6xub - Revision history

OCA at 13:12, 24 January 2024

OCA — Wed, 24 Jan 2024 13:12:50 GMT

←Older revision		Revision as of 13:12, 24 January 2024
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	<StructureSection load='6xub' size='340' side='right'caption='[[6xub]], [[Resolution\|resolution]] 1.78Å' scene=''>		<StructureSection load='6xub' size='340' side='right'caption='[[6xub]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6xub]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_diphtheriae"_kruse_in_flugge_1886 "bacillus~~ diphtheriae~~" kruse in flugge 1886~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XUB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6XUB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xub]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XUB FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=VOV:harderoheme+(III)'>VOV</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]] 1.78Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>B11Q_01470, BT093_04375 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1717~~ "~~Bacillus diphtheriae~~" ~~Kruse in Flugge 1886]~~)</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=VOV:harderoheme+(III)'>VOV</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6xub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xub OCA], [~~http~~://pdbe.org/6xub PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6xub RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6xub PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6xub 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=6xub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xub OCA], [https://pdbe.org/6xub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xub RCSB], [https://www.ebi.ac.uk/pdbsum/6xub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xub ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q6NGV6_CORDI Q6NGV6_CORDI] Involved in coproporphyrin-dependent heme b biosynthesis. Catalyzes the decarboxylation of Fe-coproporphyrin III (coproheme) to heme b (protoheme IX), the last step of the pathway. The reaction occurs in a stepwise manner with a three-propionate intermediate.[HAMAP-Rule:MF_02244]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ diphtheriae ~~kruse in flugge 1886~~]]	+	[[Category: Corynebacterium diphtheriae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Djinovic-Carugo, K]]	+	[[Category: Djinovic-Carugo K]]
-	[[Category: Furtmueller~~, P G~~]]	+	[[Category: Furtmueller PG]]
-	[[Category: Hofbauer, S]]	+	[[Category: Hofbauer S]]
-	[[Category: Lier, B]]	+	[[Category: Lier B]]
-	[[Category: Michlits, H]]	+	[[Category: Michlits H]]
-	[[Category: Obinger, C]]	+	[[Category: Obinger C]]
-	[[Category: Oostenbrink, C]]	+	[[Category: Oostenbrink C]]
-	[[Category: Pfanzagl, V]]	+	[[Category: Pfanzagl V]]
-	~~[[Category: Actinobacterial]]~~	+
-	~~[[Category: Coproheme decarboxylase]]~~	+
-	~~[[Category: Decarboxylation]]~~	+
-	~~[[Category: Ferredoxin like]]~~	+
-	~~[[Category: Heme b biosynthesis]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 06:51, 10 June 2020

OCA — Wed, 10 Jun 2020 06:51:02 GMT

←Older revision		Revision as of 06:51, 10 June 2020
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	==Structure of coproheme decarboxylase from Corynebacterium diphteriae in complex with monovinyl monopropionyl deuteroheme==		==Structure of coproheme decarboxylase from Corynebacterium diphteriae in complex with monovinyl monopropionyl deuteroheme==
-	<StructureSection load='6xub' size='340' side='right'caption='[[6xub]]' scene=''>	+	<StructureSection load='6xub' size='340' side='right'caption='[[6xub]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XUB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6XUB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xub]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_diphtheriae"_kruse_in_flugge_1886 "bacillus diphtheriae" kruse in flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XUB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6XUB FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6xub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xub OCA], [http://pdbe.org/6xub PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6xub RCSB], [http://www.ebi.ac.uk/pdbsum/6xub PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6xub ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=VOV:harderoheme+(III)'>VOV</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">B11Q_01470, BT093_04375 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1717 "Bacillus diphtheriae" Kruse in Flugge 1886])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6xub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xub OCA], [http://pdbe.org/6xub PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6xub RCSB], [http://www.ebi.ac.uk/pdbsum/6xub PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6xub ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Coproheme decarboxylases (ChdCs) catalyze the final step in heme b biosynthesis of monoderm and some diderm bacteria. In this reaction, coproheme is converted to heme b via monovinyl monopropionate deuteroheme (MMD) in two consecutive decarboxylation steps. In Firmicutes decarboxylation of propionates 2 and 4 of coproheme depend on hydrogen peroxide and the presence of a catalytic tyrosine. Here we demonstrate that ChdCs from Actinobacteria are unique in using a histidine (H118 in ChdC from Corynebacterium diphtheriae, CdChdC) as a distal base in addition to the redox-active tyrosine (Y135). We present the X-ray crystal structures of coproheme-CdChdC and MMD-CdChdC, which clearly show (i) differences in the active site architecture between Firmicutes and Actinobacteria and (ii) rotation of the redox-active reaction intermediate (MMD) after formation of the vinyl group at position 2. Distal H118 is shown to catalyze the heterolytic cleavage of hydrogen peroxide (k app = (4.90 +/- 1.25) x 10(4) M(-1) s(-1)). The resulting Compound I is rapidly converted to a catalytically active Compound I* (oxoiron(IV) Y135(*)) that initiates the radical decarboxylation reactions. As a consequence of the more efficient Compound I formation, actinobacterial ChdCs exhibit a higher catalytic efficiency in comparison to representatives from Firmicutes. On the basis of the kinetic data of wild-type CdChdC and the variants H118A, Y135A, and H118A/Y135A together with high-resolution crystal structures and molecular dynamics simulations, we present a molecular mechanism for the hydrogen peroxide dependent conversion of coproheme via MMD to heme b and discuss differences between ChdCs from Actinobacteria and Firmicutes.
		+
		+	Actinobacterial Coproheme Decarboxylases Use Histidine as a Distal Base to Promote Compound I Formation.,Michlits H, Lier B, Pfanzagl V, Djinovic-Carugo K, Furtmuller PG, Oostenbrink C, Obinger C, Hofbauer S ACS Catal. 2020 May 15;10(10):5405-5418. doi: 10.1021/acscatal.0c00411. Epub 2020, Apr 9. PMID:32440366<ref>PMID:32440366</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6xub" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus diphtheriae kruse in flugge 1886]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Djinovic-Carugo K]]	+	[[Category: Djinovic-Carugo, K]]
-	[[Category: Furtmueller PG]]	+	[[Category: Furtmueller, P G]]
-	[[Category: Hofbauer S]]	+	[[Category: Hofbauer, S]]
-	[[Category: Lier B]]	+	[[Category: Lier, B]]
-	[[Category: Michlits H]]	+	[[Category: Michlits, H]]
-	[[Category: Obinger C]]	+	[[Category: Obinger, C]]
-	[[Category: Oostenbrink C]]	+	[[Category: Oostenbrink, C]]
-	[[Category: Pfanzagl V]]	+	[[Category: Pfanzagl, V]]
		+	[[Category: Actinobacterial]]
		+	[[Category: Coproheme decarboxylase]]
		+	[[Category: Decarboxylation]]
		+	[[Category: Ferredoxin like]]
		+	[[Category: Heme b biosynthesis]]
		+	[[Category: Oxidoreductase]]

OCA at 05:49, 22 April 2020

OCA — Wed, 22 Apr 2020 05:49:16 GMT

←Older revision		Revision as of 05:49, 22 April 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6xub is ~~ON HOLD~~	+	==Structure of coproheme decarboxylase from Corynebacterium diphteriae in complex with monovinyl monopropionyl deuteroheme==
-		+	<StructureSection load='6xub' size='340' side='right'caption='[[6xub]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XUB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6XUB FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6xub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xub OCA], [http://pdbe.org/6xub PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6xub RCSB], [http://www.ebi.ac.uk/pdbsum/6xub PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6xub ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Djinovic-Carugo K]]
		+	[[Category: Furtmueller PG]]
		+	[[Category: Hofbauer S]]
		+	[[Category: Lier B]]
		+	[[Category: Michlits H]]
		+	[[Category: Obinger C]]
		+	[[Category: Oostenbrink C]]
		+	[[Category: Pfanzagl V]]

OCA at 05:30, 15 April 2020

OCA — Wed, 15 Apr 2020 05:30:26 GMT

←Older revision		Revision as of 05:30, 15 April 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6xub is ON HOLD ~~until Paper Publication~~	+	The entry 6xub is ON HOLD

	Authors:		Authors:

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

OCA — Wed, 29 Jan 2020 13:45:13 GMT

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

←Older revision

Revision as of 13:45, 29 January 2020

OCA: New page: '''Unreleased structure''' The entry 6xub is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 29 Jan 2020 13:45:11 GMT

New page: '''Unreleased structure''' The entry 6xub is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6xub is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]