5oab - Revision history

OCA at 09:38, 6 December 2023

2023-12-06T09:38:18Z

←Older revision		Revision as of 09:38, 6 December 2023
Line 3:		Line 3:
	<StructureSection load='5oab' size='340' side='right'caption='[[5oab]], [[Resolution\|resolution]] 1.11Å' scene=''>		<StructureSection load='5oab' size='340' side='right'caption='[[5oab]], [[Resolution\|resolution]] 1.11Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5oab]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OAB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5OAB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5oab]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OAB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OAB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.111Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x09\|4x09]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNASE6, RNS6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=5oab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oab OCA], [https://pdbe.org/5oab PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5oab RCSB], [https://www.ebi.ac.uk/pdbsum/5oab PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5oab 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=5oab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oab OCA], [~~http~~://pdbe.org/5oab PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5oab RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5oab PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5oab ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RNAS6_HUMAN RNAS6_HUMAN]] May have a role in host defense.	+	[https://www.uniprot.org/uniprot/RNAS6_HUMAN RNAS6_HUMAN] May have a role in host defense.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Boix, E]]	+	[[Category: Boix E]]
-	[[Category: Moussaoui, M]]	+	[[Category: Moussaoui M]]
-	[[Category: Prats-Ejarque, G]]	+	[[Category: Prats-Ejarque G]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Pancreatic ribonuclease]]~~	+
-	~~[[Category: Rnase k6~~]]	+

OCA at 12:20, 26 August 2020

2020-08-26T12:20:02Z

←Older revision		Revision as of 12:20, 26 August 2020
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	==A novel crystal form of human RNase6 at atomic resolution==		==A novel crystal form of human RNase6 at atomic resolution==
-	<StructureSection load='5oab' size='340' side='right' caption='[[5oab]], [[Resolution\|resolution]] 1.11Å' scene=''>	+	<StructureSection load='5oab' size='340' side='right'caption='[[5oab]], [[Resolution\|resolution]] 1.11Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5oab]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OAB OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OAB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5oab]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OAB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5OAB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x09\|4x09]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x09\|4x09]]</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=5oab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oab OCA], [http://pdbe.org/5oab PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oab RCSB], [http://www.ebi.ac.uk/pdbsum/5oab PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oab ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNASE6, RNS6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5oab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oab OCA], [http://pdbe.org/5oab PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oab RCSB], [http://www.ebi.ac.uk/pdbsum/5oab PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oab ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	Human ~~RNase 6~~ is a cationic ~~secreted~~ protein that belongs to the ~~RNase A~~ superfamily. ~~Its expression is induced in neutrophils and monocytes upon bacterial infection~~, ~~suggesting~~ a ~~role~~ in ~~host defence~~. ~~We present here the~~ crystal structure of ~~RNase 6 obtained at~~ a 1.~~72 A resolution~~, ~~being the first report for the protein three~~-~~dimensional structure~~ and ~~thereby setting the basis for functional studies~~. The ~~structure shows an overall kidney shaped globular fold shared~~ with ~~the other known family members. Three sulphate~~ anions ~~bound~~ to ~~RNase 6 were found, interacting to residues~~ at the ~~main~~ active site (~~His15, His122 and Gln14~~) ~~and cationic surface exposed~~ residues (His36, His39~~, Arg66 and His67~~). ~~Kinetic characterization~~, ~~together with prediction of protein~~ -~~nucleotide complexes~~ by ~~molecular dynamics, was applied to analyse~~ the ~~RNase 6 substrate nitrogenous base and phosphate selectivity. Our results reveal that, although RNase 6 is~~ a ~~moderate catalyst~~ in comparison to the pancreatic RNase type, its structure includes lineage specific features that facilitate its activity towards polymeric nucleotide substrates. In particular, enzyme interactions at the substrate 5' end can provide an endonuclease type cleavage pattern. ~~Interestingly, the~~ RNase ~~6 crystal structure revealed a novel secondary active~~ site ~~conformed by the His36-His39 dyad that~~ facilitates the ~~polynucleotide substrate catalysis~~.	+	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.

-	~~The first crystal structure~~ of ~~human~~ RNase6 ~~reveals a novel substrate binding~~ and ~~cleavage~~ site arrangement.,Prats-Ejarque G~~, Arranz-Trullen J~~, Blanco JA, ~~Pulido D~~, Nogues MV, Moussaoui M, Boix E ~~Biochem J~~. ~~2016 Mar 24~~. ~~pii~~: ~~BCJ20160245~~. PMID:~~27013146~~<ref>PMID:~~27013146~~</ref>	+	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>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	<div class="pdbe-citations 5oab" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5oab" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Boix, E]]		[[Category: Boix, E]]
	[[Category: Moussaoui, M]]		[[Category: Moussaoui, M]]

OCA at 18:33, 1 August 2018

2018-08-01T18:33:32Z

←Older revision		Revision as of 18:33, 1 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5oab is ~~ON HOLD until Paper~~ Publication	+	==A novel crystal form of human RNase6 at atomic resolution==
		+	<StructureSection load='5oab' size='340' side='right' caption='[[5oab]], [[Resolution\|resolution]] 1.11Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5oab]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OAB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OAB FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x09\|4x09]]</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=5oab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oab OCA], [http://pdbe.org/5oab PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oab RCSB], [http://www.ebi.ac.uk/pdbsum/5oab PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oab ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RNAS6_HUMAN RNAS6_HUMAN]] May have a role in host defense.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human RNase 6 is a cationic secreted protein that belongs to the RNase A superfamily. Its expression is induced in neutrophils and monocytes upon bacterial infection, suggesting a role in host defence. We present here the crystal structure of RNase 6 obtained at a 1.72 A resolution, being the first report for the protein three-dimensional structure and thereby setting the basis for functional studies. The structure shows an overall kidney shaped globular fold shared with the other known family members. Three sulphate anions bound to RNase 6 were found, interacting to residues at the main active site (His15, His122 and Gln14) and cationic surface exposed residues (His36, His39, Arg66 and His67). Kinetic characterization, together with prediction of protein -nucleotide complexes by molecular dynamics, was applied to analyse the RNase 6 substrate nitrogenous base and phosphate selectivity. Our results reveal that, although RNase 6 is a moderate catalyst in comparison to the pancreatic RNase type, its structure includes lineage specific features that facilitate its activity towards polymeric nucleotide substrates. In particular, enzyme interactions at the substrate 5' end can provide an endonuclease type cleavage pattern. Interestingly, the RNase 6 crystal structure revealed a novel secondary active site conformed by the His36-His39 dyad that facilitates the polynucleotide substrate catalysis.

-	~~Authors:~~ Prats-Ejarque, G., ~~Moussaoui~~, M., Boix, E.	+	The first crystal structure of human RNase6 reveals a novel substrate binding and cleavage site arrangement.,Prats-Ejarque G, Arranz-Trullen J, Blanco JA, Pulido D, Nogues MV, Moussaoui M, Boix E Biochem J. 2016 Mar 24. pii: BCJ20160245. PMID:27013146<ref>PMID:27013146</ref>

-	~~Description: A novel crystal form~~ of ~~human RNase6 at atomic resolution~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5oab" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Boix, E]]		[[Category: Boix, E]]
	[[Category: Moussaoui, M]]		[[Category: Moussaoui, M]]
	[[Category: Prats-Ejarque, G]]		[[Category: Prats-Ejarque, G]]
		+	[[Category: Hydrolase]]
		+	[[Category: Pancreatic ribonuclease]]
		+	[[Category: Rnase k6]]

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

2017-09-27T12:12:31Z

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

←Older revision

Revision as of 12:12, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5oab is ON HOLD until Paper Publication Authors: Prats-Ejarque, G., Moussaoui, M., Boix, E. Description: A novel crystal form of human RNase6 at at...

2017-09-27T12:12:30Z

New page: '''Unreleased structure''' The entry 5oab is ON HOLD until Paper Publication Authors: Prats-Ejarque, G., Moussaoui, M., Boix, E. Description: A novel crystal form of human RNase6 at at...

New page

'''Unreleased structure'''

The entry 5oab is ON HOLD until Paper Publication

Authors: Prats-Ejarque, G., Moussaoui, M., Boix, E.

Description: A novel crystal form of human RNase6 at atomic resolution
[[Category: Unreleased Structures]]
[[Category: Boix, E]]
[[Category: Moussaoui, M]]
[[Category: Prats-Ejarque, G]]