7npa - Revision history

OCA at 07:52, 7 February 2024

OCA — Wed, 07 Feb 2024 07:52:38 GMT

←Older revision		Revision as of 07:52, 7 February 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/A0A2Z5PF12_METMI A0A2Z5PF12_METMI]		[https://www.uniprot.org/uniprot/A0A2Z5PF12_METMI A0A2Z5PF12_METMI]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Methanogenic archaea are main actors in the carbon cycle but are sensitive to reactive sulfite. Some methanogens use a sulfite detoxification system that combines an F(420)H(2)-oxidase with a sulfite reductase, both of which are proposed precursors of modern enzymes. Here, we present snapshots of this coupled system, named coenzyme F(420)-dependent sulfite reductase (Group I Fsr), obtained from two marine methanogens. Fsr organizes as a homotetramer, harboring an intertwined six-[4Fe-4S] cluster relay characterized by spectroscopy. The wire, spanning 5.4 nm, electronically connects the flavin to the siroheme center. Despite a structural architecture similar to dissimilatory sulfite reductases, Fsr shows a siroheme coordination and a reaction mechanism identical to assimilatory sulfite reductases. Accordingly, the reaction of Fsr is unidirectional, reducing sulfite or nitrite with F(420)H(2). Our results provide structural insights into this unique fusion, in which a primitive sulfite reductase turns a poison into an elementary block of life.
-
-	Structures of the sulfite detoxifying F(420)-dependent enzyme from Methanococcales.,Jespersen M, Pierik AJ, Wagner T Nat Chem Biol. 2023 Jan 19. doi: 10.1038/s41589-022-01232-y. PMID:36658338<ref>PMID:36658338</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7npa" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 09:00, 6 December 2023

OCA — Wed, 06 Dec 2023 09:00:37 GMT

←Older revision		Revision as of 09:00, 6 December 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7npa]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermococcus_thermolithotrophicus_DSM_2095 Methanothermococcus thermolithotrophicus DSM 2095]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NPA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NPA FirstGlance]. <br>		<table><tr><td colspan='2'>[[7npa]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermococcus_thermolithotrophicus_DSM_2095 Methanothermococcus thermolithotrophicus DSM 2095]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NPA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NPA 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</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=SRM:SIROHEME'>SRM</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.55Å</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</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=SRM:SIROHEME'>SRM</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=7npa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7npa OCA], [https://pdbe.org/7npa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7npa RCSB], [https://www.ebi.ac.uk/pdbsum/7npa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7npa 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=7npa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7npa OCA], [https://pdbe.org/7npa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7npa RCSB], [https://www.ebi.ac.uk/pdbsum/7npa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7npa ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:36, 7 April 2023

OCA — Fri, 07 Apr 2023 06:36:36 GMT

←Older revision		Revision as of 06:36, 7 April 2023
Line 1:		Line 1:

	==Crystal structure of the Coenzyme F420-dependent sulfite reductase from Methanothermococcus thermolithotrophicus at 1.55-A resolution==		==Crystal structure of the Coenzyme F420-dependent sulfite reductase from Methanothermococcus thermolithotrophicus at 1.55-A resolution==
-	<StructureSection load='7npa' size='340' side='right'caption='[[7npa]]' scene=''>	+	<StructureSection load='7npa' size='340' side='right'caption='[[7npa]], [[Resolution\|resolution]] 1.55Å' 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=7NPA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NPA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7npa]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermococcus_thermolithotrophicus_DSM_2095 Methanothermococcus thermolithotrophicus DSM 2095]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NPA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NPA FirstGlance]. <br>
-	</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=7npa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7npa OCA], [https://pdbe.org/7npa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7npa RCSB], [https://www.ebi.ac.uk/pdbsum/7npa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7npa 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</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=SRM:SIROHEME'>SRM</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=7npa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7npa OCA], [https://pdbe.org/7npa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7npa RCSB], [https://www.ebi.ac.uk/pdbsum/7npa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7npa ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A2Z5PF12_METMI A0A2Z5PF12_METMI]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Methanogenic archaea are main actors in the carbon cycle but are sensitive to reactive sulfite. Some methanogens use a sulfite detoxification system that combines an F(420)H(2)-oxidase with a sulfite reductase, both of which are proposed precursors of modern enzymes. Here, we present snapshots of this coupled system, named coenzyme F(420)-dependent sulfite reductase (Group I Fsr), obtained from two marine methanogens. Fsr organizes as a homotetramer, harboring an intertwined six-[4Fe-4S] cluster relay characterized by spectroscopy. The wire, spanning 5.4 nm, electronically connects the flavin to the siroheme center. Despite a structural architecture similar to dissimilatory sulfite reductases, Fsr shows a siroheme coordination and a reaction mechanism identical to assimilatory sulfite reductases. Accordingly, the reaction of Fsr is unidirectional, reducing sulfite or nitrite with F(420)H(2). Our results provide structural insights into this unique fusion, in which a primitive sulfite reductase turns a poison into an elementary block of life.
		+
		+	Structures of the sulfite detoxifying F(420)-dependent enzyme from Methanococcales.,Jespersen M, Pierik AJ, Wagner T Nat Chem Biol. 2023 Jan 19. doi: 10.1038/s41589-022-01232-y. PMID:36658338<ref>PMID:36658338</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7npa" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Methanothermococcus thermolithotrophicus DSM 2095]]
	[[Category: Jespersen M]]		[[Category: Jespersen M]]
	[[Category: Wagner T]]		[[Category: Wagner T]]

OCA at 11:17, 23 March 2022

OCA — Wed, 23 Mar 2022 11:17:43 GMT

←Older revision		Revision as of 11:17, 23 March 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7npa is ON HOLD~~	+	==Crystal structure of the Coenzyme F420-dependent sulfite reductase from Methanothermococcus thermolithotrophicus at 1.55-A resolution==
-		+	<StructureSection load='7npa' size='340' side='right'caption='[[7npa]]' scene=''>
-	~~Authors: Jespersen, M., Wagner, T.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NPA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NPA FirstGlance]. <br>
-	~~Description:~~ Crystal structure of the Coenzyme F420-dependent sulfite reductase from Methanothermococcus thermolithotrophicus at 1.55-A resolution	+	</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=7npa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7npa OCA], [https://pdbe.org/7npa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7npa RCSB], [https://www.ebi.ac.uk/pdbsum/7npa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7npa ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Wagner~~, T]]	+	__TOC__
-	[[Category: Jespersen, M]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Jespersen M]]
		+	[[Category: Wagner T]]

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

OCA — Wed, 10 Mar 2021 15:00:56 GMT

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

←Older revision

Revision as of 15:00, 10 March 2021

OCA: New page: '''Unreleased structure''' The entry 7npa is ON HOLD Authors: Jespersen, M., Wagner, T. Description: Crystal structure of the Coenzyme F420-dependent sulfite reductase from Methanother...

OCA — Wed, 10 Mar 2021 15:00:54 GMT

New page: '''Unreleased structure''' The entry 7npa is ON HOLD Authors: Jespersen, M., Wagner, T. Description: Crystal structure of the Coenzyme F420-dependent sulfite reductase from Methanother...

New page

'''Unreleased structure'''

The entry 7npa is ON HOLD

Authors: Jespersen, M., Wagner, T.

Description: Crystal structure of the Coenzyme F420-dependent sulfite reductase from Methanothermococcus thermolithotrophicus at 1.55-A resolution
[[Category: Unreleased Structures]]
[[Category: Wagner, T]]
[[Category: Jespersen, M]]