5y7m - Revision history

OCA at 09:19, 20 March 2024

2024-03-20T09:19:57Z

←Older revision		Revision as of 09:19, 20 March 2024
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	== Function ==		== Function ==
	[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>		[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;">
-	== 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<ref>PMID:29372908</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5y7m" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:24, 22 November 2023

2023-11-22T08:24:08Z

←Older revision		Revision as of 08:24, 22 November 2023
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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~~]]	+

OCA at 10:16, 26 February 2020

2020-02-26T10:16:05Z

←Older revision		Revision as of 10:16, 26 February 2020
Line 1:		Line 1:

	==Crystal structure of PhoRpp38 bound to a K-turn in P12.1 helix==		==Crystal structure of PhoRpp38 bound to a K-turn in P12.1 helix==
-	<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. 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 [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>
	</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='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>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xtm\|5xtm]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xtm\|5xtm]]</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'>[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>		<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>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Pyrococcus horikoshii]]
	[[Category: Kimura, M]]		[[Category: Kimura, M]]
	[[Category: Oshima, K]]		[[Category: Oshima, K]]

OCA at 06:16, 7 February 2018

2018-02-07T06:16:13Z

←Older revision		Revision as of 06:16, 7 February 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5y7m is ~~ON HOLD~~ ~~until Aug 01 2019~~	+	==Crystal structure of PhoRpp38 bound to a K-turn in P12.1 helix==
		+	<StructureSection load='5y7m' size='340' side='right' caption='[[5y7m]], [[Resolution\|resolution]] 3.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5y7m]] is a 4 chain structure. 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>
		+	</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>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xtm\|5xtm]]</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>
		+	== 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>
		+	<div style="background-color:#fffaf0;">
		+	== 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.

-	~~Authors: Oshima,~~ K., ~~Kimura~~, M.	+	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<ref>PMID:29372908</ref>

-	~~Description: RNA-Protein crystal structure~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Oshima, K]]~~	+	<div class="pdbe-citations 5y7m" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Kimura, M]]		[[Category: Kimura, M]]
		+	[[Category: Oshima, K]]
		+	[[Category: Kink-turn rna]]
		+	[[Category: Ribonuclease p]]
		+	[[Category: Rna binding protein]]

OCA: Protected "5y7m" [edit=sysop:move=sysop]

2017-09-27T16:14:17Z

Protected "5y7m" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:14, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5y7m is ON HOLD until Aug 01 2019 Authors: Oshima, K., Kimura, M. Description: RNA-Protein crystal structure Category: Unreleased Structures [[...

2017-09-27T16:14:16Z

New page: '''Unreleased structure''' The entry 5y7m is ON HOLD until Aug 01 2019 Authors: Oshima, K., Kimura, M. Description: RNA-Protein crystal structure Category: Unreleased Structures [[...

New page

'''Unreleased structure'''

The entry 5y7m is ON HOLD until Aug 01 2019

Authors: Oshima, K., Kimura, M.

Description: RNA-Protein crystal structure
[[Category: Unreleased Structures]]
[[Category: Oshima, K]]
[[Category: Kimura, M]]