6qkb - Revision history

OCA at 12:02, 24 January 2024

OCA — Wed, 24 Jan 2024 12:02:41 GMT

←Older revision		Revision as of 12:02, 24 January 2024
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	<StructureSection load='6qkb' size='340' side='right'caption='[[6qkb]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='6qkb' size='340' side='right'caption='[[6qkb]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6qkb]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_17741 Atcc 17741~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QKB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6QKB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6qkb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QKB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QKB FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=MG:MAGNESIUM+ION'>MG</scene~~>, ~~<scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 1.701Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Pden_3919 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=266 ATCC 17741])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=6qkb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qkb OCA], [~~http~~://pdbe.org/6qkb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6qkb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6qkb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6qkb 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=6qkb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qkb OCA], [https://pdbe.org/6qkb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qkb RCSB], [https://www.ebi.ac.uk/pdbsum/6qkb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qkb ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/BHCC_PARDP BHCC_PARDP] Catalyzes the condensation of glyoxylate and glycine into (2R,3S)-beta-hydroxyaspartate ((3S)-3-hydroxy-D-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). Is also able to catalyze the reverse reaction in vitro, i.e. the cleavage of (3S)-3-hydroxy-D-aspartate, and that of D-threonine to a lesser extent.<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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	</div>		</div>
	<div class="pdbe-citations 6qkb" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6qkb" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aldolase 3D structures\|Aldolase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 17741]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Borzyskowski, L Schada von~~]]	+	[[Category: Paracoccus denitrificans]]
-	[[Category: Erb~~, T J~~]]	+	[[Category: Erb TJ]]
-	[[Category: Gilardet, A]]	+	[[Category: Gilardet A]]
-	[[Category: ~~Zarzycki, J~~]]	+	[[Category: Schada von Borzyskowski L]]
-	[[Category: ~~Beta-hydroxyaspartate aldolase]]~~	+	[[Category: Zarzycki J]]
-	~~[[Category: Lyase~~]]	+

OCA at 09:22, 27 November 2019

OCA — Wed, 27 Nov 2019 09:22:25 GMT

←Older revision		Revision as of 09:22, 27 November 2019
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	<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=6qkb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qkb OCA], [http://pdbe.org/6qkb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qkb RCSB], [http://www.ebi.ac.uk/pdbsum/6qkb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qkb 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=6qkb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qkb OCA], [http://pdbe.org/6qkb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qkb RCSB], [http://www.ebi.ac.uk/pdbsum/6qkb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qkb 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 6qkb" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:35, 16 October 2019

OCA — Wed, 16 Oct 2019 07:35:03 GMT

←Older revision		Revision as of 07:35, 16 October 2019
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	<StructureSection load='6qkb' size='340' side='right'caption='[[6qkb]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='6qkb' size='340' side='right'caption='[[6qkb]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6qkb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QKB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QKB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6qkb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_17741 Atcc 17741]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QKB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QKB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pden_3919 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266 ATCC 17741])</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=6qkb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qkb OCA], [http://pdbe.org/6qkb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qkb RCSB], [http://www.ebi.ac.uk/pdbsum/6qkb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qkb 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=6qkb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qkb OCA], [http://pdbe.org/6qkb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qkb RCSB], [http://www.ebi.ac.uk/pdbsum/6qkb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qkb ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 17741]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Borzyskowski, L Schada von]]		[[Category: Borzyskowski, L Schada von]]

OCA at 16:44, 14 August 2019

OCA — Wed, 14 Aug 2019 16:44:33 GMT

←Older revision		Revision as of 16:44, 14 August 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6qkb ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of the beta-hydroxyaspartate aldolase of Paracoccus denitrificans==
-		+	<StructureSection load='6qkb' size='340' side='right'caption='[[6qkb]], [[Resolution\|resolution]] 1.70Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6qkb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QKB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QKB FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=6qkb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qkb OCA], [http://pdbe.org/6qkb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qkb RCSB], [http://www.ebi.ac.uk/pdbsum/6qkb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qkb ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Borzyskowski, L Schada von]]
		+	[[Category: Erb, T J]]
		+	[[Category: Gilardet, A]]
		+	[[Category: Zarzycki, J]]
		+	[[Category: Beta-hydroxyaspartate aldolase]]
		+	[[Category: Lyase]]

OCA at 05:48, 6 March 2019

OCA — Wed, 06 Mar 2019 05:48:45 GMT

←Older revision		Revision as of 05:48, 6 March 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6qkb is ON HOLD	+	The entry 6qkb is ON HOLD until Paper Publication

	Authors:		Authors:

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

OCA — Wed, 13 Feb 2019 07:59:08 GMT

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

←Older revision

Revision as of 07:59, 13 February 2019

OCA: New page: '''Unreleased structure''' The entry 6qkb is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 13 Feb 2019 07:59:06 GMT

New page: '''Unreleased structure''' The entry 6qkb is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6qkb is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]