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==Solution structure of the 2'-5' RNA ligase-like protein from Pyrococcus furiosus==
==Solution structure of the 2'-5' RNA ligase-like protein from Pyrococcus furiosus==
<StructureSection load='2fyh' size='340' side='right'caption='[[2fyh]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
<StructureSection load='2fyh' size='340' side='right'caption='[[2fyh]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2fyh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FYH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FYH FirstGlance]. <br>
<table><tr><td colspan='2'>[[2fyh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FYH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FYH FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PF0027 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2fyh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fyh OCA], [https://pdbe.org/2fyh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fyh RCSB], [https://www.ebi.ac.uk/pdbsum/2fyh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fyh ProSAT], [https://www.topsan.org/Proteins/RSGI/2fyh TOPSAN]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2fyh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fyh OCA], [https://pdbe.org/2fyh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fyh RCSB], [https://www.ebi.ac.uk/pdbsum/2fyh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fyh ProSAT], [https://www.topsan.org/Proteins/RSGI/2fyh TOPSAN]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/THPR_PYRFU THPR_PYRFU] Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'-phosphomonoester. In vitro, ligates 5' and 3' half-tRNA molecules with 2',3'-cyclic phosphate and 5'-hydroxyl termini, respectively, to the product containing the 2'-5' phosphodiester linkage. Ligase activity requires GTP, but GTP hydrolysis is not required for the reaction, which is reversible. Ligase activity is weak compared to the phosphodiesterase activity.<ref>PMID:19155324</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2fyh ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2fyh ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Using an expression protein library of a hyperthermophilic archaeon, Pyrococcus furiosus, we identified a gene (PF0027) that encodes a protein with heat-stable cyclic nucleotide phosphodiesterase (CPDase) activity. The PF0027 gene encoded a 21-kDa protein and an amino acid sequence that showed approximately 27% identity to that of the 2'-5' tRNA ligase protein, ligT (20 kDa), from Escherichia coli. We found that the purified PF0027 protein possessed GTP-dependent RNA ligase activity and that synthetic tRNA halves bearing 2',3'-cyclic phosphate and 5'-OH termini were substrates for the ligation reaction in vitro. GTP hydrolysis was not required for the reaction, and GTPgammaS enhanced the tRNA ligation activity of PF0027 protein, suggesting that the ligation step is regulated by a novel mechanism. In comparison to the strong CPDase activity of the PF0027 protein, the RNA ligase activity itself was quite weak, and the ligation product was unstable during in vitro reaction. Finally, we used NMR to determine the solution structure of the PF0027 protein and discuss the implications of our results in understanding the role of the PF0027 protein.
Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus.,Kanai A, Sato A, Fukuda Y, Okada K, Matsuda T, Sakamoto T, Muto Y, Yokoyama S, Kawai G, Tomita M RNA. 2009 Mar;15(3):420-31. Epub 2009 Jan 20. PMID:19155324<ref>PMID:19155324</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2fyh" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Pyrfu]]
[[Category: Pyrococcus furiosus DSM 3638]]
[[Category: Kanai, A]]
[[Category: Kanai A]]
[[Category: Kawai, G]]
[[Category: Kawai G]]
[[Category: Matsuda, T]]
[[Category: Matsuda T]]
[[Category: Muto, Y]]
[[Category: Muto Y]]
[[Category: Okada, K]]
[[Category: Okada K]]
[[Category: Structural genomic]]
[[Category: Sakamoto T]]
[[Category: Sakamoto, T]]
[[Category: Yokoyama S]]
[[Category: Yokoyama, S]]
[[Category: 2'-5' rna ligase-like protein]]
[[Category: Hxtx motif]]
[[Category: Ligase]]
[[Category: National project on protein structural and functional analyse]]
[[Category: Nppsfa]]
[[Category: Pyrococcus furiosus]]
[[Category: Rsgi]]

Latest revision as of 09:40, 1 May 2024

Solution structure of the 2'-5' RNA ligase-like protein from Pyrococcus furiosusSolution structure of the 2'-5' RNA ligase-like protein from Pyrococcus furiosus

Structural highlights

2fyh is a 1 chain structure with sequence from Pyrococcus furiosus DSM 3638. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

THPR_PYRFU Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'-phosphomonoester. In vitro, ligates 5' and 3' half-tRNA molecules with 2',3'-cyclic phosphate and 5'-hydroxyl termini, respectively, to the product containing the 2'-5' phosphodiester linkage. Ligase activity requires GTP, but GTP hydrolysis is not required for the reaction, which is reversible. Ligase activity is weak compared to the phosphodiesterase activity.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ Kanai A, Sato A, Fukuda Y, Okada K, Matsuda T, Sakamoto T, Muto Y, Yokoyama S, Kawai G, Tomita M. Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus. RNA. 2009 Mar;15(3):420-31. Epub 2009 Jan 20. PMID:19155324 doi:10.1261/rna.1122109
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