title: Crystal structure of Pyrococcus horikoshii tryptophanyl-tRNA synthetase and structure-based phylogenetic analysis suggest an archaeal origin of tryptophanyl-tRNA synthetase.
abstract: The ancient and ubiquitous aminoacyl-tRNA synthetases constitute a valuable model system for studying early evolutionary events. So far, the evolutionary relationship of tryptophanyl- and tyrosyl-tRNA synthetase (TrpRS and TyrRS) remains controversial. As TrpRS and TyrRS share low sequence homology but high structural similarity, a structure-based method would be advantageous for phylogenetic analysis of the enzymes. Here, we present the first crystal structure of an archaeal TrpRS, the structure of Pyrococcus horikoshii TrpRS (pTrpRS) in complex with tryptophanyl-5' AMP (TrpAMP) at 3.0 A resolution which demonstrates more similarities to its eukaryotic counterparts. With the pTrpRS structure, we perform a more complete structure-based phylogenetic study of TrpRS and TyrRS, which for the first time includes representatives from all three domains of life. Individually, each enzyme shows a similar evolutionary profile as observed in the sequence-based phylogenetic studies. However, TyrRSs from Archaea/Eucarya cluster with TrpRSs rather than their bacterial counterparts, and the root of TrpRS locates in the archaeal branch of TyrRS, indicating the archaeal origin of TrpRS. Moreover, the short distance between TrpRS and archaeal TyrRS and that between bacterial and archaeal TrpRS, together with the wide distribution of TrpRS, suggest that the emergence of TrpRS and subsequent acquisition by Bacteria occurred at early stages of evolution.
authors: State Key Laboratory of Molecular Biology and Research Center for Structural Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Graduate School of Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China.
authors: Xianchi
authors: X
authors: Dong
authors: Minyun
authors: M
authors: Zhou
authors: Chen
authors: C
authors: Zhong
authors: Bei
authors: B
authors: Yang
authors: Ning
authors: N
authors: Shen
authors: Jianping
authors: J
authors: Ding
mesh_terms: D000249:Adenosine Monophosphate / Q000031:analogs & derivatives / Q000737:chemistry; D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000737:chemistry* / Q000145:classification* / Q000235:genetics; D018360:Crystallography, X-Ray; D008969:Molecular Sequence Data; D010802:Phylogeny; D043902:Pyrococcus horikoshii / Q000201:enzymology*; D017386:Sequence Homology, Amino Acid; D014364:Tryptophan / Q000031:analogs & derivatives / Q000737:chemistry; D014369:Tryptophan-tRNA Ligase / Q000737:chemistry* / Q000145:classification* / Q000235:genetics; D014448:Tyrosine-tRNA Ligase / Q000737:chemistry / Q000145:classification / Q000235:genetics
chemical_list: D019843:Archaeal Proteins; C548317:tryptophanyl-5'-adenosine monophosphate; D000249:Adenosine Monophosphate; D014364:Tryptophan; D014448:Tyrosine-tRNA Ligase; D014369:Tryptophan-tRNA Ligase