6cxt - Revision history

OCA at 15:13, 4 October 2023

OCA — Wed, 04 Oct 2023 15:13:30 GMT

←Older revision		Revision as of 15:13, 4 October 2023
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	<StructureSection load='6cxt' size='340' side='right'caption='[[6cxt]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='6cxt' size='340' side='right'caption='[[6cxt]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cxt]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Marm1 Marm1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CXT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6CXT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cxt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Marinomonas_mediterranea_MMB-1 Marinomonas mediterranea MMB-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CXT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FK4:S-[2-({N-[(2R)-2-hydroxy-4-{[(R)-hydroxy(oxo)-lambda~5~-phosphanyl]oxy}-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl]+1H-pyrrole-2-carbothioate'>FK4</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]] 1.9Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Marme_4088 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=717774 MARM1]), Marme_4091 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=717774 MARM1])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FK4:S-[2-({N-[(2R)-2-hydroxy-4-{[(R)-hydroxy(oxo)-lambda~5~-phosphanyl]oxy}-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl]+1H-pyrrole-2-carbothioate'>FK4</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Short-chain_acyl-CoA_dehydrogenase Short-chain acyl-CoA dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.8.1 1.3.8.1] </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=6cxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cxt OCA], [https://pdbe.org/6cxt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cxt RCSB], [https://www.ebi.ac.uk/pdbsum/6cxt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cxt 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=6cxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cxt OCA], [~~http~~://pdbe.org/6cxt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6cxt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6cxt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6cxt ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/F2K077_MARM1 F2K077_MARM1]
	<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: ~~Marm1]]~~	+	[[Category: Marinomonas mediterranea MMB-1]]
-	~~[[Category: Short-chain acyl~~-~~CoA dehydrogenase~~]]	+	[[Category: Agarwal V]]
-	[[Category: Agarwal, V]]	+
-	~~[[Category: Acyl carrier protein]]~~	+
-	~~[[Category: Fad-dependent enzyme]]~~	+
-	~~[[Category: Natural product biosynthesis]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 09:53, 18 December 2019

OCA — Wed, 18 Dec 2019 09:53:12 GMT

←Older revision		Revision as of 09:53, 18 December 2019
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	==Crystal structure of FAD-dependent dehydrogenase==		==Crystal structure of FAD-dependent dehydrogenase==
-	<StructureSection load='6cxt' size='340' side='right' caption='[[6cxt]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='6cxt' size='340' side='right'caption='[[6cxt]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6cxt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Marm1 Marm1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CXT FirstGlance]. <br>		<table><tr><td colspan='2'>[[6cxt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Marm1 Marm1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CXT FirstGlance]. <br>
Line 25:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Marm1]]		[[Category: Marm1]]
	[[Category: Short-chain acyl-CoA dehydrogenase]]		[[Category: Short-chain acyl-CoA dehydrogenase]]

OCA at 08:19, 6 March 2019

OCA — Wed, 06 Mar 2019 08:19:34 GMT

←Older revision		Revision as of 08:19, 6 March 2019
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	==Crystal structure of FAD-dependent dehydrogenase==		==Crystal structure of FAD-dependent dehydrogenase==
-	<StructureSection load='6cxt' size='340' side='right' caption='[[6cxt]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='6cxt' size='340' side='right' caption='[[6cxt]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cxt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CXT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cxt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Marm1 Marm1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CXT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FK4:S-[2-({N-[(2R)-2-hydroxy-4-{[(R)-hydroxy(oxo)-lambda~5~-phosphanyl]oxy}-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl]+1H-pyrrole-2-carbothioate'>FK4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FK4:S-[2-({N-[(2R)-2-hydroxy-4-{[(R)-hydroxy(oxo)-lambda~5~-phosphanyl]oxy}-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl]+1H-pyrrole-2-carbothioate'>FK4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Marme_4088 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=717774 MARM1]), Marme_4091 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=717774 MARM1])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Short-chain_acyl-CoA_dehydrogenase Short-chain acyl-CoA dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.8.1 1.3.8.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Short-chain_acyl-CoA_dehydrogenase Short-chain acyl-CoA dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.8.1 1.3.8.1] </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=6cxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cxt OCA], [http://pdbe.org/6cxt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cxt RCSB], [http://www.ebi.ac.uk/pdbsum/6cxt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cxt 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=6cxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cxt OCA], [http://pdbe.org/6cxt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cxt RCSB], [http://www.ebi.ac.uk/pdbsum/6cxt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cxt ProSAT]</span></td></tr>
Line 17:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 6cxt" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6cxt" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Acyl-CoA dehydrogenase 3D structures\|Acyl-CoA dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Marm1]]
	[[Category: Short-chain acyl-CoA dehydrogenase]]		[[Category: Short-chain acyl-CoA dehydrogenase]]
	[[Category: Agarwal, V]]		[[Category: Agarwal, V]]

OCA at 12:05, 16 January 2019

OCA — Wed, 16 Jan 2019 12:05:43 GMT

←Older revision		Revision as of 12:05, 16 January 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6cxt is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of FAD-dependent dehydrogenase==
		+	<StructureSection load='6cxt' size='340' side='right' caption='[[6cxt]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6cxt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CXT FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FK4:S-[2-({N-[(2R)-2-hydroxy-4-{[(R)-hydroxy(oxo)-lambda~5~-phosphanyl]oxy}-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl]+1H-pyrrole-2-carbothioate'>FK4</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Short-chain_acyl-CoA_dehydrogenase Short-chain acyl-CoA dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.8.1 1.3.8.1] </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=6cxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cxt OCA], [http://pdbe.org/6cxt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cxt RCSB], [http://www.ebi.ac.uk/pdbsum/6cxt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cxt ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Sequential enzymatic reactions on substrates tethered to carrier proteins (CPs) generates thiotemplated building blocks that are then delivered to non-ribosomal peptide synthetases (NRPSs) to generate peptidic natural products. The underlying diversity of these thiotemplated building blocks is the principal driver of the chemical diversity of NRPS-derived natural products. Structural insights into recognition of CPs by tailoring enzymes that generate these building blocks are sparse. Here we present the crystal structure of a flavin-dependent prolyl oxidase that furnishes thiotemplated pyrrole as the product, in complex with its cognate CP in the holo- and product bound states. The thiotemplated pyrrole is an intermediate that is well represented in natural product biosynthetic pathways. Our results delineate the interactions between the CP and the oxidase, while also providing insights into the stereospecificity of the enzymatic oxidation of the prolyl heterocycle to the aromatic pyrrole. Biochemical validation of the interaction between the CP and the oxidase demonstrates that NRPSs recognize and bind to their CPs using interactions quite different to that from fatty acid and polyketide biosynthetic enzymes. Our results posit that structural diversity in natural product biosynthesis can be, and is, derived from subtle modifications of primary metabolic enzymes.

-	~~Authors~~:	+	Insights into thiotemplated pyrrole biosynthesis gained by crystal structure of flavin-dependent oxidase in complex with carrier protein.,Thapa HR, Robbins JM, Moore BS, Agarwal V Biochemistry. 2019 Jan 8. doi: 10.1021/acs.biochem.8b01177. PMID:30620182<ref>PMID:30620182</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6cxt" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Short-chain acyl-CoA dehydrogenase]]
		+	[[Category: Agarwal, V]]
		+	[[Category: Acyl carrier protein]]
		+	[[Category: Fad-dependent enzyme]]
		+	[[Category: Natural product biosynthesis]]
		+	[[Category: Oxidoreductase]]

OCA at 04:49, 9 May 2018

OCA — Wed, 09 May 2018 04:49:02 GMT

←Older revision		Revision as of 04:49, 9 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 11 Apr 2018 12:33:15 GMT

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

←Older revision

Revision as of 12:33, 11 April 2018

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

OCA — Wed, 11 Apr 2018 12:33:14 GMT

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

New page

'''Unreleased structure'''

The entry 6cxt is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]