1oqk - Revision history

OCA at 08:56, 22 May 2024

OCA — Wed, 22 May 2024 08:56:54 GMT

←Older revision		Revision as of 08:56, 22 May 2024
Line 19:		Line 19:
	</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=1oqk 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=1oqk ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We have determined the solution structure of Mth11 (Mth Rpp29), an essential subunit of the RNase P enzyme from the archaebacterium Methanothermobacter thermoautotrophicus (Mth). RNase P is a ubiquitous ribonucleoprotein enzyme primarily responsible for cleaving the 5' leader sequence during maturation of tRNAs in all three domains of life. In eubacteria, this enzyme is made up of two subunits: a large RNA ( approximately 120 kDa) responsible for mediating catalysis, and a small protein cofactor ( approximately 15 kDa) that modulates substrate recognition and is required for efficient in vivo catalysis. In contrast, multiple proteins are associated with eukaryotic and archaeal RNase P, and these proteins exhibit no recognizable homology to the conserved bacterial protein subunit. In reconstitution experiments with recombinantly expressed and purified protein subunits, we found that Mth Rpp29, a homolog of the Rpp29 protein subunit from eukaryotic RNase P, is an essential protein component of the archaeal holoenzyme. Consistent with its role in mediating protein-RNA interactions, we report that Mth Rpp29 is a member of the oligonucleotide/oligosaccharide binding fold family. In addition to a structured beta-barrel core, it possesses unstructured N- and C-terminal extensions bearing several highly conserved amino acid residues. To identify possible RNA contacts in the protein-RNA complex, we examined the interaction of the 11-kDa protein with the full 100-kDa Mth RNA subunit by using NMR chemical shift perturbation. Our findings represent a critical step toward a structural model of the RNase P holoenzyme from archaebacteria and higher organisms.
		+
		+	Structure of Mth11/Mth Rpp29, an essential protein subunit of archaeal and eukaryotic RNase P.,Boomershine WP, McElroy CA, Tsai HY, Wilson RC, Gopalan V, Foster MP Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15398-403. Epub 2003 Dec 12. PMID:14673079<ref>PMID:14673079</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1oqk" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:49, 17 April 2024

OCA — Wed, 17 Apr 2024 05:49:46 GMT

←Older revision		Revision as of 05:49, 17 April 2024
Line 1:		Line 1:

	==Structure of Mth11: A homologue of human RNase P protein Rpp29==		==Structure of Mth11: A homologue of human RNase P protein Rpp29==
-	<StructureSection load='1oqk' size='340' side='right'caption='[[1oqk~~]], [[NMR_Ensembles_of_Models \| 22 NMR models~~]]' scene=''>	+	<StructureSection load='1oqk' size='340' side='right'caption='[[1oqk]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1oqk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OQK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OQK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1oqk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OQK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OQK FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>MTH11 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~145262~~ "~~Methanobacterium thermoautotrophicus~~" ~~(sic) Zeikus and Wolfe 1972])</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonuclease_P Ribonuclease P], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.5 3.1.26.5] </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=1oqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oqk OCA], [https://pdbe.org/1oqk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oqk RCSB], [https://www.ebi.ac.uk/pdbsum/1oqk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oqk ProSAT]</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=1oqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oqk OCA], [https://pdbe.org/1oqk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oqk RCSB], [https://www.ebi.ac.uk/pdbsum/1oqk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oqk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RNP1_METTH RNP1_METTH]] Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends.<ref>PMID:12003490</ref> <ref>PMID:14673079</ref>	+	[https://www.uniprot.org/uniprot/RNP1_METTH RNP1_METTH] Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends.<ref>PMID:12003490</ref> <ref>PMID:14673079</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 19:
	</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=1oqk 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=1oqk ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	We have determined the solution structure of Mth11 (Mth Rpp29), an essential subunit of the RNase P enzyme from the archaebacterium Methanothermobacter thermoautotrophicus (Mth). RNase P is a ubiquitous ribonucleoprotein enzyme primarily responsible for cleaving the 5' leader sequence during maturation of tRNAs in all three domains of life. In eubacteria, this enzyme is made up of two subunits: a large RNA ( approximately 120 kDa) responsible for mediating catalysis, and a small protein cofactor ( approximately 15 kDa) that modulates substrate recognition and is required for efficient in vivo catalysis. In contrast, multiple proteins are associated with eukaryotic and archaeal RNase P, and these proteins exhibit no recognizable homology to the conserved bacterial protein subunit. In reconstitution experiments with recombinantly expressed and purified protein subunits, we found that Mth Rpp29, a homolog of the Rpp29 protein subunit from eukaryotic RNase P, is an essential protein component of the archaeal holoenzyme. Consistent with its role in mediating protein-RNA interactions, we report that Mth Rpp29 is a member of the oligonucleotide/oligosaccharide binding fold family. In addition to a structured beta-barrel core, it possesses unstructured N- and C-terminal extensions bearing several highly conserved amino acid residues. To identify possible RNA contacts in the protein-RNA complex, we examined the interaction of the 11-kDa protein with the full 100-kDa Mth RNA subunit by using NMR chemical shift perturbation. Our findings represent a critical step toward a structural model of the RNase P holoenzyme from archaebacteria and higher organisms.
-
-	Structure of Mth11/Mth Rpp29, an essential protein subunit of archaeal and eukaryotic RNase P.,Boomershine WP, McElroy CA, Tsai HY, Wilson RC, Gopalan V, Foster MP Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15398-403. Epub 2003 Dec 12. PMID:14673079<ref>PMID:14673079</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1oqk" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ribonuclease P~~]]	+	[[Category: Methanothermobacter thermautotrophicus]]
-	[[Category: Boomershine~~, W P~~]]	+	[[Category: Boomershine WP]]
-	[[Category: Foster~~, M P~~]]	+	[[Category: Foster MP]]
-	[[Category: Gopalan, V]]	+	[[Category: Gopalan V]]
-	[[Category: McElroy~~, C A~~]]	+	[[Category: McElroy CA]]
-	[[Category: Tsai, H]]	+	[[Category: Tsai H]]
-	~~[[Category: Archaeal rnase p protein subunit]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Ob fold~~]]	+

OCA at 08:26, 23 February 2022

OCA — Wed, 23 Feb 2022 08:26:13 GMT

←Older revision		Revision as of 08:26, 23 February 2022
Line 3:		Line 3:
	<StructureSection load='1oqk' size='340' side='right'caption='[[1oqk]], [[NMR_Ensembles_of_Models \| 22 NMR models]]' scene=''>		<StructureSection load='1oqk' size='340' side='right'caption='[[1oqk]], [[NMR_Ensembles_of_Models \| 22 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1oqk]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OQK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1OQK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1oqk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OQK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OQK FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTH11 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 "Methanobacterium thermoautotrophicus" (sic) Zeikus and Wolfe 1972])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTH11 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 "Methanobacterium thermoautotrophicus" (sic) Zeikus and Wolfe 1972])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Ribonuclease_P Ribonuclease P], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.5 3.1.26.5] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonuclease_P Ribonuclease P], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.5 3.1.26.5] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1oqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oqk OCA], [~~http~~://pdbe.org/1oqk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1oqk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1oqk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1oqk ProSAT]</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=1oqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oqk OCA], [https://pdbe.org/1oqk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oqk RCSB], [https://www.ebi.ac.uk/pdbsum/1oqk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oqk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RNP1_METTH RNP1_METTH]] Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends.<ref>PMID:12003490</ref> <ref>PMID:14673079</ref>	+	[[https://www.uniprot.org/uniprot/RNP1_METTH RNP1_METTH]] Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends.<ref>PMID:12003490</ref> <ref>PMID:14673079</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:13, 9 December 2020

OCA — Wed, 09 Dec 2020 07:13:33 GMT

←Older revision		Revision as of 07:13, 9 December 2020
Line 1:		Line 1:

	==Structure of Mth11: A homologue of human RNase P protein Rpp29==		==Structure of Mth11: A homologue of human RNase P protein Rpp29==
-	<StructureSection load='1oqk' size='340' side='right' caption='[[1oqk]], [[NMR_Ensembles_of_Models \| 22 NMR models]]' scene=''>	+	<StructureSection load='1oqk' size='340' side='right'caption='[[1oqk]], [[NMR_Ensembles_of_Models \| 22 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1oqk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OQK OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1OQK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1oqk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OQK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1OQK FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTH11 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 "Methanobacterium thermoautotrophicus" (sic) Zeikus and Wolfe 1972])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTH11 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 "Methanobacterium thermoautotrophicus" (sic) Zeikus and Wolfe 1972])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_P Ribonuclease P], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.5 3.1.26.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_P Ribonuclease P], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.5 3.1.26.5] </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=1oqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oqk OCA], [http://pdbe.org/1oqk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1oqk RCSB], [http://www.ebi.ac.uk/pdbsum/1oqk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1oqk ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1oqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oqk OCA], [http://pdbe.org/1oqk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1oqk RCSB], [http://www.ebi.ac.uk/pdbsum/1oqk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1oqk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 33:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Ribonuclease P]]		[[Category: Ribonuclease P]]
	[[Category: Boomershine, W P]]		[[Category: Boomershine, W P]]

OCA at 07:43, 15 February 2018

OCA — Thu, 15 Feb 2018 07:43:14 GMT

←Older revision		Revision as of 07:43, 15 February 2018
Line 1:		Line 1:
		+
	==Structure of Mth11: A homologue of human RNase P protein Rpp29==		==Structure of Mth11: A homologue of human RNase P protein Rpp29==
	<StructureSection load='1oqk' size='340' side='right' caption='[[1oqk]], [[NMR_Ensembles_of_Models \| 22 NMR models]]' scene=''>		<StructureSection load='1oqk' size='340' side='right' caption='[[1oqk]], [[NMR_Ensembles_of_Models \| 22 NMR models]]' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTH11 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 "Methanobacterium thermoautotrophicus" (sic) Zeikus and Wolfe 1972])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTH11 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 "Methanobacterium thermoautotrophicus" (sic) Zeikus and Wolfe 1972])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_P Ribonuclease P], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.5 3.1.26.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_P Ribonuclease P], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.5 3.1.26.5] </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=1oqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oqk OCA], [http://pdbe.org/1oqk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1oqk RCSB], [http://www.ebi.ac.uk/pdbsum/1oqk PDBsum]</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=1oqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oqk OCA], [http://pdbe.org/1oqk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1oqk RCSB], [http://www.ebi.ac.uk/pdbsum/1oqk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1oqk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oq/1oqk_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oq/1oqk_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 23:54, 9 February 2016

OCA — Tue, 09 Feb 2016 23:54:54 GMT

←Older revision		Revision as of 23:54, 9 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ 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=1oqk ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:19, 11 September 2015

OCA — Fri, 11 Sep 2015 03:19:05 GMT

←Older revision		Revision as of 03:19, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1oqk' size='340' side='right' caption='[[1oqk]], [[NMR_Ensembles_of_Models \| 22 NMR models]]' scene=''>		<StructureSection load='1oqk' size='340' side='right' caption='[[1oqk]], [[NMR_Ensembles_of_Models \| 22 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1oqk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OQK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OQK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1oqk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OQK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OQK FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTH11 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 ~~Methanothermobacter thermautotrophicus~~])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTH11 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 "Methanobacterium thermoautotrophicus" (sic) Zeikus and Wolfe 1972])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_P Ribonuclease P], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.5 3.1.26.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_P Ribonuclease P], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.5 3.1.26.5] </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=1oqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oqk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1oqk RCSB], [http://www.ebi.ac.uk/pdbsum/1oqk PDBsum]</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=1oqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oqk OCA], [http://pdbe.org/1oqk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1oqk RCSB], [http://www.ebi.ac.uk/pdbsum/1oqk PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1oqk" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Methanothermobacter thermautotrophicus]]
	[[Category: Ribonuclease P]]		[[Category: Ribonuclease P]]
	[[Category: Boomershine, W P]]		[[Category: Boomershine, W P]]

OCA at 10:23, 25 December 2014

OCA — Thu, 25 Dec 2014 10:23:29 GMT

←Older revision		Revision as of 10:23, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1oqk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OQK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OQK FirstGlance]. <br>		<table><tr><td colspan='2'>[[1oqk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OQK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OQK FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTH11 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 Methanothermobacter thermautotrophicus])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTH11 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 Methanothermobacter thermautotrophicus])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_P Ribonuclease P], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.5 3.1.26.5] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_P Ribonuclease P], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.5 3.1.26.5] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1oqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oqk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1oqk RCSB], [http://www.ebi.ac.uk/pdbsum/1oqk PDBsum]</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=1oqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oqk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1oqk RCSB], [http://www.ebi.ac.uk/pdbsum/1oqk PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RNP1_METTH RNP1_METTH]] Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends.<ref>PMID:12003490</ref> <ref>PMID:14673079</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	[[Category: Methanothermobacter thermautotrophicus]]		[[Category: Methanothermobacter thermautotrophicus]]
	[[Category: Ribonuclease P]]		[[Category: Ribonuclease P]]
-	[[Category: Boomershine, W P.]]	+	[[Category: Boomershine, W P]]
-	[[Category: Foster, M P.]]	+	[[Category: Foster, M P]]
-	[[Category: Gopalan, V.]]	+	[[Category: Gopalan, V]]
-	[[Category: McElroy, C A.]]	+	[[Category: McElroy, C A]]
-	[[Category: Tsai, H.]]	+	[[Category: Tsai, H]]
	[[Category: Archaeal rnase p protein subunit]]		[[Category: Archaeal rnase p protein subunit]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Ob fold]]		[[Category: Ob fold]]

OCA at 23:25, 28 September 2014

OCA — Sun, 28 Sep 2014 23:25:05 GMT

←Older revision		Revision as of 23:25, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1oqk.~~png\|left~~\|200px]]	+	==Structure of Mth11: A homologue of human RNase P protein Rpp29==
		+	<StructureSection load='1oqk' size='340' side='right' caption='[[1oqk]], [[NMR_Ensembles_of_Models \| 22 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1oqk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OQK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OQK FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTH11 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 Methanothermobacter thermautotrophicus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_P Ribonuclease P], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.5 3.1.26.5] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1oqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oqk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1oqk RCSB], [http://www.ebi.ac.uk/pdbsum/1oqk PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oq/1oqk_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</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/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We have determined the solution structure of Mth11 (Mth Rpp29), an essential subunit of the RNase P enzyme from the archaebacterium Methanothermobacter thermoautotrophicus (Mth). RNase P is a ubiquitous ribonucleoprotein enzyme primarily responsible for cleaving the 5' leader sequence during maturation of tRNAs in all three domains of life. In eubacteria, this enzyme is made up of two subunits: a large RNA ( approximately 120 kDa) responsible for mediating catalysis, and a small protein cofactor ( approximately 15 kDa) that modulates substrate recognition and is required for efficient in vivo catalysis. In contrast, multiple proteins are associated with eukaryotic and archaeal RNase P, and these proteins exhibit no recognizable homology to the conserved bacterial protein subunit. In reconstitution experiments with recombinantly expressed and purified protein subunits, we found that Mth Rpp29, a homolog of the Rpp29 protein subunit from eukaryotic RNase P, is an essential protein component of the archaeal holoenzyme. Consistent with its role in mediating protein-RNA interactions, we report that Mth Rpp29 is a member of the oligonucleotide/oligosaccharide binding fold family. In addition to a structured beta-barrel core, it possesses unstructured N- and C-terminal extensions bearing several highly conserved amino acid residues. To identify possible RNA contacts in the protein-RNA complex, we examined the interaction of the 11-kDa protein with the full 100-kDa Mth RNA subunit by using NMR chemical shift perturbation. Our findings represent a critical step toward a structural model of the RNase P holoenzyme from archaebacteria and higher organisms.

-	~~{{STRUCTURE_1oqk\| PDB=1oqk \| SCENE= }}~~	+	Structure of Mth11/Mth Rpp29, an essential protein subunit of archaeal and eukaryotic RNase P.,Boomershine WP, McElroy CA, Tsai HY, Wilson RC, Gopalan V, Foster MP Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15398-403. Epub 2003 Dec 12. PMID:14673079<ref>PMID:14673079</ref>

-	~~===Structure~~ of ~~Mth11: A homologue of human RNase P protein Rpp29===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_14673079}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1oqk]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]~~. ~~Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1OQK OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:014673079<~~/~~ref~~><~~ref group="xtra">PMID:012963372</ref><references group="xtra"~~/>	+
	[[Category: Methanothermobacter thermautotrophicus]]		[[Category: Methanothermobacter thermautotrophicus]]
	[[Category: Ribonuclease P]]		[[Category: Ribonuclease P]]

OCA: Protected "1oqk" [edit=sysop:move=sysop]

OCA — Wed, 12 Dec 2012 21:39:35 GMT

Protected "1oqk" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:39, 12 December 2012