This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
2cxi
From Proteopedia
| Line 1: | Line 1: | ||
[[Image:2cxi.gif|left|200px]] | [[Image:2cxi.gif|left|200px]] | ||
| - | + | <!-- | |
| - | + | The line below this paragraph, containing "STRUCTURE_2cxi", creates the "Structure Box" on the page. | |
| - | + | You may change the PDB parameter (which sets the PDB file loaded into the applet) | |
| - | + | or the SCENE parameter (which sets the initial scene displayed when the page is loaded), | |
| - | + | or leave the SCENE parameter empty for the default display. | |
| - | | | + | --> |
| - | | | + | {{STRUCTURE_2cxi| PDB=2cxi | SCENE= }} |
| - | + | ||
| - | + | ||
| - | }} | + | |
'''Crystal Structure Of An N-terminal Fragment Of The Phenylalanyl-tRNA Synthetase Beta-Subunit From Pyrococcus Horikoshii''' | '''Crystal Structure Of An N-terminal Fragment Of The Phenylalanyl-tRNA Synthetase Beta-Subunit From Pyrococcus Horikoshii''' | ||
| Line 30: | Line 27: | ||
[[Category: Sekine, S.]] | [[Category: Sekine, S.]] | ||
[[Category: Yokoyama, S.]] | [[Category: Yokoyama, S.]] | ||
| - | [[Category: | + | [[Category: Aminoacyl-trna synthetase]] |
| - | [[Category: | + | [[Category: Ligase]] |
| - | [[Category: | + | [[Category: National project on protein structural and functional analyse]] |
| - | [[Category: | + | [[Category: Nppsfa]] |
| - | [[Category: | + | [[Category: Riken structural genomics/proteomics initiative]] |
| - | [[Category: | + | [[Category: Rsgi]] |
| - | [[Category: | + | [[Category: Structural genomic]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 23:17:35 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 20:17, 3 May 2008
Crystal Structure Of An N-terminal Fragment Of The Phenylalanyl-tRNA Synthetase Beta-Subunit From Pyrococcus Horikoshii
Overview
To achieve accurate aminoacylation of tRNAs with their cognate amino acids, errors in aminoacylation are corrected by the "editing" mechanism in several aminoacyl-tRNA synthetases. Phenylalanyl-tRNA synthetase (PheRS) hydrolyzes, or edits, misformed tyrosyl-tRNA with its editing domain in the beta subunit. We report the crystal structure of an N-terminal fragment of the PheRS beta subunit (PheRS-beta(N)) from the archaeon, Pyrococcus horikoshii, at 1.94-A resolution. PheRS-beta(N) includes the editing domain B3/4, which has archaea/eukarya-specific insertions/deletions and adopts a different orientation relative to other domains, as compared with that of bacterial PheRS. Surprisingly, most residues constituting the editing active-site pocket were substituted between the archaeal/eukaryal and bacterial PheRSs. We prepared Ala-substituted mutants of P. horikoshii PheRS for 16 editing-pocket residues, of which 12 are archaea/eukarya-specific and four are more widely conserved. On the basis of their activities, Tyr-adenosine was modeled on the B3/4-domain structure. First, the mutations of Leu-202, Ser-211, Asp-234, and Thr-236 made the PheRS incorrectly hydrolyze the cognate Phe-tRNA(Phe), indicating that these residues participate in the Tyr hydroxy group recognition and are responsible for discrimination against Phe. Second, the mutations of Leu-168 and Arg-223, which could interact with the tRNA 3'-terminal adenosine, reduced Tyr-tRNA(Phe) deacylation activity. Third, the mutations of archaea/eukarya-specific Gln-126, Glu-127, Arg-137, and Asn-217, which are proximal to the ester bond to be cleaved, also reduced Tyr-tRNA(Phe) deacylation activity. In particular, the replacement of Asn-217 abolished the activity, revealing its absolute requirement for the catalysis.
About this Structure
2CXI is a Single protein structure of sequence from Pyrococcus horikoshii. Full crystallographic information is available from OCA.
Reference
Structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-tRNA synthetase., Sasaki HM, Sekine S, Sengoku T, Fukunaga R, Hattori M, Utsunomiya Y, Kuroishi C, Kuramitsu S, Shirouzu M, Yokoyama S, Proc Natl Acad Sci U S A. 2006 Oct 3;103(40):14744-9. Epub 2006 Sep 26. PMID:17003130 Page seeded by OCA on Sat May 3 23:17:35 2008
Categories: Phenylalanine--tRNA ligase | Pyrococcus horikoshii | Single protein | RSGI, RIKEN Structural Genomics/Proteomics Initiative. | Sasaki, H. | Sekine, S. | Yokoyama, S. | Aminoacyl-trna synthetase | Ligase | National project on protein structural and functional analyse | Nppsfa | Riken structural genomics/proteomics initiative | Rsgi | Structural genomic
