2cxi: Difference between revisions
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'''Crystal Structure Of An N-terminal Fragment Of The Phenylalanyl-tRNA Synthetase Beta-Subunit From Pyrococcus Horikoshii''' | {{Structure | ||
|PDB= 2cxi |SIZE=350|CAPTION= <scene name='initialview01'>2cxi</scene>, resolution 1.94Å | |||
|SITE= | |||
|LIGAND= | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/Phenylalanine--tRNA_ligase Phenylalanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.20 6.1.1.20] | |||
|GENE= PH0657 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 Pyrococcus horikoshii]) | |||
}} | |||
'''Crystal Structure Of An N-terminal Fragment Of The Phenylalanyl-tRNA Synthetase Beta-Subunit From Pyrococcus Horikoshii''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2CXI is a [ | 2CXI is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CXI OCA]. | ||
==Reference== | ==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:[http:// | 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:[http://www.ncbi.nlm.nih.gov/pubmed/17003130 17003130] | ||
[[Category: Phenylalanine--tRNA ligase]] | [[Category: Phenylalanine--tRNA ligase]] | ||
[[Category: Pyrococcus horikoshii]] | [[Category: Pyrococcus horikoshii]] | ||
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[[Category: aminoacyl-trna synthetase]] | [[Category: aminoacyl-trna synthetase]] | ||
[[Category: ligase]] | [[Category: ligase]] | ||
[[Category: national project on protein structural and functional | [[Category: national project on protein structural and functional analyse]] | ||
[[Category: nppsfa]] | [[Category: nppsfa]] | ||
[[Category: riken structural genomics/proteomics initiative]] | [[Category: riken structural genomics/proteomics initiative]] | ||
[[Category: rsgi]] | [[Category: rsgi]] | ||
[[Category: structural | [[Category: structural genomic]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:20:57 2008'' | ||
Revision as of 14:20, 20 March 2008
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| 2cxi, resolution 1.94Å | |||||||||||||
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| Gene: | PH0657 (Pyrococcus horikoshii) | ||||||||||||
| Activity: | Phenylalanine--tRNA ligase, with EC number 6.1.1.20 | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
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
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Proteopedia Page Contributors and Editors (what is this?)
- Pages with broken file links
- 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
