>TIGR00467 lysS_arch lysyl-tRNA synthetase; InterPro: IPR002904 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). A refined crystal structures shows that 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=92.03  E-value=0.93  Score=24.26  Aligned_cols=80  Identities=18%  Similarity=0.255  Sum_probs=57.9

Q ss_pred             HHHHHHHHH-HHCCCCCCCEEEECCHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCC--HHHHHHHHH
Q ss_conf             999999999-72266345115311011012211000001223302456777776321123455542000--123334477
Q gi|254780285|r  364 VKRLEAVAA-AVSEKKAQINVLLCELVRLYRDGMPIKMSKRAGDFITLRHVVDEVGSDSVRFMMLWRKN--SELLDFDFC  440 (586)
Q Consensus       364 ~~~v~~~~~-~lg~~~~~~~~~~~~~v~l~~dg~~~kmstR~G~~v~l~dll~evg~~aiky~~L~~~~--~~~~~Fd~d  440 (586)
T Consensus       248 ~d~~~~~~~~~~~~~pp--~~~~~~~~~~~~gd~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~p~~~~~~~~d~~  325 (539)
T TIGR00467       248 YDTGVLIAKEIFDYEPP--YPVPYEWISLKGGDKGGPLSSSKGDVLPVKDWLEVYPPEILRFLLLRTKPNTEKHIDFDLG  325 (539)
T ss_pred             CHHHHHHHHHHHCCCCC--CCEEEEEEEEECCCCCCCCCCCCCCEEEHHHHHHHCCHHHHHHHHHHCCCCCCEEEECCHH
T ss_conf             10246788887505788--4202324565025423323234563232334544214357555453116775212202402


Q ss_pred             HHHHH
Q ss_conf             76532
Q gi|254780285|r  441 KVKEQ  445 (586)
Q Consensus       441 ~~l~~  445 (586)
T Consensus       326 ~~~d~  330 (539)
T TIGR00467       326 KIPDL  330 (539)
T ss_pred             HHHHH
T ss_conf             32356