6ple - Revision history

OCA at 07:31, 11 October 2023

OCA — Wed, 11 Oct 2023 07:31:38 GMT

←Older revision		Revision as of 07:31, 11 October 2023
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	<StructureSection load='6ple' size='340' side='right'caption='[[6ple]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='6ple' size='340' side='right'caption='[[6ple]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ple]] 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=6PLE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6PLE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ple]] 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=6PLE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PLE FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</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]] 2.5Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">mhuD, Rv3592 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5&~~id=83332 MYCTU])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene></td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>[http://en.wikipedia.org/wiki/Heme_oxygenase_(mycobilin-producing) Heme oxygenase (mycobilin-producing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.57 1.14.99.57] </~~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=6ple FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ple OCA], [https://pdbe.org/6ple PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ple RCSB], [https://www.ebi.ac.uk/pdbsum/6ple PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ple 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=6ple FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ple OCA], [~~http~~://pdbe.org/6ple PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ple RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ple PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ple ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MHUD_MYCTU MHUD_MYCTU]] Catalyzes the oxidative degradation of the heme macrocyclic porphyrin ring in the presence of a suitable electron donor such as ascorbate or NADPH--cytochrome P450 reductase, with subsequent release of free iron.	+	[https://www.uniprot.org/uniprot/MHUD_MYCTU MHUD_MYCTU] Catalyzes the oxidative degradation of the heme macrocyclic porphyrin ring in the presence of a suitable electron donor such as ascorbate or NADPH--cytochrome P450 reductase, with subsequent release of free iron.
	<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 6ple" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6ple" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Heme oxygenase 3D structures\|Heme oxygenase 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: Chao, A]]	+	[[Category: Chao A]]
-	[[Category: Goulding~~, C W]]~~	+	[[Category: Goulding CW]]
-	~~[[Category: Biliverdin]]~~	+
-	~~[[Category: Cell wall]]~~	+
-	~~[[Category: Heme binding]]~~	+
-	~~[[Category: Heme catabolic process]]~~	+
-	~~[[Category: Metal binding protein]]~~	+
-	~~[[Category: Metal ion binding]]~~	+
-	~~[[Category: Monooxygenase activity]]~~	+
-	~~[[Category: Oxidation reduction process]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Oxidoreductase activity]]~~	+
-	~~[[Category: Plasma membrane~~]]	+

OCA at 17:51, 20 November 2019

OCA — Wed, 20 Nov 2019 17:51:43 GMT

←Older revision		Revision as of 17:51, 20 November 2019
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	<StructureSection load='6ple' size='340' side='right'caption='[[6ple]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='6ple' size='340' side='right'caption='[[6ple]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ple]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PLE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PLE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ple]] 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=6PLE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PLE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mhuD, Rv3592 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Heme_oxygenase_(mycobilin-producing) Heme oxygenase (mycobilin-producing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.57 1.14.99.57] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Heme_oxygenase_(mycobilin-producing) Heme oxygenase (mycobilin-producing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.57 1.14.99.57] </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=6ple FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ple OCA], [http://pdbe.org/6ple PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ple RCSB], [http://www.ebi.ac.uk/pdbsum/6ple PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ple 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=6ple FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ple OCA], [http://pdbe.org/6ple PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ple RCSB], [http://www.ebi.ac.uk/pdbsum/6ple PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ple ProSAT]</span></td></tr>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Myctu]]
	[[Category: Chao, A]]		[[Category: Chao, A]]
	[[Category: Goulding, C W]]		[[Category: Goulding, C W]]

OCA at 06:46, 6 November 2019

OCA — Wed, 06 Nov 2019 06:46:09 GMT

←Older revision		Revision as of 06:46, 6 November 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6ple is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of MhuD R26S mutant in complex with biliverdin==
		+	<StructureSection load='6ple' size='340' side='right'caption='[[6ple]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6ple]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PLE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PLE FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Heme_oxygenase_(mycobilin-producing) Heme oxygenase (mycobilin-producing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.57 1.14.99.57] </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=6ple FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ple OCA], [http://pdbe.org/6ple PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ple RCSB], [http://www.ebi.ac.uk/pdbsum/6ple PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ple ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MHUD_MYCTU MHUD_MYCTU]] Catalyzes the oxidative degradation of the heme macrocyclic porphyrin ring in the presence of a suitable electron donor such as ascorbate or NADPH--cytochrome P450 reductase, with subsequent release of free iron.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mycobacterium tuberculosis(Mtb), the causative agent of tuberculosis, requires iron for survival. In Mtb, MhuD is the cytosolic protein that degrades imported heme. MhuD is distinct, both in sequence and structure, from canonical heme oxygenases (HOs) but homologous with IsdG-type proteins. Canonical HO is found mainly in eukaryotes, while IsdG-type proteins are predominantly found in prokaryotes including pathogens. While there are several published structures of MhuD and other IsdG-type proteins in complex with heme substrate, no structures have been reported of IsdG-type proteins in complex with product, unlike HOs. We recently showed that the Mtb variant MhuD-R26S produces biliverdin IXalpha (alphaBV) rather than the wild-type mycobilin isomers as product. Given that mycobilin and other IsdG-type protein products like staphylobilin are difficult to isolate in quantities sufficient for structure determination, here we use the MhuD-R26S variant and its product alphaBV as a proxy to study the IsdG-type protein/product complex. First we show that alphaBV has nanomolar affinity for MhuD and the R26S variant. Second we determined the MhuD-R26S-BV complex structure to 2.5 A, which reveals two notable features (1) two alphaBV molecules bound per active site and (2) a novel alpha-helix (alpha3) unobserved in previous MhuD-heme structures. Finally, through molecular dynamics simulations we show that alpha3 is stable with the proximal alphaBV alone. With MhuD's high affinity for product along with observed structural and electrostatic changes that accompany substrate turnover suggest that there may be an unidentified class of proteins responsible for product extraction from MhuD and other IsdG-type proteins.

-	~~Authors~~:	+	The structure of a Mycobacterium tuberculosis heme-degrading protein, MhuD, variant in complex with its product.,Chao A, Burley K, Sieminski PJ, de Miranda R, Chen X, Mobley DL, Goulding C Biochemistry. 2019 Oct 22. doi: 10.1021/acs.biochem.9b00726. PMID:31638374<ref>PMID:31638374</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6ple" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Chao, A]]
		+	[[Category: Goulding, C W]]
		+	[[Category: Biliverdin]]
		+	[[Category: Cell wall]]
		+	[[Category: Heme binding]]
		+	[[Category: Heme catabolic process]]
		+	[[Category: Metal binding protein]]
		+	[[Category: Metal ion binding]]
		+	[[Category: Monooxygenase activity]]
		+	[[Category: Oxidation reduction process]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Oxidoreductase activity]]
		+	[[Category: Plasma membrane]]

OCA at 13:44, 28 August 2019

OCA — Wed, 28 Aug 2019 13:44:04 GMT

←Older revision		Revision as of 13:44, 28 August 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 10 Jul 2019 04:13:17 GMT

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

←Older revision

Revision as of 04:13, 10 July 2019

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

OCA — Wed, 10 Jul 2019 04:13:16 GMT

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

New page

'''Unreleased structure'''

The entry 6ple is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]