Crystal structure of the N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase from Helicobacter pylori.
The N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase (ND-AspRS) plays a crucial role in the recognition of both tRNAAspand tRNAAsn. Here, the first X-ray crystal structure of the N-terminal domain of this enzyme (ND-AspRS1-104) from the human-pathogenic bacterium Helicobacter pylori is reported at 2.0 Å resolution. The apo form of H. pylori ND-AspRS1-104shares high structural similarity with the N-terminal anticodon-binding domains of the discriminating aspartyl-tRNA synthetase (D-AspRS) from Escherichia coli and ND-AspRS from Pseudomonas aeruginosa, allowing recognition elements to be proposed for tRNAAspand tRNAAsn. It is proposed that a long loop (Arg77-Lys90) in this H. pylori domain influences its relaxed tRNA specificity, such that it is classified as nondiscriminating. A structural comparison between D-AspRS from E. coli and ND-AspRS from P. aeruginosa suggests that turns E and F (78GAGL81and83NPKL86) in H. pylori ND-AspRS play a crucial role in anticodon recognition. Accordingly, the conserved Pro84 in turn F facilitates the recognition of the anticodons of tRNAAsp(34GUC36) and tRNAAsn(34GUU36). The absence of the amide H atom allows both C and U bases to be accommodated in the tRNA-recognition site.
Synchrotron Light Research Institute (Public Organization), 111 University Avenue, Nakhon Ratchasima 30000, Thailand.
Chomphunuch
C
Songsiriritthigul
Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, and Special Research Unit for Advanced Magnetic Resonance, Kasetsart University, 50 Ngamwongwan Road, Chatuchak, Bangkok 10900, Thailand.
Suwimon
S
Suebka
Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan.
Chun Jung
CJ
Chen
Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, and Special Research Unit for Advanced Magnetic Resonance, Kasetsart University, 50 Ngamwongwan Road, Chatuchak, Bangkok 10900, Thailand.
Pitchayada
P
Fuengfuloy
Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, and Special Research Unit for Advanced Magnetic Resonance, Kasetsart University, 50 Ngamwongwan Road, Chatuchak, Bangkok 10900, Thailand.
Pitak
P
Chuawong
D000595:Amino Acid Sequence; D000926:Anticodon / Q000737:chemistry* / Q000378:metabolism; D001059:Apoproteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001226:Aspartate-tRNA Ligase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics; D015870:Gene Expression; D016480:Helicobacter pylori / Q000737:chemistry* / Q000201:enzymology; D008958:Models, Molecular; D010957:Plasmids / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D054730:Protein Interaction Domains and Motifs; D011550:Pseudomonas aeruginosa / Q000201:enzymology / Q000235:genetics; D012348:RNA, Transfer, Asn / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012349:RNA, Transfer, Asp / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D040681:Structural Homology, Protein
D000926:Anticodon; D001059:Apoproteins; D001426:Bacterial Proteins; D012348:RNA, Transfer, Asn; D012349:RNA, Transfer, Asp; D011994:Recombinant Proteins; D001226:Aspartate-tRNA Ligase
Helicobacter pylori; anticodon-binding domain; crystal structure; nondiscriminating aspartyl-tRNA synthetase