_conf 11225778877764013-67787643331046654457530245567765108899998999999999875321100112 Q ss_pred ---------CCCCEEECCCCCCCEEEEECCCC----CCCCCCCCCCCCHHHHHHHHHHHCC---CC-CCC--CCHHHHHH Q ss_conf ---------11753411332210000000233----4488621543321677765652023---54-332--23189998 Q gi|254781118|r 305 ---------PFGEKVISFKAPFACKSMLQLVK----EATGLDFMLLKSDQEARVAAQSIGI---TV-END--ALWGEVMM 365 (502) Q Consensus 305 ---------~~~~~~~d~~~~f~~~~~~e~i~----~~~g~~~~~~~~~e~~~~~~~~~g~---~~-~~~--~~~g~l~~ 365 (502) T Consensus 321 p~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 400 (538) T TIGR00499 321 PVPKTFPELTYGDLELDLKKPWKRITMLDALKKYDLLETGIDFDDLKDDETAKALAKELGIKYFEVAEDSGPLTLGHILN 400 (538) T ss_pred CCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHH T ss_conf 56654311220321002355400224567776520000465400100257888888875433202234577420688999 Q ss_pred HHHHHCCCHHEEC--CEEEECCCHHHHHHHCCCCCCHHHEEECCEEECCEEEEECHHEECCHHHHHHHHHHHHHHHH-C- Q ss_conf 8765213010105--43565580023453035796721101113555578720021100579999999999998873-0- Q gi|254781118|r 366 TIFEEKIEKNIVN--PTHITDFPKDISPFAKEVAGEKRLVERFETYCNGWEICNAFSELNDPVEQRIRMEQQVEQSH-Q- 441 (502) Q Consensus 366 ~~~e~~ie~~~~~--p~fI~dfP~~~~Pf~~~~~~~~~~~~~fdl~~~G~Ei~~G~~e~~dp~~q~~r~~~~~~~~~-~- 441 (502) T Consensus 401 ~~~~~~~e~~~~~~~p~~~~~~p~~~~pl~~~~~~~p~~~~~fe~f~~g~e~~n~~~e~~~p~~~~~~~~~~~~~~~~gg 480 (538) T TIGR00499 401 ELFEEFLEHTLIQTLPTFITGYPAEISPLAKRNPSNPELTDRFELFIGGKEIANAFSELNDPLDQRERFEAQLAEKEAGG 480 (538) T ss_pred HHHHHHHHHHHHHHHHHHHHCCCHHHCCHHCCCCCCCCHHHHHHHEECCHHHHCCHHHHCCHHHHHHHHHHHHHHHHCCC T ss_conf 98888775566653214340464122210005777753011111001011220101220462788999999888875067 Q ss_pred ---CCCCCCCCHHHHHHHHCCCCCCCCEECCHHHHHHHHCCCCCCEECCCCCCCCCC Q ss_conf ---573354508999997608698461324689998998262884041278675766 Q gi|254781118|r 442 ---RGEHTILDEDFLDAMTYGMPPASGLGLGIDRLIMLLTNAPSIRDVILFPAQRVK 495 (502) Q Consensus 442 ---~~~~~~~~~~yl~a~~yG~PPhgG~glGldRL~m~l~g~~~IRdvi~FP~~k~~ 495 (502) T Consensus 481 ~~~~~~~~~~d~~~~~~l~~g~pp~~g~g~g~d~l~~l~~~~~~~~~~~~fp~~~~~ 537 (538) T TIGR00499 481 NKTDDEAPLLDEDFVEALEYGLPPTGGLGIGIDRLVMLLTDSPSIRDVLLFPALRPD 537 (538) T ss_pred CCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHCCCCCCC T ss_conf 754103444336788888716886565443277787766167510133202531357

HHsearch alignment for GI: 254781118 and conserved domain: TIGR00499