6p5x - Revision history

OCA at 07:23, 11 October 2023

2023-10-11T07:23:37Z

←Older revision		Revision as of 07:23, 11 October 2023
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	<StructureSection load='6p5x' size='340' side='right'caption='[[6p5x]], [[Resolution\|resolution]] 1.97Å' scene=''>		<StructureSection load='6p5x' size='340' side='right'caption='[[6p5x]], [[Resolution\|resolution]] 1.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6p5x]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P5X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6P5X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6p5x]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P5X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6P5X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SHN:3,3,3,3-[(7S,8S,12S,13S)-3,8,13,17-tetrakis(carboxymethyl)-8,13-dimethyl-7,8,12,13-tetrahydroporphyrin-2,7,12,18-tetrayl]tetrapropanoic+acid'>SHN</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]] 1.97Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uroporphyrinogen-III_C-methyltransferase Uroporphyrinogen-III C-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.107 2.1.1.107] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SHN:3,3,3,3-[(7S,8S,12S,13S)-3,8,13,17-tetrakis(carboxymethyl)-8,13-dimethyl-7,8,12,13-tetrahydroporphyrin-2,7,12,18-tetrayl]tetrapropanoic+acid'>SHN</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=6p5x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p5x OCA], [~~http~~://pdbe.org/6p5x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6p5x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6p5x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6p5x 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=6p5x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p5x OCA], [https://pdbe.org/6p5x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6p5x RCSB], [https://www.ebi.ac.uk/pdbsum/6p5x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6p5x ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~A0A0F7JCI1_SALER A0A0F7JCI1_SALER]~~] Multifunctional enzyme that catalyzes the SAM-dependent methylations of uroporphyrinogen III at position C-2 and C-7 to form precorrin-2 via precorrin-1. Then it catalyzes the NAD-dependent ring dehydrogenation of precorrin-2 to yield sirohydrochlorin. Finally, it catalyzes the ferrochelation of sirohydrochlorin to yield siroheme.~~[HAMAP-Rule~~:~~MF_01646][SAAS:SAAS00971394]~~	+	[https://www.uniprot.org/uniprot/CYSG_SALTY CYSG_SALTY] Multifunctional enzyme that catalyzes the SAM-dependent methylations of uroporphyrinogen III at position C-2 and C-7 to form precorrin-2 via precorrin-1. Then it catalyzes the NAD-dependent ring dehydrogenation of precorrin-2 to yield sirohydrochlorin. Finally, it catalyzes the ferrochelation of sirohydrochlorin to yield siroheme.<ref>PMID:14595395</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 6p5x" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6p5x" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Siroheme synthase\|Siroheme synthase]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Uroporphyrinogen-III C-methyltransferase~~]]	+	[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
-	[[Category: Pennington~~, J M~~]]	+	[[Category: Pennington JM]]
-	[[Category: Stroupe~~, M E]]~~	+	[[Category: Stroupe ME]]
-	~~[[Category: Biosynthetic protein]]~~	+
-	~~[[Category: Cysg]]~~	+
-	~~[[Category: Precorrin-2]]~~	+
-	~~[[Category: Sirohydrochlorin]]~~	+
-	~~[[Category: Tetrapyrrole biosynthesis~~]]	+

OCA at 09:19, 26 February 2020

2020-02-26T09:19:08Z

←Older revision		Revision as of 09:19, 26 February 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6p5x is ~~ON HOLD until Paper~~ Publication	+	==Sirohydrochlorin-bound S. typhimurium siroheme synthase==
		+	<StructureSection load='6p5x' size='340' side='right'caption='[[6p5x]], [[Resolution\|resolution]] 1.97Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6p5x]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P5X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P5X FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SHN:3,3,3,3-[(7S,8S,12S,13S)-3,8,13,17-tetrakis(carboxymethyl)-8,13-dimethyl-7,8,12,13-tetrahydroporphyrin-2,7,12,18-tetrayl]tetrapropanoic+acid'>SHN</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uroporphyrinogen-III_C-methyltransferase Uroporphyrinogen-III C-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.107 2.1.1.107] </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=6p5x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p5x OCA], [http://pdbe.org/6p5x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p5x RCSB], [http://www.ebi.ac.uk/pdbsum/6p5x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p5x ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0A0F7JCI1_SALER A0A0F7JCI1_SALER]] Multifunctional enzyme that catalyzes the SAM-dependent methylations of uroporphyrinogen III at position C-2 and C-7 to form precorrin-2 via precorrin-1. Then it catalyzes the NAD-dependent ring dehydrogenation of precorrin-2 to yield sirohydrochlorin. Finally, it catalyzes the ferrochelation of sirohydrochlorin to yield siroheme.[HAMAP-Rule:MF_01646][SAAS:SAAS00971394]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Siroheme is the central cofactor in a conserved class of sulfite and nitrite reductases that catalyze the six-electron reduction of sulfite to sulfide and nitrite to ammonia. In Salmonella enterica serovar Typhimurium, siroheme is produced by a trifunctional enzyme, siroheme synthase (CysG). A bifunctional active site that is distinct from its methyltransferase activity catalyzes the final two steps, NAD(+)-dependent dehydrogenation and iron chelation. How this active site performs such different chemistries is unknown. Here, we report the structures of CysG bound to precorrin-2, the initial substrate; sirohydrochlorin, the dehydrogenation product/chelation substrate; and a cobalt-sirohydrochlorin product. We identified binding poses for all three tetrapyrroles and tested the roles of specific amino acids in both activities to give insights into how a bifunctional active site catalyzes two different chemistries and acts as an iron-specific chelatase in the final step of siroheme synthesis.

-	~~Authors:~~ Pennington, J.M., ~~Stroupe~~, M.E.	+	Siroheme synthase orients substrates for dehydrogenase and chelatase activities in a common active site.,Pennington JM, Kemp M, McGarry L, Chen Y, Stroupe ME Nat Commun. 2020 Feb 13;11(1):864. doi: 10.1038/s41467-020-14722-1. PMID:32054833<ref>PMID:32054833</ref>

-	~~Description: Sirohydrochlorin-bound~~ S. ~~typhimurium siroheme synthase~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Pennington, J.M]]	+	<div class="pdbe-citations 6p5x" style="background-color:#fffaf0;"></div>
-	[[Category: Stroupe, M.E]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Uroporphyrinogen-III C-methyltransferase]]
		+	[[Category: Pennington, J M]]
		+	[[Category: Stroupe, M E]]
		+	[[Category: Biosynthetic protein]]
		+	[[Category: Cysg]]
		+	[[Category: Precorrin-2]]
		+	[[Category: Sirohydrochlorin]]
		+	[[Category: Tetrapyrrole biosynthesis]]

OCA at 13:33, 20 November 2019

2019-11-20T13:33:44Z

←Older revision		Revision as of 13:33, 20 November 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6p5x is ON HOLD	+	The entry 6p5x is ON HOLD until Paper Publication

	Authors: Pennington, J.M., Stroupe, M.E.		Authors: Pennington, J.M., Stroupe, M.E.

OCA at 04:21, 24 July 2019

2019-07-24T04:21:25Z

←Older revision		Revision as of 04:21, 24 July 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6p5x is ON HOLD ~~until sometime in the future~~	+	The entry 6p5x is ON HOLD

	Authors: Pennington, J.M., Stroupe, M.E.		Authors: Pennington, J.M., Stroupe, M.E.

OCA at 05:12, 26 June 2019

2019-06-26T05:12:43Z

←Older revision		Revision as of 05:12, 26 June 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6p5x is ON HOLD	+	The entry 6p5x is ON HOLD until sometime in the future

	Authors: Pennington, J.M., Stroupe, M.E.		Authors: Pennington, J.M., Stroupe, M.E.

OCA: Protected "6p5x" [edit=sysop:move=sysop]

2019-06-12T04:03:01Z

Protected "6p5x" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:03, 12 June 2019

OCA: New page: '''Unreleased structure''' The entry 6p5x is ON HOLD Authors: Pennington, J.M., Stroupe, M.E. Description: Sirohydrochlorin-bound S. typhimurium siroheme synthase [[Category: Unrelease...

2019-06-12T04:03:00Z

New page: '''Unreleased structure''' The entry 6p5x is ON HOLD Authors: Pennington, J.M., Stroupe, M.E. Description: Sirohydrochlorin-bound S. typhimurium siroheme synthase [[Category: Unrelease...

New page

'''Unreleased structure'''

The entry 6p5x is ON HOLD

Authors: Pennington, J.M., Stroupe, M.E.

Description: Sirohydrochlorin-bound S. typhimurium siroheme synthase
[[Category: Unreleased Structures]]
[[Category: Pennington, J.M]]
[[Category: Stroupe, M.E]]