6cyj - Revision history

OCA at 15:13, 4 October 2023

2023-10-04T15:13:50Z

←Older revision		Revision as of 15:13, 4 October 2023
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	<StructureSection load='6cyj' size='340' side='right'caption='[[6cyj]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='6cyj' size='340' side='right'caption='[[6cyj]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cyj]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Myctu Myctu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CYJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6CYJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cyj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CYJ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=SCA:SUCCINYL~~-~~COENZYME+A'>SCA</scene>~~, ~~<scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 2.699Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[6cz6\|6cz6]], [[6cyy\|6cyy]], [[6d2s\|6d2s]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SCA:SUCCINYL-COENZYME+A'>SCA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]<~~/b></td>~~<td class="sblockDat">prpR, Rv1129c, RVBD_1129c, P425_01178 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])~~</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=6cyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cyj OCA], [https://pdbe.org/6cyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cyj RCSB], [https://www.ebi.ac.uk/pdbsum/6cyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cyj 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=6cyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cyj OCA], [~~http~~://pdbe.org/6cyj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6cyj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6cyj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6cyj ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PRPR_MYCTU PRPR_MYCTU]] Plays a key role in regulating expression of enzymes involved in the catabolism of short chain fatty acids (SCFA) via both the glyoxylate (acetyl degradation route) and the methylcitrate cycle (propionate degradation route) (PubMed:22916289, PubMed:24705740). Required for intracellular growth in macrophages and for the assimilation of cholesterol-derived propionate (PubMed:22365605). PrpR acts as a transcriptional activator of prpDC and icl genes when propionate is the main carbon source, and as a ramB repressor (PubMed:22916289). During growth on propionate, PrpR also acts as a transcriptional repressor of dnaA, which encodes the DnaA initiator protein responsible for initiating chromosomal replication (PubMed:24705740). It is possibly involved in the regulation of genes responsible for controlling cholesterol utilization (PubMed:22365605).<ref>PMID:22365605</ref> <ref>PMID:22916289</ref> <ref>PMID:24705740</ref>	+	[https://www.uniprot.org/uniprot/PRPR_MYCTU PRPR_MYCTU] Plays a key role in regulating expression of enzymes involved in the catabolism of short chain fatty acids (SCFA) via both the glyoxylate (acetyl degradation route) and the methylcitrate cycle (propionate degradation route) (PubMed:22916289, PubMed:24705740). Required for intracellular growth in macrophages and for the assimilation of cholesterol-derived propionate (PubMed:22365605). PrpR acts as a transcriptional activator of prpDC and icl genes when propionate is the main carbon source, and as a ramB repressor (PubMed:22916289). During growth on propionate, PrpR also acts as a transcriptional repressor of dnaA, which encodes the DnaA initiator protein responsible for initiating chromosomal replication (PubMed:24705740). It is possibly involved in the regulation of genes responsible for controlling cholesterol utilization (PubMed:22365605).<ref>PMID:22365605</ref> <ref>PMID:22916289</ref> <ref>PMID:24705740</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 6cyj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6cyj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Transcriptional activator 3D structures\|Transcriptional activator 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Myctu~~]]	+	[[Category: Mycobacterium tuberculosis H37Rv]]
-	[[Category: Sacchettini, J]]	+	[[Category: Sacchettini J]]
-	[[Category: Tang, S]]	+	[[Category: Tang S]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcriptional regulator~~]]	+

OCA at 09:27, 30 October 2019

2019-10-30T09:27:09Z

←Older revision		Revision as of 09:27, 30 October 2019
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	<StructureSection load='6cyj' size='340' side='right'caption='[[6cyj]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='6cyj' size='340' side='right'caption='[[6cyj]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cyj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CYJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cyj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CYJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SCA:SUCCINYL-COENZYME+A'>SCA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SCA:SUCCINYL-COENZYME+A'>SCA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6cz6\|6cz6]], [[6cyy\|6cyy]], [[6d2s\|6d2s]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6cz6\|6cz6]], [[6cyy\|6cyy]], [[6d2s\|6d2s]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">prpR, Rv1129c, RVBD_1129c, P425_01178 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</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=6cyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cyj OCA], [http://pdbe.org/6cyj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cyj RCSB], [http://www.ebi.ac.uk/pdbsum/6cyj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cyj 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=6cyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cyj OCA], [http://pdbe.org/6cyj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cyj RCSB], [http://www.ebi.ac.uk/pdbsum/6cyj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cyj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/PRPR_MYCTU PRPR_MYCTU]] Plays a key role in regulating expression of enzymes involved in the catabolism of short chain fatty acids (SCFA) via both the glyoxylate (acetyl degradation route) and the methylcitrate cycle (propionate degradation route) (PubMed:22916289, PubMed:24705740). Required for intracellular growth in macrophages and for the assimilation of cholesterol-derived propionate (PubMed:22365605). PrpR acts as a transcriptional activator of prpDC and icl genes when propionate is the main carbon source, and as a ramB repressor (PubMed:22916289). During growth on propionate, PrpR also acts as a transcriptional repressor of dnaA, which encodes the DnaA initiator protein responsible for initiating chromosomal replication (PubMed:24705740). It is possibly involved in the regulation of genes responsible for controlling cholesterol utilization (PubMed:22365605).<ref>PMID:22365605</ref> <ref>PMID:22916289</ref> <ref>PMID:24705740</ref>		[[http://www.uniprot.org/uniprot/PRPR_MYCTU PRPR_MYCTU]] Plays a key role in regulating expression of enzymes involved in the catabolism of short chain fatty acids (SCFA) via both the glyoxylate (acetyl degradation route) and the methylcitrate cycle (propionate degradation route) (PubMed:22916289, PubMed:24705740). Required for intracellular growth in macrophages and for the assimilation of cholesterol-derived propionate (PubMed:22365605). PrpR acts as a transcriptional activator of prpDC and icl genes when propionate is the main carbon source, and as a ramB repressor (PubMed:22916289). During growth on propionate, PrpR also acts as a transcriptional repressor of dnaA, which encodes the DnaA initiator protein responsible for initiating chromosomal replication (PubMed:24705740). It is possibly involved in the regulation of genes responsible for controlling cholesterol utilization (PubMed:22365605).<ref>PMID:22365605</ref> <ref>PMID:22916289</ref> <ref>PMID:24705740</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The pathogenicity of Mycobacterium tuberculosis depends upon its ability to catabolize host cholesterol. Upregulation of the methylcitrate cycle (MCC) is required to assimilate and detoxify propionyl-CoA, a cholesterol degradation product. The transcription of key genes prpC and prpD in MCC is activated by MtPrpR, a member of a family of prokaryotic transcription factors whose structures and modes of action have not been clearly defined. We show that MtPrpR has a novel overall structure and directly binds to CoA or short-chain acyl-CoA derivatives to form a homotetramer that covers the binding cavity and locks CoA tightly inside the protein. The regulation of this process involves a [4Fe4S] cluster located close to the CoA-binding cavity on a neighboring chain. Mutations in the [4Fe4S] cluster binding residues rendered MtPrpR incapable of regulating MCC gene transcription. The structure of MtPrpR without the [4Fe4S] cluster-binding region shows a conformational change that prohibits CoA binding. The stability of this cluster means it is unlikely a redox sensor but may function by sensing ambient iron levels. These results provide mechanistic insights into this family of critical transcription factors who share similar structures and regulate gene transcription using a combination of acyl-CoAs and [4Fe4S] cluster.
		+
		+	Structural and functional insight into the Mycobacterium tuberculosis protein PrpR reveals a novel type of transcription factor.,Tang S, Hicks ND, Cheng YS, Silva A, Fortune SM, Sacchettini JC Nucleic Acids Res. 2019 Oct 10;47(18):9934-9949. doi: 10.1093/nar/gkz724. PMID:31504787<ref>PMID:31504787</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6cyj" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Myctu]]
	[[Category: Sacchettini, J]]		[[Category: Sacchettini, J]]
	[[Category: Tang, S]]		[[Category: Tang, S]]

OCA at 05:50, 17 April 2019

2019-04-17T05:50:51Z

←Older revision		Revision as of 05:50, 17 April 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6cyj is ~~ON HOLD until Paper Publication~~	+	==Mycobacterium tuberculosis transcriptional regulator==
-		+	<StructureSection load='6cyj' size='340' side='right'caption='[[6cyj]], [[Resolution\|resolution]] 2.70Å' scene=''>
-	~~Authors~~: ~~Tang~~, S., ~~Sacchettini~~, J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6cyj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CYJ FirstGlance]. <br>
-	~~Description~~: ~~Mycobacterium tuberculosis~~ transcriptional ~~regulator~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SCA:SUCCINYL-COENZYME+A'>SCA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6cz6\|6cz6]], [[6cyy\|6cyy]], [[6d2s\|6d2s]]</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=6cyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cyj OCA], [http://pdbe.org/6cyj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cyj RCSB], [http://www.ebi.ac.uk/pdbsum/6cyj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cyj ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PRPR_MYCTU PRPR_MYCTU]] Plays a key role in regulating expression of enzymes involved in the catabolism of short chain fatty acids (SCFA) via both the glyoxylate (acetyl degradation route) and the methylcitrate cycle (propionate degradation route) (PubMed:22916289, PubMed:24705740). Required for intracellular growth in macrophages and for the assimilation of cholesterol-derived propionate (PubMed:22365605). PrpR acts as a transcriptional activator of prpDC and icl genes when propionate is the main carbon source, and as a ramB repressor (PubMed:22916289). During growth on propionate, PrpR also acts as a transcriptional repressor of dnaA, which encodes the DnaA initiator protein responsible for initiating chromosomal replication (PubMed:24705740). It is possibly involved in the regulation of genes responsible for controlling cholesterol utilization (PubMed:22365605).<ref>PMID:22365605</ref> <ref>PMID:22916289</ref> <ref>PMID:24705740</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Sacchettini, J]]
	[[Category: Tang, S]]		[[Category: Tang, S]]
-	[[Category: ~~Sacchettini, J~~]]	+	[[Category: Dna binding protein]]
		+	[[Category: Transcription]]
		+	[[Category: Transcriptional regulator]]

OCA at 04:03, 25 April 2018

2018-04-25T04:03:44Z

←Older revision		Revision as of 04:03, 25 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Tang, S., Sacchettini, J.		Authors: Tang, S., Sacchettini, J.

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

2018-04-11T12:34:56Z

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

←Older revision

Revision as of 12:34, 11 April 2018

OCA: New page: '''Unreleased structure''' The entry 6cyj is ON HOLD Authors: Tang, S., Sacchettini, J. Description: Mycobacterium tuberculosis transcriptional regulator [[Category: Unreleased Structu...

2018-04-11T12:34:55Z

New page: '''Unreleased structure''' The entry 6cyj is ON HOLD Authors: Tang, S., Sacchettini, J. Description: Mycobacterium tuberculosis transcriptional regulator [[Category: Unreleased Structu...

New page

'''Unreleased structure'''

The entry 6cyj is ON HOLD

Authors: Tang, S., Sacchettini, J.

Description: Mycobacterium tuberculosis transcriptional regulator
[[Category: Unreleased Structures]]
[[Category: Tang, S]]
[[Category: Sacchettini, J]]