6rqa - Revision history

OCA at 12:26, 24 January 2024

OCA — Wed, 24 Jan 2024 12:26:21 GMT

←Older revision		Revision as of 12:26, 24 January 2024
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	<StructureSection load='6rqa' size='340' side='right'caption='[[6rqa]], [[Resolution\|resolution]] 2.56Å' scene=''>		<StructureSection load='6rqa' size='340' side='right'caption='[[6rqa]], [[Resolution\|resolution]] 2.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6rqa]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pardp Pardp~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RQA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6RQA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6rqa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans_PD1222 Paracoccus denitrificans PD1222]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RQA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RQA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7MT:Tb-Xo4'>7MT</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=TB:TERBIUM(III)+ION'>TB</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]] 2.56Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pden_3918 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318586 PARDP])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7MT:Tb-Xo4'>7MT</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=TB:TERBIUM(III)+ION'>TB</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=6rqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rqa OCA], [~~http~~://pdbe.org/6rqa PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6rqa RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6rqa PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6rqa 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=6rqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rqa OCA], [https://pdbe.org/6rqa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rqa RCSB], [https://www.ebi.ac.uk/pdbsum/6rqa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rqa ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/BHCD_PARDP BHCD_PARDP] Imine reductase that catalyzes the NADH-dependent reduction of iminosuccinate to L-aspartate. Is essential for the growth of P.denitrificans in the presence of glycolate and glyoxylate since it functions in glyoxylate assimilation via the beta-hydroxyaspartate cycle (BHAC). Thereby BhcD regenerates the amino group donor for the first step of the BHAC.<ref>PMID:31723261</ref>
	<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: ~~Pardp~~]]	+	[[Category: Paracoccus denitrificans PD1222]]
-	[[Category: ~~Borzyskowski, L Schada von~~]]	+	[[Category: Erb TJ]]
-	[[Category: ~~Erb, T J~~]]	+	[[Category: Schada von Borzyskowski L]]
-	[[Category: Severi, F]]	+	[[Category: Severi F]]
-	[[Category: Zarzycki, J]]	+	[[Category: Zarzycki J]]
-	~~[[Category: Iminosuccinate reductase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 09:25, 27 November 2019

OCA — Wed, 27 Nov 2019 09:25:02 GMT

←Older revision		Revision as of 09:25, 27 November 2019
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	<StructureSection load='6rqa' size='340' side='right'caption='[[6rqa]], [[Resolution\|resolution]] 2.56Å' scene=''>		<StructureSection load='6rqa' size='340' side='right'caption='[[6rqa]], [[Resolution\|resolution]] 2.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6rqa]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RQA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RQA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6rqa]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pardp Pardp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RQA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RQA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7MT:Tb-Xo4'>7MT</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=TB:TERBIUM(III)+ION'>TB</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7MT:Tb-Xo4'>7MT</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=TB:TERBIUM(III)+ION'>TB</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pden_3918 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318586 PARDP])</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=6rqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rqa OCA], [http://pdbe.org/6rqa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rqa RCSB], [http://www.ebi.ac.uk/pdbsum/6rqa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rqa 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=6rqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rqa OCA], [http://pdbe.org/6rqa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rqa RCSB], [http://www.ebi.ac.uk/pdbsum/6rqa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rqa ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	One of the most abundant sources of organic carbon in the ocean is glycolate, the secretion of which by marine phytoplankton results in an estimated annual flux of one petagram of glycolate in marine environments(1). Although it is generally accepted that glycolate is oxidized to glyoxylate by marine bacteria(2-4), the further fate of this C2 metabolite is not well understood. Here we show that ubiquitous marine Proteobacteria are able to assimilate glyoxylate via the beta-hydroxyaspartate cycle (BHAC) that was originally proposed 56 years ago(5). We elucidate the biochemistry of the BHAC and describe the structure of its key enzymes, including a previously unknown primary imine reductase. Overall, the BHAC enables the direct production of oxaloacetate from glyoxylate through only four enzymatic steps, representing-to our knowledge-the most efficient glyoxylate assimilation route described to date. Analysis of marine metagenomes shows that the BHAC is globally distributed and on average 20-fold more abundant than the glycerate pathway, the only other known pathway for net glyoxylate assimilation. In a field study of a phytoplankton bloom, we show that glycolate is present in high nanomolar concentrations and taken up by prokaryotes at rates that allow a full turnover of the glycolate pool within one week. During the bloom, genes that encode BHAC key enzymes are present in up to 1.5% of the bacterial community and actively transcribed, supporting the role of the BHAC in glycolate assimilation and suggesting a previously undescribed trophic interaction between autotrophic phytoplankton and heterotrophic bacterioplankton.
		+
		+	Marine Proteobacteria metabolize glycolate via the beta-hydroxyaspartate cycle.,Schada von Borzyskowski L, Severi F, Kruger K, Hermann L, Gilardet A, Sippel F, Pommerenke B, Claus P, Cortina NS, Glatter T, Zauner S, Zarzycki J, Fuchs BM, Bremer E, Maier UG, Amann RI, Erb TJ Nature. 2019 Nov;575(7783):500-504. doi: 10.1038/s41586-019-1748-4. Epub 2019 Nov, 13. PMID:31723261<ref>PMID:31723261</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6rqa" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Pardp]]
	[[Category: Borzyskowski, L Schada von]]		[[Category: Borzyskowski, L Schada von]]
	[[Category: Erb, T J]]		[[Category: Erb, T J]]

OCA at 16:45, 14 August 2019

OCA — Wed, 14 Aug 2019 16:45:51 GMT

←Older revision		Revision as of 16:45, 14 August 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6rqa ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of the iminosuccinate reductase of Paracoccus denitrificans in complex with NAD+==
-		+	<StructureSection load='6rqa' size='340' side='right'caption='[[6rqa]], [[Resolution\|resolution]] 2.56Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6rqa]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RQA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RQA FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7MT:Tb-Xo4'>7MT</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=TB:TERBIUM(III)+ION'>TB</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=6rqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rqa OCA], [http://pdbe.org/6rqa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rqa RCSB], [http://www.ebi.ac.uk/pdbsum/6rqa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rqa ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Borzyskowski, L Schada von]]
		+	[[Category: Erb, T J]]
		+	[[Category: Severi, F]]
		+	[[Category: Zarzycki, J]]
		+	[[Category: Iminosuccinate reductase]]
		+	[[Category: Oxidoreductase]]

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

OCA — Wed, 22 May 2019 04:21:27 GMT

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

←Older revision

Revision as of 04:21, 22 May 2019

OCA: New page: '''Unreleased structure''' The entry 6rqa is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 22 May 2019 04:21:25 GMT

New page: '''Unreleased structure''' The entry 6rqa is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6rqa is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]