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| | <StructureSection load='5y7m' size='340' side='right'caption='[[5y7m]], [[Resolution|resolution]] 3.10Å' scene=''> | | <StructureSection load='5y7m' size='340' side='right'caption='[[5y7m]], [[Resolution|resolution]] 3.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5y7m]] is a 4 chain structure with 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=5Y7M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y7M FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5y7m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y7M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y7M FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5xtm|5xtm]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpl7ae, PH1496 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</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=5y7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y7m OCA], [https://pdbe.org/5y7m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y7m RCSB], [https://www.ebi.ac.uk/pdbsum/5y7m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y7m ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5y7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y7m OCA], [http://pdbe.org/5y7m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y7m RCSB], [http://www.ebi.ac.uk/pdbsum/5y7m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y7m ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RL7A_PYRHO RL7A_PYRHO]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs (By similarity). When added to reconstituted ribonuclease P (RNase P) it increases the optimum temperature to that of the partially purified enzyme and causes a 5-fold increase in apparent Vmax. Binds the RNase P catalytic RNA.<ref>PMID:16829535</ref> <ref>PMID:16574071</ref> | + | [https://www.uniprot.org/uniprot/RL7A_PYRHO RL7A_PYRHO] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs (By similarity). When added to reconstituted ribonuclease P (RNase P) it increases the optimum temperature to that of the partially purified enzyme and causes a 5-fold increase in apparent Vmax. Binds the RNase P catalytic RNA.<ref>PMID:16829535</ref> <ref>PMID:16574071</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pyrococcus horikoshii]] | + | [[Category: Pyrococcus horikoshii OT3]] |
| - | [[Category: Kimura, M]] | + | [[Category: Kimura M]] |
| - | [[Category: Oshima, K]] | + | [[Category: Oshima K]] |
| - | [[Category: Kink-turn rna]]
| + | |
| - | [[Category: Ribonuclease p]]
| + | |
| - | [[Category: Rna binding protein]]
| + | |
| Structural highlights
Function
RL7A_PYRHO Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs (By similarity). When added to reconstituted ribonuclease P (RNase P) it increases the optimum temperature to that of the partially purified enzyme and causes a 5-fold increase in apparent Vmax. Binds the RNase P catalytic RNA.[1] [2]
Publication Abstract from PubMed
A characteristic feature of archaeal ribonuclease P (RNase P) RNAs is that they have extended helices P12.1 and P12.2 containing kink-turn (K-turn) motifs to which the archaeal RNase P protein Rpp38, a homologue of the human RNase P protein Rpp38, specifically binds. PhoRpp38 from the hyperthermophilic archaeon Pyrococcus horikoshii is involved in the elevation of the optimum temperature of the reconstituted RNase P by binding the K-turns in P12.1 and P12.2. Previously, the crystal structure of PhoRpp38 in complex with the K-turn in P12.2 was determined at 3.4 A resolution. In this study, the crystal structure of PhoRpp38 in complex with the K-turn in P12.2 was improved to 2.1 A resolution and the structure of PhoRpp38 in complex with the K-turn in P12.1 was also determined at a resolution of 3.1 A. Both structures revealed that Lys35, Asn38 and Glu39 in PhoRpp38 interact with characteristic G.A and A.G pairs in the K-turn, while Thr37, Asp59, Lys84, Glu94, Ala96 and Ala98 in PhoRpp38 interact with the three-nucleotide bulge in the K-turn. Moreover, an extended stem-loop containing P10-P12.2 in complex with PhoRpp38, as well as PhoRpp21 and PhoRpp29, which are the archaeal homologues of the human proteins Rpp21 and Rpp29, respectively, was affinity-purified and crystallized. The crystals thus grown diffracted to a resolution of 6.35 A. Structure determination of the crystals will demonstrate the previously proposed secondary structure of stem-loops including helices P12.1 and P12.2 and will also provide insight into the structural organization of the specificity domain in P. horikoshii RNase P RNA.
Crystal structures of the archaeal RNase P protein Rpp38 in complex with RNA fragments containing a K-turn motif.,Oshima K, Gao X, Hayashi S, Ueda T, Nakashima T, Kimura M Acta Crystallogr F Struct Biol Commun. 2018 Jan 1;74(Pt 1):57-64. doi:, 10.1107/S2053230X17018039. Epub 2018 Jan 1. PMID:29372908[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Terada A, Honda T, Fukuhara H, Hada K, Kimura M. Characterization of the archaeal ribonuclease P proteins from Pyrococcus horikoshii OT3. J Biochem. 2006 Aug;140(2):293-8. Epub 2006 Jul 7. PMID:16829535 doi:http://dx.doi.org/10.1093/jb/mvj144
- ↑ Fukuhara H, Kifusa M, Watanabe M, Terada A, Honda T, Numata T, Kakuta Y, Kimura M. A fifth protein subunit Ph1496p elevates the optimum temperature for the ribonuclease P activity from Pyrococcus horikoshii OT3. Biochem Biophys Res Commun. 2006 May 12;343(3):956-64. Epub 2006 Mar 15. PMID:16574071 doi:10.1016/j.bbrc.2006.02.192
- ↑ Oshima K, Gao X, Hayashi S, Ueda T, Nakashima T, Kimura M. Crystal structures of the archaeal RNase P protein Rpp38 in complex with RNA fragments containing a K-turn motif. Acta Crystallogr F Struct Biol Commun. 2018 Jan 1;74(Pt 1):57-64. doi:, 10.1107/S2053230X17018039. Epub 2018 Jan 1. PMID:29372908 doi:http://dx.doi.org/10.1107/S2053230X17018039
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