6b9v - Revision history

OCA at 14:36, 4 October 2023

OCA — Wed, 04 Oct 2023 14:36:17 GMT

←Older revision		Revision as of 14:36, 4 October 2023
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	<StructureSection load='6b9v' size='340' side='right'caption='[[6b9v]], [[Resolution\|resolution]] 1.88Å' scene=''>		<StructureSection load='6b9v' size='340' side='right'caption='[[6b9v]], [[Resolution\|resolution]] 1.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6b9v]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Acidobacteria_bacterium_ellin345 Acidobacteria bacterium ellin345~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B9V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6B9V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6b9v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Candidatus_Koribacter_versatilis_Ellin345 Candidatus Koribacter versatilis Ellin345]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B9V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6B9V 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>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.88Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Acid345_2630 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=204669 Acidobacteria bacterium Ellin345])</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>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6b9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b9v OCA], [~~http~~://pdbe.org/6b9v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6b9v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6b9v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6b9v 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=6b9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b9v OCA], [https://pdbe.org/6b9v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6b9v RCSB], [https://www.ebi.ac.uk/pdbsum/6b9v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6b9v ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q1INB9_KORVE Q1INB9_KORVE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Acidobacteria bacterium ellin345~~]]	+	[[Category: Candidatus Koribacter versatilis Ellin345]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bruner~~, S D~~]]	+	[[Category: Bruner SD]]
-	[[Category: Li, Q]]	+	[[Category: Li Q]]
-	~~[[Category: Diphosphatase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Metallo-beta-lactamase-like hydrolase~~]]	+

OCA at 13:21, 10 May 2019

OCA — Fri, 10 May 2019 13:21:05 GMT

←Older revision		Revision as of 13:21, 10 May 2019
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	==Crystal Structure of a New Diphosphatase from the PhnP Family==		==Crystal Structure of a New Diphosphatase from the PhnP Family==
-	<StructureSection load='6b9v' size='340' side='right' caption='[[6b9v]], [[Resolution\|resolution]] 1.88Å' scene=''>	+	<StructureSection load='6b9v' size='340' side='right'caption='[[6b9v]], [[Resolution\|resolution]] 1.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6b9v]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B9V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B9V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6b9v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acidobacteria_bacterium_ellin345 Acidobacteria bacterium ellin345]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B9V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B9V 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>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Acid345_2630 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=204669 Acidobacteria bacterium Ellin345])</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=6b9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b9v OCA], [http://pdbe.org/6b9v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b9v RCSB], [http://www.ebi.ac.uk/pdbsum/6b9v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b9v 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=6b9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b9v OCA], [http://pdbe.org/6b9v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b9v RCSB], [http://www.ebi.ac.uk/pdbsum/6b9v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b9v ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Flavins are notoriously photolabile, but while the photoproducts derived from the iso-alloxazine ring are well known the other photoproducts are not. In the case of FAD, typically the main cellular flavin, the other photoproducts are predicted to include four- and five-carbon sugars linked to ADP. These FAD photoproducts were shown to be potent glycating agents, more so than ADP-ribose. Such toxic compounds would require disposal via an ADP-sugar diphosphatase or other route. Comparative analysis of bacterial genomes uncovered a candidate disposal gene that is chromosomally clustered with genes for FAD synthesis or transport and is predicted to encode a protein of the PhnP cyclic phosphodiesterase family. The representative PhnP family enzyme from Koribacter versatilis (here named Fpd, FAD photoproduct diphosphatase) was found to have high, Mn(2+)-dependent diphosphatase activity against FAD photoproducts, FAD, and ADP-ribose, but almost no phosphodiesterase activity against riboflavin 4',5'-cyclic phosphate, a chemical breakdown product of FAD. To provide a structural basis of the unique Fpd activity, the crystal structure of K. versatilis Fpd was determined. The results place Fpd in the broad metallo-beta-lactamase-like family of hydrolases, a diverse family commonly using two metals for hydrolytic catalysis. The active site of Fpd contains two Mn(2+) ions and a bound phosphate, consistent with a diphosphatase mechanism. Our results characterize the first PhnP family member that is a diphosphatase rather than a cyclic phosphodiesterase and suggest its involvement in a cellular damage-control system that efficiently hydrolyzes the reactive, ADP-ribose-like products of FAD photodegradation.
		+
		+	An unusual diphosphatase from the PhnP family cleaves reactive FAD photoproducts.,Beaudoin GAW, Li Q, Bruner SD, Hanson AD Biochem J. 2018 Jan 11;475(1):261-272. doi: 10.1042/BCJ20170817. PMID:29229761<ref>PMID:29229761</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6b9v" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Acidobacteria bacterium ellin345]]
		+	[[Category: Large Structures]]
	[[Category: Bruner, S D]]		[[Category: Bruner, S D]]
	[[Category: Li, Q]]		[[Category: Li, Q]]

OCA at 07:54, 17 October 2018

OCA — Wed, 17 Oct 2018 07:54:06 GMT

←Older revision		Revision as of 07:54, 17 October 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 6b9v is ~~ON HOLD until Paper Publication~~	+	==Crystal Structure of a New Diphosphatase from the PhnP Family==
-		+	<StructureSection load='6b9v' size='340' side='right' caption='[[6b9v]], [[Resolution\|resolution]] 1.88Å' scene=''>
-	~~Authors~~: Li, Q., ~~Bruner~~, S.D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6b9v]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B9V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B9V FirstGlance]. <br>
-	~~Description: Crystal Structure of a New Diphosphatase from the PhnP Family~~	+	</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>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6b9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b9v OCA], [http://pdbe.org/6b9v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b9v RCSB], [http://www.ebi.ac.uk/pdbsum/6b9v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b9v ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bruner, S D]]
	[[Category: Li, Q]]		[[Category: Li, Q]]
-	[[Category: ~~Bruner, S.D~~]]	+	[[Category: Diphosphatase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Metallo-beta-lactamase-like hydrolase]]

OCA: Protected "6b9v" [edit=sysop:move=sysop]

OCA — Wed, 01 Nov 2017 04:52:52 GMT

Protected "6b9v" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:52, 1 November 2017

OCA: New page: '''Unreleased structure''' The entry 6b9v is ON HOLD until Paper Publication Authors: Li, Q., Bruner, S.D. Description: Crystal Structure of a New Diphosphatase from the PhnP Family [[...

OCA — Wed, 01 Nov 2017 04:52:51 GMT

New page: '''Unreleased structure''' The entry 6b9v is ON HOLD until Paper Publication Authors: Li, Q., Bruner, S.D. Description: Crystal Structure of a New Diphosphatase from the PhnP Family [[...

New page

'''Unreleased structure'''

The entry 6b9v is ON HOLD until Paper Publication

Authors: Li, Q., Bruner, S.D.

Description: Crystal Structure of a New Diphosphatase from the PhnP Family
[[Category: Unreleased Structures]]
[[Category: Li, Q]]
[[Category: Bruner, S.D]]