5et4 - Revision history

OCA at 08:21, 12 July 2023

OCA — Wed, 12 Jul 2023 08:21:59 GMT

←Older revision		Revision as of 08:21, 12 July 2023
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	<StructureSection load='5et4' size='340' side='right'caption='[[5et4]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5et4' size='340' side='right'caption='[[5et4]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5et4]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bovin Bovin~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ET4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ET4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5et4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ET4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ET4 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=C3P:CYTIDINE-3-MONOPHOSPHATE'>C3P</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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]] 2.1Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[4u7r\|4u7r~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C3P:CYTIDINE-3-MONOPHOSPHATE'>C3P</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>RNASE1, RNS1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9913 BOVIN])</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=5et4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5et4 OCA], [https://pdbe.org/5et4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5et4 RCSB], [https://www.ebi.ac.uk/pdbsum/5et4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5et4 ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease]~~, ~~with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5]~~ </~~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=5et4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5et4 OCA], [~~http~~://pdbe.org/5et4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5et4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5et4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5et4 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN]] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</ref>	+	[https://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: Human RNase6 is a small cationic antimicrobial protein that belongs to the vertebrate RNaseA superfamily. All members share a common catalytic mechanism, which involves a conserved catalytic triad, constituted by two histidines and a lysine (His15/His122/Lys38 in RNase6 corresponding to His12/His119/Lys41 in RNaseA). Recently, our first crystal structure of human RNase6 identified an additional His pair (His36/His39) and suggested the presence of a secondary active site. METHODS: In this work we have explored RNase6 and RNaseA subsite architecture by X-ray crystallography, site-directed mutagenesis and kinetic characterization. RESULTS: The analysis of two novel crystal structures of RNase6 in complex with phosphate anions at atomic resolution locates a total of nine binding sites and reveals the contribution of Lys87 to phosphate-binding at the secondary active center. Contribution of the second catalytic triad residues to the enzyme activity is confirmed by mutagenesis. RNase6 catalytic site architecture has been compared with an RNaseA engineered variant where a phosphate-binding subsite is converted into a secondary catalytic center (RNaseA-K7H/R10H). CONCLUSIONS: We have identified the residues that participate in RNase6 second catalytic triad (His36/His39/Lys87) and secondary phosphate-binding sites. To note, residues His39 and Lys87 are unique within higher primates. The RNaseA/RNase6 side-by-side comparison correlates the presence of a dual active site in RNase6 with a favored endonuclease-type cleavage pattern. GENERAL SIGNIFICANCE: An RNase dual catalytic and extended binding site arrangement facilitates the cleavage of polymeric substrates. This is the first report of the presence of two catalytic centers in a single monomer within the RNaseA superfamily.
		+
		+	Characterization of an RNase with two catalytic centers. Human RNase6 catalytic and phosphate-binding site arrangement favors the endonuclease cleavage of polymeric substrates.,Prats-Ejarque G, Blanco JA, Salazar VA, Nogues VM, Moussaoui M, Boix E Biochim Biophys Acta Gen Subj. 2018 Oct 1;1863(1):105-117. doi:, 10.1016/j.bbagen.2018.09.021. PMID:30287244<ref>PMID:30287244</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5et4" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[Ribonuclease\|Ribonuclease]]	+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bovin~~]]	+	[[Category: Bos taurus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Pancreatic ribonuclease]]~~	+	[[Category: Blanco JA]]
-	[[Category: Blanco~~, J A~~]]	+	[[Category: Boix E]]
-	[[Category: Boix, E]]	+	[[Category: Moussaoui M]]
-	[[Category: Moussaoui, M]]	+	[[Category: Salazar VA]]
-	[[Category: Salazar~~, V A]]~~	+
-	~~[[Category: Exonuclease activity]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: P2 subsite]]~~	+
-	~~[[Category: Rnase some~~]]	+

OCA at 12:23, 17 July 2019

OCA — Wed, 17 Jul 2019 12:23:39 GMT

←Older revision		Revision as of 12:23, 17 July 2019
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	==Structure of RNase A-K7H/R10H in complex with 3'-CMP==		==Structure of RNase A-K7H/R10H in complex with 3'-CMP==
-	<StructureSection load='5et4' size='340' side='right' caption='[[5et4]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5et4' size='340' side='right'caption='[[5et4]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5et4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ET4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ET4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5et4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ET4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ET4 FirstGlance]. <br>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN]] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</ref>		[[http://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN]] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</ref>
		+
		+	==See Also==
		+	*[[Ribonuclease\|Ribonuclease]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Bovin]]		[[Category: Bovin]]
		+	[[Category: Large Structures]]
	[[Category: Pancreatic ribonuclease]]		[[Category: Pancreatic ribonuclease]]
	[[Category: Blanco, J A]]		[[Category: Blanco, J A]]

OCA at 20:30, 24 January 2018

OCA — Wed, 24 Jan 2018 20:30:29 GMT

←Older revision		Revision as of 20:30, 24 January 2018
Line 3:		Line 3:
	<StructureSection load='5et4' size='340' side='right' caption='[[5et4]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5et4' size='340' side='right' caption='[[5et4]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5et4]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ET4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ET4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5et4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ET4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ET4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C3P:CYTIDINE-3-MONOPHOSPHATE'>C3P</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C3P:CYTIDINE-3-MONOPHOSPHATE'>C3P</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4u7r\|4u7r]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4u7r\|4u7r]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNASE1, RNS1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9913 BOVIN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] </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=5et4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5et4 OCA], [http://pdbe.org/5et4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5et4 RCSB], [http://www.ebi.ac.uk/pdbsum/5et4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5et4 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=5et4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5et4 OCA], [http://pdbe.org/5et4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5et4 RCSB], [http://www.ebi.ac.uk/pdbsum/5et4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5et4 ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bovin]]
	[[Category: Pancreatic ribonuclease]]		[[Category: Pancreatic ribonuclease]]
	[[Category: Blanco, J A]]		[[Category: Blanco, J A]]

OCA at 18:30, 10 December 2016

OCA — Sat, 10 Dec 2016 18:30:17 GMT

←Older revision		Revision as of 18:30, 10 December 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5et4 is ~~ON HOLD until Nov 17 2017~~	+	==Structure of RNase A-K7H/R10H in complex with 3'-CMP==
-		+	<StructureSection load='5et4' size='340' side='right' caption='[[5et4]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~Authors~~: ~~Blanco~~, J.A., ~~Salazar, V~~.A., ~~Moussaoui~~, M., ~~Boix~~, E.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5et4]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ET4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ET4 FirstGlance]. <br>
-	~~Description~~: ~~Structure of RNase A-K7H~~/~~R10H in complex with~~ 3'~~-CMP~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C3P:CYTIDINE-3-MONOPHOSPHATE'>C3P</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4u7r\|4u7r]]</td></tr>
-	[[Category: Blanco, J.A]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] </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=5et4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5et4 OCA], [http://pdbe.org/5et4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5et4 RCSB], [http://www.ebi.ac.uk/pdbsum/5et4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5et4 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN]] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Pancreatic ribonuclease]]
		+	[[Category: Blanco, J A]]
	[[Category: Boix, E]]		[[Category: Boix, E]]
-	[[Category: Salazar, V.A]]
	[[Category: Moussaoui, M]]		[[Category: Moussaoui, M]]
		+	[[Category: Salazar, V A]]
		+	[[Category: Exonuclease activity]]
		+	[[Category: Hydrolase]]
		+	[[Category: P2 subsite]]
		+	[[Category: Rnase some]]

OCA at 14:59, 2 December 2015

OCA — Wed, 02 Dec 2015 14:59:03 GMT

←Older revision		Revision as of 14:59, 2 December 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5et4 is ON HOLD	+	The entry 5et4 is ON HOLD until Nov 17 2017

	Authors: Blanco, J.A., Salazar, V.A., Moussaoui, M., Boix, E.		Authors: Blanco, J.A., Salazar, V.A., Moussaoui, M., Boix, E.

OCA: Protected "5et4" [edit=sysop:move=sysop]

OCA — Tue, 01 Dec 2015 03:20:02 GMT

Protected "5et4" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:20, 1 December 2015

OCA: New page: '''Unreleased structure''' The entry 5et4 is ON HOLD Authors: Blanco, J.A., Salazar, V.A., Moussaoui, M., Boix, E. Description: Structure of RNase A-K7H/R10H in complex with 3'-CMP [[C...

OCA — Tue, 01 Dec 2015 03:20:00 GMT

New page: '''Unreleased structure''' The entry 5et4 is ON HOLD Authors: Blanco, J.A., Salazar, V.A., Moussaoui, M., Boix, E. Description: Structure of RNase A-K7H/R10H in complex with 3'-CMP [[C...

New page

'''Unreleased structure'''

The entry 5et4 is ON HOLD

Authors: Blanco, J.A., Salazar, V.A., Moussaoui, M., Boix, E.

Description: Structure of RNase A-K7H/R10H in complex with 3'-CMP
[[Category: Unreleased Structures]]
[[Category: Blanco, J.A]]
[[Category: Boix, E]]
[[Category: Salazar, V.A]]
[[Category: Moussaoui, M]]