6ied - Revision history

OCA at 09:39, 22 November 2023

OCA — Wed, 22 Nov 2023 09:39:23 GMT

←Older revision		Revision as of 09:39, 22 November 2023
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	==Crystal structure of heme A synthase from Bacillus subtilis==		==Crystal structure of heme A synthase from Bacillus subtilis==
-	<StructureSection load='6ied' size='340' side='right' caption='[[6ied]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='6ied' size='340' side='right'caption='[[6ied]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ied]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacsu Bacsu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IED OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6IED FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ied]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IED FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 3Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6a2j\|6a2j]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ctaA, BSU14870 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])~~</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=6ied FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ied OCA], [https://pdbe.org/6ied PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ied RCSB], [https://www.ebi.ac.uk/pdbsum/6ied PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ied 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=6ied FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ied OCA], [~~http~~://pdbe.org/6ied PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ied RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ied PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ied ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CTAA_BACSU CTAA_BACSU]] Catalyzes the oxidation of the C8 methyl side group on heme O porphyrin ring into a formyl group. Also involved in the sporulation.<ref>PMID:12206660</ref>	+	[https://www.uniprot.org/uniprot/CTAA_BACSU CTAA_BACSU] Catalyzes the oxidation of the C8 methyl side group on heme O porphyrin ring into a formyl group. Also involved in the sporulation.<ref>PMID:12206660</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacsu~~]]	+	[[Category: Bacillus subtilis subsp. subtilis str. 168]]
-	[[Category: Kosugi, M]]	+	[[Category: Large Structures]]
-	[[Category: Miki, K]]	+	[[Category: Kosugi M]]
-	[[Category: Niwa, S]]	+	[[Category: Miki K]]
-	[[Category: Takeda, K]]	+	[[Category: Niwa S]]
-	[[Category: Tsutsumi, E]]	+	[[Category: Takeda K]]
-	~~[[Category: Heam biosynthesis]]~~	+	[[Category: Tsutsumi E]]
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:18, 12 December 2018

OCA — Wed, 12 Dec 2018 07:18:57 GMT

←Older revision		Revision as of 07:18, 12 December 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 6ied is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of heme A synthase from Bacillus subtilis==
		+	<StructureSection load='6ied' size='340' side='right' caption='[[6ied]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6ied]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IED OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IED FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6a2j\|6a2j]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ctaA, BSU14870 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=6ied FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ied OCA], [http://pdbe.org/6ied PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ied RCSB], [http://www.ebi.ac.uk/pdbsum/6ied PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ied ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CTAA_BACSU CTAA_BACSU]] Catalyzes the oxidation of the C8 methyl side group on heme O porphyrin ring into a formyl group. Also involved in the sporulation.<ref>PMID:12206660</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Heme A is an essential cofactor for respiratory terminal oxidases and vital for respiration in aerobic organisms. The final step of heme A biosynthesis is formylation of the C-8 methyl group of heme molecule by heme A synthase (HAS). HAS is a heme-containing integral membrane protein, and its structure and reaction mechanisms have remained unknown. Thus, little is known about HAS despite of its importance. Here we report the crystal structure of HAS from Bacillus subtilis at 2.2-A resolution. The N- and C-terminal halves of HAS consist of four-helix bundles and they align in a pseudo twofold symmetry manner. Each bundle contains a pair of histidine residues and forms a heme-binding domain. The C-half domain binds a cofactor-heme molecule, while the N-half domain is vacant. Many water molecules are found in the transmembrane region and around the substrate-binding site, and some of them interact with the main chain of transmembrane helix. Comparison of these two domain structures enables us to construct a substrate-heme binding state structure. This structure implies that a completely conserved glutamate, Glu57 in B. subtilis, is the catalytic residue for the formylation reaction. These results provide valuable suggestions of the substrate-heme binding mechanism. Our results present significant insight into the heme A biosynthesis.

-	~~Authors: Niwa~~, S., Takeda, K., Kosugi, M., Tsutsumi, E., ~~Miki~~, K.	+	Crystal structure of heme A synthase from Bacillus subtilis.,Niwa S, Takeda K, Kosugi M, Tsutsumi E, Mogi T, Miki K Proc Natl Acad Sci U S A. 2018 Nov 20;115(47):11953-11957. doi:, 10.1073/pnas.1813346115. Epub 2018 Nov 5. PMID:30397130<ref>PMID:30397130</ref>

-	~~Description: Crystal structure~~ of ~~heme A synthase from Bacillus subtilis~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Takeda, K]]~~	+	<div class="pdbe-citations 6ied" style="background-color:#fffaf0;"></div>
-	~~[[Category: Niwa, S]]~~	+	== References ==
-	[[Category: ~~Tsutsumi, E~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bacsu]]
	[[Category: Kosugi, M]]		[[Category: Kosugi, M]]
	[[Category: Miki, K]]		[[Category: Miki, K]]
		+	[[Category: Niwa, S]]
		+	[[Category: Takeda, K]]
		+	[[Category: Tsutsumi, E]]
		+	[[Category: Heam biosynthesis]]
		+	[[Category: Membrane protein]]
		+	[[Category: Oxidoreductase]]

OCA at 04:18, 24 October 2018

OCA — Wed, 24 Oct 2018 04:18:11 GMT

←Older revision		Revision as of 04:18, 24 October 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Niwa, S., Takeda, K., Kosugi, M., Tsutsumi, E., Miki, K.		Authors: Niwa, S., Takeda, K., Kosugi, M., Tsutsumi, E., Miki, K.
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Takeda, K]]		[[Category: Takeda, K]]
-	[[Category: Miki, K]]
	[[Category: Niwa, S]]		[[Category: Niwa, S]]
	[[Category: Tsutsumi, E]]		[[Category: Tsutsumi, E]]
	[[Category: Kosugi, M]]		[[Category: Kosugi, M]]
		+	[[Category: Miki, K]]

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

OCA — Wed, 19 Sep 2018 18:20:28 GMT

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

←Older revision

Revision as of 18:20, 19 September 2018

OCA: New page: '''Unreleased structure''' The entry 6ied is ON HOLD Authors: Niwa, S., Takeda, K., Kosugi, M., Tsutsumi, E., Miki, K. Description: Crystal structure of heme A synthase from Bacillus s...

OCA — Wed, 19 Sep 2018 18:20:26 GMT

New page: '''Unreleased structure''' The entry 6ied is ON HOLD Authors: Niwa, S., Takeda, K., Kosugi, M., Tsutsumi, E., Miki, K. Description: Crystal structure of heme A synthase from Bacillus s...

New page

'''Unreleased structure'''

The entry 6ied is ON HOLD

Authors: Niwa, S., Takeda, K., Kosugi, M., Tsutsumi, E., Miki, K.

Description: Crystal structure of heme A synthase from Bacillus subtilis
[[Category: Unreleased Structures]]
[[Category: Takeda, K]]
[[Category: Miki, K]]
[[Category: Niwa, S]]
[[Category: Tsutsumi, E]]
[[Category: Kosugi, M]]