6nvo - Revision history

OCA at 07:00, 11 October 2023

OCA — Wed, 11 Oct 2023 07:00:36 GMT

←Older revision		Revision as of 07:00, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6nvo' size='340' side='right'caption='[[6nvo]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6nvo' size='340' side='right'caption='[[6nvo]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nvo]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Psepk Psepk~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NVO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6NVO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nvo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida_KT2440 Pseudomonas putida KT2440]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NVO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NVO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.196Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~PP_1102 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=160488 PSEPK]~~)</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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=6nvo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nvo OCA], [~~http~~://pdbe.org/6nvo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6nvo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6nvo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6nvo 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=6nvo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nvo OCA], [https://pdbe.org/6nvo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nvo RCSB], [https://www.ebi.ac.uk/pdbsum/6nvo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nvo ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q88NV2_PSEPK Q88NV2_PSEPK]
	<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: ~~Psepk~~]]	+	[[Category: Pseudomonas putida KT2440]]
-	[[Category: Ejaz, A]]	+	[[Category: Ejaz A]]
-	[[Category: Goldgur, Y]]	+	[[Category: Goldgur Y]]
-	[[Category: Shuman, S]]	+	[[Category: Shuman S]]
-	~~[[Category: Binuclear metallo-phosphodiesterase/nuclease]]~~	+
-	~~[[Category: Dna binding protein~~]]	+

OCA at 07:03, 17 April 2019

OCA — Wed, 17 Apr 2019 07:03:56 GMT

←Older revision		Revision as of 07:03, 17 April 2019
Line 3:		Line 3:
	<StructureSection load='6nvo' size='340' side='right'caption='[[6nvo]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6nvo' size='340' side='right'caption='[[6nvo]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nvo]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NVO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NVO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nvo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Psepk Psepk]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NVO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NVO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PP_1102 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=160488 PSEPK])</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=6nvo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nvo OCA], [http://pdbe.org/6nvo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nvo RCSB], [http://www.ebi.ac.uk/pdbsum/6nvo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nvo 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=6nvo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nvo OCA], [http://pdbe.org/6nvo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nvo RCSB], [http://www.ebi.ac.uk/pdbsum/6nvo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nvo ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A recently identified and widely prevalent prokaryal gene cluster encodes a suite of enzymes with imputed roles in nucleic acid repair. The enzymes are: MPE, a DNA endonuclease; Lhr-Core, a 3'-5' DNA helicase; LIG, an ATP-dependent DNA ligase; and Exo, a metallo-beta-lactamase-family nuclease. Bacterial and archaeal MPE proteins belong to the binuclear metallophosphoesterase superfamily that includes the well-studied DNA repair nucleases Mre11 and SbcD. Here we report that the Pseudomonas putida MPE protein is a manganese-dependent DNA endonuclease that incises either linear single strands or the single-strand loops of stem-loop DNA structures. MPE has feeble activity on duplex DNA. A crystal structure of MPE at 2.2 A resolution revealed that the active site includes two octahedrally coordinated manganese ions. Seven signature amino acids of the binuclear metallophosphoesterase superfamily serve as the enzymic metal ligands in MPE: Asp33, His35, Asp78, Asn112, His124, His146, and His158. A swath of positive surface potential on either side of the active site pocket suggests a binding site for the single-strand DNA substrate. The structure of MPE differs significantly from Mre11 and SbcD in several key respects: (i) MPE is a monomer, whereas Mre11 and SbcD are homodimers; (ii) MPE lacks the capping domain present in Mre11 and SbcD; and (iii) the topology of the bsandwich that comprises the core of the metallophosphoesterase fold differs in MPE vis-a-vis Mre11 and SbcD. We surmise that MPE exemplifies a novel clade of DNA endonuclease within the binuclear metallophosphoesterase superfamily.
		+
		+	Activity and structure of Pseudomonas putida MPE, a manganese-dependent single-strand DNA endonuclease encoded in a nucleic acid repair gene cluster.,Ejaz A, Goldgur Y, Shuman S J Biol Chem. 2019 Mar 20. pii: RA119.008049. doi: 10.1074/jbc.RA119.008049. PMID:30894417<ref>PMID:30894417</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6nvo" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Psepk]]
	[[Category: Ejaz, A]]		[[Category: Ejaz, A]]
	[[Category: Goldgur, Y]]		[[Category: Goldgur, Y]]

OCA at 06:45, 27 March 2019

OCA — Wed, 27 Mar 2019 06:45:42 GMT

←Older revision		Revision as of 06:45, 27 March 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6nvo is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of Pseudomonas putida nuclease MPE==
-		+	<StructureSection load='6nvo' size='340' side='right'caption='[[6nvo]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~Authors~~: ~~Goldgur~~, Y., ~~Shuman~~, S., ~~Ejaz~~, A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6nvo]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NVO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NVO FirstGlance]. <br>
-	~~Description: Crystal structure of Pseudomonas putida nuclease MPE~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6nvo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nvo OCA], [http://pdbe.org/6nvo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nvo RCSB], [http://www.ebi.ac.uk/pdbsum/6nvo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nvo ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ejaz, A]]
	[[Category: Goldgur, Y]]		[[Category: Goldgur, Y]]
-	[[Category: Ejaz, A]]
	[[Category: Shuman, S]]		[[Category: Shuman, S]]
		+	[[Category: Binuclear metallo-phosphodiesterase/nuclease]]
		+	[[Category: Dna binding protein]]

OCA: Protected "6nvo" [edit=sysop:move=sysop]

OCA — Wed, 13 Feb 2019 07:49:56 GMT

Protected "6nvo" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:49, 13 February 2019

OCA: New page: '''Unreleased structure''' The entry 6nvo is ON HOLD until Paper Publication Authors: Goldgur, Y., Shuman, S., Ejaz, A. Description: Crystal structure of Pseudomonas putida nuclease MP...

OCA — Wed, 13 Feb 2019 07:49:54 GMT

New page: '''Unreleased structure''' The entry 6nvo is ON HOLD until Paper Publication Authors: Goldgur, Y., Shuman, S., Ejaz, A. Description: Crystal structure of Pseudomonas putida nuclease MP...

New page

'''Unreleased structure'''

The entry 6nvo is ON HOLD until Paper Publication

Authors: Goldgur, Y., Shuman, S., Ejaz, A.

Description: Crystal structure of Pseudomonas putida nuclease MPE
[[Category: Unreleased Structures]]
[[Category: Goldgur, Y]]
[[Category: Ejaz, A]]
[[Category: Shuman, S]]