>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=97.59  E-value=0.0018  Score=44.78  Aligned_cols=87  Identities=18%  Similarity=0.232  Sum_probs=60.2

Q ss_pred             EEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCHH-----HHH---HHH-HCCC------C--
Q ss_conf             1799788899998832224789789999999988589803623643702279-----999---999-8399------9--
Q gi|255764461|r    6 KLYISTAIAYPNAQPHIGHAYEMIIADVLARFHRLDGLDVLFTTGTDEHGQK-----IAK---AAQ-NAGV------T--   68 (511)
Q Consensus         6 ~~~vt~~~Py~ng~lHlGH~~~~i~~D~~~R~~r~~G~~v~~~~g~D~hg~~-----i~~---~A~-~~g~------~--   68 (511)
T Consensus        20 ~~~~~~g-~~p~g~~~~g~~~~~~~~d~~~~~l~~~g~~~~~~~~~d~~d~~~~~~~~~p~~~~~~~~~~~~~~~~p~~~   98 (539)
T TIGR00467        20 LYTVASG-ITPSGHIHLGNLREVLTADAIARALLDSGGEAKLIYIADDYDPLRKLYPFLPEQEELETYLGLPLTKIPDPE   98 (539)
T ss_pred             CEEEECC-CCCCCCEEECCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCC
T ss_conf             1033204-676660330421456768888888750676147888524510344304567506788887410122067854


Q ss_pred             --HHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             --8999999999999999980889886
Q gi|255764461|r   69 --TKVFVDQNSRNFRDMADVLDISYDD   93 (511)
Q Consensus        69 --p~e~~~~~~~~~~~~~~~~~i~~D~   93 (511)
T Consensus        99 ~~~~~~~~~~~~~~~~~l~~~g~~~~~  125 (539)
T TIGR00467        99 GCCDSYAEHFLRPFLESLPVLGIPPEF  125 (539)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCHH
T ss_conf             202456666665667642211676021