7yzm - Revision history

OCA at 13:27, 1 February 2024

2024-02-01T13:27:48Z

←Older revision		Revision as of 13:27, 1 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7yzm]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Carboxydothermus_hydrogenoformans_Z-2901 Carboxydothermus hydrogenoformans Z-2901]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7YZM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YZM FirstGlance]. <br>		<table><tr><td colspan='2'>[[7yzm]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Carboxydothermus_hydrogenoformans_Z-2901 Carboxydothermus hydrogenoformans Z-2901]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7YZM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YZM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=BJ8:Double+cubane+cluster'>BJ8</scene>, <scene name='pdbligand=BU3:(R,R)-2,3-BUTANEDIOL'>BU3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TAM:TRIS(HYDROXYETHYL)AMINOMETHANE'>TAM</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]] 1.82Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=BJ8:Double+cubane+cluster'>BJ8</scene>, <scene name='pdbligand=BU3:(R,R)-2,3-BUTANEDIOL'>BU3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TAM:TRIS(HYDROXYETHYL)AMINOMETHANE'>TAM</scene></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=7yzm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yzm OCA], [https://pdbe.org/7yzm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yzm RCSB], [https://www.ebi.ac.uk/pdbsum/7yzm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yzm 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=7yzm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yzm OCA], [https://pdbe.org/7yzm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yzm RCSB], [https://www.ebi.ac.uk/pdbsum/7yzm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yzm ProSAT]</span></td></tr>
	</table>		</table>

OCA at 09:00, 28 December 2022

2022-12-28T09:00:07Z

←Older revision		Revision as of 09:00, 28 December 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7yzm is ~~ON HOLD~~	+	==MgADPNP-bound DCCP:DCCP-R complex==
		+	<StructureSection load='7yzm' size='340' side='right'caption='[[7yzm]], [[Resolution\|resolution]] 1.82Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7yzm]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Carboxydothermus_hydrogenoformans_Z-2901 Carboxydothermus hydrogenoformans Z-2901]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7YZM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YZM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=BJ8:Double+cubane+cluster'>BJ8</scene>, <scene name='pdbligand=BU3:(R,R)-2,3-BUTANEDIOL'>BU3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TAM:TRIS(HYDROXYETHYL)AMINOMETHANE'>TAM</scene></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=7yzm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yzm OCA], [https://pdbe.org/7yzm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yzm RCSB], [https://www.ebi.ac.uk/pdbsum/7yzm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yzm ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q3AET9_CARHZ Q3AET9_CARHZ]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Electron transfers coupled to the hydrolysis of ATP allow various metalloenzymes to catalyze reductions at very negative reduction potentials. The double-cubane cluster protein (DCCP) catalyzes the reduction of small molecules, such as acetylene and hydrazine, with electrons provided by its cognate ATP-hydrolyzing reductase (DCCP-R). How ATP-driven electron transfer occurs is not known. To resolve the structural basis for ATP-driven electron transfer, we solved the structures of the DCCP:DCCP-R complex in three different states. The structures show that the DCCP-R homodimer is covalently bridged by a [4Fe4S] cluster that is aligned with the twofold axis of the DCCP homodimer, positioning the [4Fe4S] cluster to enable electron transfer to both double-cubane clusters in the DCCP dimer. DCCP and DCCP-R form stable complexes independent of oxidation state or nucleotides present, and electron transfer requires the hydrolysis of ATP. Electron transfer appears to be additionally driven by modulating the angle between the helices binding the [4Fe4S] cluster. We observed hydrogen bond networks running from the ATP binding site via the [4Fe4S] cluster in DCCP-R to the double-cubane cluster in DCCP, allowing the propagation of conformational changes. Remarkable similarities between the DCCP:DCCP-R complex and the nonhomologous nitrogenases suggest a convergent evolution of catalytic strategies to achieve ATP-driven electron transfers between iron-sulfur clusters.

-	~~Authors: Jeoung, J.~~-H., ~~Dobbek~~, H.	+	Structural basis for coupled ATP-driven electron transfer in the double-cubane cluster protein.,Jeoung JH, Nicklisch S, Dobbek H Proc Natl Acad Sci U S A. 2022 Aug 2;119(31):e2203576119. doi: , 10.1073/pnas.2203576119. Epub 2022 Jul 29. PMID:35905315<ref>PMID:35905315</ref>

-	~~Description: MgADPNP~~-~~bound DCCP~~:~~DCCP~~-~~R complex~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Dobbek, H]]	+	<div class="pdbe-citations 7yzm" style="background-color:#fffaf0;"></div>
-	[[Category: Jeoung, J.-H]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Carboxydothermus hydrogenoformans Z-2901]]
		+	[[Category: Large Structures]]
		+	[[Category: Dobbek H]]
		+	[[Category: Jeoung J-H]]

OCA: Protected "7yzm" [edit=sysop:move=sysop]

2022-03-02T05:20:28Z

Protected "7yzm" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:20, 2 March 2022

OCA: New page: '''Unreleased structure''' The entry 7yzm is ON HOLD Authors: Jeoung, J.-H., Dobbek, H. Description: MgADPNP-bound DCCP:DCCP-R complex Category: Unreleased Structures [[Category: D...

2022-03-02T05:20:27Z

New page: '''Unreleased structure''' The entry 7yzm is ON HOLD Authors: Jeoung, J.-H., Dobbek, H. Description: MgADPNP-bound DCCP:DCCP-R complex Category: Unreleased Structures [[Category: D...

New page

'''Unreleased structure'''

The entry 7yzm is ON HOLD

Authors: Jeoung, J.-H., Dobbek, H.

Description: MgADPNP-bound DCCP:DCCP-R complex
[[Category: Unreleased Structures]]
[[Category: Dobbek, H]]
[[Category: Jeoung, J.-H]]