6uyk - Revision history

OCA at 08:00, 11 October 2023

OCA — Wed, 11 Oct 2023 08:00:52 GMT

←Older revision		Revision as of 08:00, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6uyk' size='340' side='right'caption='[[6uyk]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='6uyk' size='340' side='right'caption='[[6uyk]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6uyk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"luteovulum_sphaeroides"_(van_niel_1944)_suresh_et_al._2019 "luteovulum~~ sphaeroides~~" (van niel 1944) suresh et al. 2019~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UYK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6uyk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Cereibacter_sphaeroides Cereibacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UYK FirstGlance]. <br>
-	</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=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]] 2.6Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>bchL, RHOS4_18930, RSP_0288 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1063~~ "~~Luteovulum sphaeroides~~" ~~(van Niel 1944) Suresh et al. 2019])</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=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[https://en.wikipedia.org/wiki/Ferredoxin:protochlorophyllide_reductase_(ATP-dependent) Ferredoxin:protochlorophyllide reductase (ATP-dependent)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.7.7 1.3.7.7] </~~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=6uyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uyk OCA], [https://pdbe.org/6uyk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6uyk RCSB], [https://www.ebi.ac.uk/pdbsum/6uyk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6uyk 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=6uyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uyk OCA], [https://pdbe.org/6uyk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6uyk RCSB], [https://www.ebi.ac.uk/pdbsum/6uyk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6uyk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~BCHL_RHOS4 BCHL_RHOS4]~~] Component of the dark-operative protochlorophyllide reductase (DPOR) that uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This reaction is light-independent. The L component serves as a unique electron donor to the NB-component of the complex, and binds Mg-ATP.[HAMAP-Rule:MF_00355]<ref>PMID:19006326</ref>	+	[https://www.uniprot.org/uniprot/BCHL_CERS4 BCHL_CERS4] Component of the dark-operative protochlorophyllide reductase (DPOR) that uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This reaction is light-independent. The L component serves as a unique electron donor to the NB-component of the complex, and binds Mg-ATP.[HAMAP-Rule:MF_00355]<ref>PMID:19006326</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: Cereibacter sphaeroides]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ando, N]]	+	[[Category: Ando N]]
-	[[Category: Antony, E]]	+	[[Category: Antony E]]
-	[[Category: Bacik~~, J P~~]]	+	[[Category: Bacik JP]]
-	[[Category: Corless, E]]	+	[[Category: Corless E]]
-	[[Category: Imran~~, S M.S~~]]	+	[[Category: Imran SMS]]
-	[[Category: Watkins~~, M B]]~~	+	[[Category: Watkins MB]]
-	~~[[Category: Dpor]]~~	+
-	~~[[Category: Electron transfer]]~~	+
-	~~[[Category: Iron-sulfur cluster]]~~	+
-	~~[[Category: Nitrogenase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Photosynthesis~~]]	+

OCA at 09:58, 14 July 2021

OCA — Wed, 14 Jul 2021 09:58:54 GMT

←Older revision		Revision as of 09:58, 14 July 2021
Line 3:		Line 3:
	<StructureSection load='6uyk' size='340' side='right'caption='[[6uyk]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='6uyk' size='340' side='right'caption='[[6uyk]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6uyk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"~~rhodococcus_capsulatus~~"~~_molisch_1907~~ "~~rhodococcus capsulatus~~" ~~molisch 1907~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UYK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6uyk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"luteovulum_sphaeroides"_(van_niel_1944)_suresh_et_al._2019 "luteovulum sphaeroides" (van niel 1944) suresh et al. 2019]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UYK FirstGlance]. <br>
	</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=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>		</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=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bchL, RHOS4_18930, RSP_0288 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1063 "~~Rhodococcus capsulatus~~" ~~Molisch 1907~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bchL, RHOS4_18930, RSP_0288 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1063 "Luteovulum sphaeroides" (van Niel 1944) Suresh et al. 2019])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/~~Oxidoreductase Oxidoreductase~~], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.7.7 1.3.7.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ferredoxin:protochlorophyllide_reductase_(ATP-dependent) Ferredoxin:protochlorophyllide reductase (ATP-dependent)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.7.7 1.3.7.7] </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=6uyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uyk OCA], [https://pdbe.org/6uyk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6uyk RCSB], [https://www.ebi.ac.uk/pdbsum/6uyk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6uyk 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=6uyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uyk OCA], [https://pdbe.org/6uyk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6uyk RCSB], [https://www.ebi.ac.uk/pdbsum/6uyk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6uyk ProSAT]</span></td></tr>
	</table>		</table>
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Rhodococcus capsulatus molisch 1907]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Oxidoreductase]]
	[[Category: Ando, N]]		[[Category: Ando, N]]
	[[Category: Antony, E]]		[[Category: Antony, E]]
Line 37:		Line 35:
	[[Category: Iron-sulfur cluster]]		[[Category: Iron-sulfur cluster]]
	[[Category: Nitrogenase]]		[[Category: Nitrogenase]]
		+	[[Category: Oxidoreductase]]
	[[Category: Photosynthesis]]		[[Category: Photosynthesis]]

OCA at 05:27, 28 April 2021

OCA — Wed, 28 Apr 2021 05:27:46 GMT

←Older revision		Revision as of 05:27, 28 April 2021
Line 1:		Line 1:

	==Dark-operative protochlorophyllide oxidoreductase in the nucleotide-free form.==		==Dark-operative protochlorophyllide oxidoreductase in the nucleotide-free form.==
-	<StructureSection load='6uyk' size='340' side='right'caption='[[6uyk]]' scene=''>	+	<StructureSection load='6uyk' size='340' side='right'caption='[[6uyk]], [[Resolution\|resolution]] 2.60Å' 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=6UYK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6UYK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6uyk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"rhodococcus_capsulatus"_molisch_1907 "rhodococcus capsulatus" molisch 1907]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UYK 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=6uyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uyk OCA], [~~http~~://pdbe.org/6uyk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6uyk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6uyk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6uyk 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=CL:CHLORIDE+ION'>CL</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">bchL, RHOS4_18930, RSP_0288 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1063 "Rhodococcus capsulatus" Molisch 1907])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.7.7 1.3.7.7] </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=6uyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uyk OCA], [https://pdbe.org/6uyk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6uyk RCSB], [https://www.ebi.ac.uk/pdbsum/6uyk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6uyk ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/BCHL_RHOS4 BCHL_RHOS4]] Component of the dark-operative protochlorophyllide reductase (DPOR) that uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This reaction is light-independent. The L component serves as a unique electron donor to the NB-component of the complex, and binds Mg-ATP.[HAMAP-Rule:MF_00355]<ref>PMID:19006326</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A key step in bacteriochlorophyll biosynthesis is the reduction of protochlorophyllide to chlorophyllide, catalyzed by dark-operative protochlorophyllide oxidoreductase (DPOR). DPOR contains two [4Fe-4S]-containing component proteins (BchL and BchNB) that assemble upon ATP binding to BchL to coordinate electron transfer and protochlorophyllide reduction. But the precise nature of the ATP-induced conformational changes are poorly understood. We present a crystal structure of BchL in the nucleotide-free form where a conserved, flexible region in the N-terminus masks the [4Fe-4S] cluster at the docking interface between BchL and BchNB. Amino acid substitutions in this region produce a hyper-active enzyme complex, suggesting a role for the N-terminus in auto-inhibition. Hydrogen deuterium exchange mass spectrometry shows that ATP-binding to BchL produces specific conformational changes leading to release of the flexible N-terminus from the docking interface. The release also promotes changes within the local environment surrounding the [4Fe-4S] cluster and promotes BchL complex formation with BchNB. A key patch of amino acids, Asp-Phe-Asp (the 'DFD patch'), situated at the mouth of the BchL ATP-binding pocket promotes inter-subunit cross stabilization of the two subunits. A linked BchL dimer with one defective ATP-binding site does not support protochlorophyllide reduction, illustrating nucleotide binding to both subunits as a prerequisite for the inter-subunit cross stabilization. The masking of the [4Fe-4S] cluster by the flexible N-terminal region and the associated inhibition of activity is a novel mechanism of regulation in metalloproteins. Such mechanisms are possibly an adaptation to the anaerobic nature of eubacterial cells with poor tolerance for oxygen.
		+
		+	The flexible N-terminus of BchL autoinhibits activity through interaction with its [4Fe-4S] cluster and relieved upon ATP binding.,Corless EI, Saad Imran SM, Watkins MB, Bacik JP, Mattice J, Patterson A, Danyal K, Soffe M, Kitelinger R, Seefeldt LC, Origanti SS, Bennett B, Bothner B, Ando N, Antony E J Biol Chem. 2020 Nov 20:100107. doi: 10.1074/jbc.RA120.016278. PMID:33219127<ref>PMID:33219127</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6uyk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Rhodococcus capsulatus molisch 1907]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ando N]]	+	[[Category: Oxidoreductase]]
-	[[Category: Antony E]]	+	[[Category: Ando, N]]
-	[[Category: Bacik JP]]	+	[[Category: Antony, E]]
-	[[Category: Corless E]]	+	[[Category: Bacik, J P]]
-	[[Category: Imran ~~SMS~~]]	+	[[Category: Corless, E]]
-	[[Category: Watkins MB]]	+	[[Category: Imran, S M.S]]
		+	[[Category: Watkins, M B]]
		+	[[Category: Dpor]]
		+	[[Category: Electron transfer]]
		+	[[Category: Iron-sulfur cluster]]
		+	[[Category: Nitrogenase]]
		+	[[Category: Photosynthesis]]

OCA at 07:44, 2 December 2020

OCA — Wed, 02 Dec 2020 07:44:41 GMT

←Older revision		Revision as of 07:44, 2 December 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6uyk is ~~ON HOLD until Paper Publication~~	+	==Dark-operative protochlorophyllide oxidoreductase in the nucleotide-free form.==
-		+	<StructureSection load='6uyk' size='340' side='right'caption='[[6uyk]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UYK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6UYK 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=6uyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uyk OCA], [http://pdbe.org/6uyk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6uyk RCSB], [http://www.ebi.ac.uk/pdbsum/6uyk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6uyk ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ando N]]
		+	[[Category: Antony E]]
		+	[[Category: Bacik JP]]
		+	[[Category: Corless E]]
		+	[[Category: Imran SMS]]
		+	[[Category: Watkins MB]]

OCA at 03:49, 13 May 2020

OCA — Wed, 13 May 2020 03:49:09 GMT

←Older revision		Revision as of 03:49, 13 May 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 20 Nov 2019 13:56:44 GMT

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

←Older revision

Revision as of 13:56, 20 November 2019

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

OCA — Wed, 20 Nov 2019 13:56:43 GMT

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

New page

'''Unreleased structure'''

The entry 6uyk is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]