5b48 - Revision history

OCA at 15:59, 8 November 2023

OCA — Wed, 08 Nov 2023 15:59:37 GMT

←Older revision		Revision as of 15:59, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5b48]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfurisphaera_tokodaii_str._7 Sulfurisphaera tokodaii str. 7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B48 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B48 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5b48]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfurisphaera_tokodaii_str._7 Sulfurisphaera tokodaii str. 7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B48 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B48 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TDN:2-[(2E)-3-[(4-AZANYL-2-METHYL-PYRIMIDIN-5-YL)METHYL]-4-METHYL-2-(1-OXIDANYLPROPYLIDENE)-1,3-THIAZOL-5-YL]ETHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>TDN</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]] 2.5Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TDN:2-[(2E)-3-[(4-AZANYL-2-METHYL-PYRIMIDIN-5-YL)METHYL]-4-METHYL-2-(1-OXIDANYLPROPYLIDENE)-1,3-THIAZOL-5-YL]ETHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>TDN</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=5b48 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b48 OCA], [https://pdbe.org/5b48 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b48 RCSB], [https://www.ebi.ac.uk/pdbsum/5b48 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b48 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=5b48 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b48 OCA], [https://pdbe.org/5b48 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b48 RCSB], [https://www.ebi.ac.uk/pdbsum/5b48 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b48 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:38, 31 May 2023

OCA — Wed, 31 May 2023 06:38:13 GMT

←Older revision		Revision as of 06:38, 31 May 2023
Line 3:		Line 3:
	<StructureSection load='5b48' size='340' side='right'caption='[[5b48]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5b48' size='340' side='right'caption='[[5b48]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5b48]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Sulto Sulto~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B48 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5B48 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5b48]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfurisphaera_tokodaii_str._7 Sulfurisphaera tokodaii str. 7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B48 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B48 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TDN:2-[(2E)-3-[(4-AZANYL-2-METHYL-PYRIMIDIN-5-YL)METHYL]-4-METHYL-2-(1-OXIDANYLPROPYLIDENE)-1,3-THIAZOL-5-YL]ETHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>TDN</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TDN:2-[(2E)-3-[(4-AZANYL-2-METHYL-PYRIMIDIN-5-YL)METHYL]-4-METHYL-2-(1-OXIDANYLPROPYLIDENE)-1,3-THIAZOL-5-YL]ETHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>TDN</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5b46\|5b46]], [[5b47\|5b47]]</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=5b48 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b48 OCA], [https://pdbe.org/5b48 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b48 RCSB], [https://www.ebi.ac.uk/pdbsum/5b48 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b48 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">STK_23000 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273063 SULTO]), STK_22980 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273063 SULTO])</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=5b48 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b48 OCA], [~~http~~://pdbe.org/5b48 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5b48 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5b48 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5b48 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/OFOA1_SULTO OFOA1_SULTO] Catalyzes the coenzyme A-dependent oxidative decarboxylation of different 2-oxoacids such as 2-oxoglutarate, pyruvate and 2-oxobutyrate to form their CoA derivatives.<ref>PMID:19027887</ref> <ref>PMID:27619895</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Sulto~~]]	+	[[Category: Sulfurisphaera tokodaii str. 7]]
-	[[Category: Arakawa, T]]	+	[[Category: Arakawa T]]
-	[[Category: Fushinobu, S]]	+	[[Category: Fushinobu S]]
-	[[Category: Maruyama, A]]	+	[[Category: Maruyama A]]
-	[[Category: Wakagi, T]]	+	[[Category: Wakagi T]]
-	[[Category: Yan, Z]]	+	[[Category: Yan Z]]
-	~~[[Category: Ferredoxin]]~~	+
-	~~[[Category: Iron-sulfur cluster]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Thiamin pyrophosphate~~]]	+

OCA at 10:03, 26 February 2020

OCA — Wed, 26 Feb 2020 10:03:48 GMT

←Older revision		Revision as of 10:03, 26 February 2020
Line 1:		Line 1:

	==2-Oxoacid:Ferredoxin Oxidoreductase 1 from Sulfolobus tokodai==		==2-Oxoacid:Ferredoxin Oxidoreductase 1 from Sulfolobus tokodai==
-	<StructureSection load='5b48' size='340' side='right' caption='[[5b48]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5b48' size='340' side='right'caption='[[5b48]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5b48]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B48 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B48 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5b48]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulto Sulto]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B48 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B48 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TDN:2-[(2E)-3-[(4-AZANYL-2-METHYL-PYRIMIDIN-5-YL)METHYL]-4-METHYL-2-(1-OXIDANYLPROPYLIDENE)-1,3-THIAZOL-5-YL]ETHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>TDN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TDN:2-[(2E)-3-[(4-AZANYL-2-METHYL-PYRIMIDIN-5-YL)METHYL]-4-METHYL-2-(1-OXIDANYLPROPYLIDENE)-1,3-THIAZOL-5-YL]ETHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>TDN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5b46\|5b46]], [[5b47\|5b47]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5b46\|5b46]], [[5b47\|5b47]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">STK_23000 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273063 SULTO]), STK_22980 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273063 SULTO])</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=5b48 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b48 OCA], [http://pdbe.org/5b48 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b48 RCSB], [http://www.ebi.ac.uk/pdbsum/5b48 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b48 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=5b48 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b48 OCA], [http://pdbe.org/5b48 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b48 RCSB], [http://www.ebi.ac.uk/pdbsum/5b48 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b48 ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Sulto]]
	[[Category: Arakawa, T]]		[[Category: Arakawa, T]]
	[[Category: Fushinobu, S]]		[[Category: Fushinobu, S]]

OCA at 16:53, 3 October 2016

OCA — Mon, 03 Oct 2016 16:53:50 GMT

←Older revision		Revision as of 16:53, 3 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5b48 is ~~ON HOLD until Paper~~ Publication	+	==2-Oxoacid:Ferredoxin Oxidoreductase 1 from Sulfolobus tokodai==
		+	<StructureSection load='5b48' size='340' side='right' caption='[[5b48]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5b48]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B48 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B48 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TDN:2-[(2E)-3-[(4-AZANYL-2-METHYL-PYRIMIDIN-5-YL)METHYL]-4-METHYL-2-(1-OXIDANYLPROPYLIDENE)-1,3-THIAZOL-5-YL]ETHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>TDN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5b46\|5b46]], [[5b47\|5b47]]</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=5b48 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b48 OCA], [http://pdbe.org/5b48 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b48 RCSB], [http://www.ebi.ac.uk/pdbsum/5b48 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b48 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	As the first three-dimensional structure of the two-subunit type 2-oxoacid:ferredoxin oxidoreductases (OFOR) from archaea, we solved the crystal structures of STK_23000/STK_22980 (StOFOR1) and STK_24350/STK_24330 (StOFOR2) from Sulfolobus tokodaii. They showed similar overall structures, consisting of two a- and b-subunit heterodimers containing thiamin pyrophosphate (TPP) cofactor and [4Fe-4S] cluster, but lack an intramolecular ferredoxin domain. Unlike other OFORs, StOFORs can utilize both pyruvate and 2-oxoglutarate, playing a key role in the central metabolism. In the structure of StOFOR2 in unreacted pyruvate complex form, carboxylate group of pyruvate is recognized by Arg344 and Thr257 from the a-subunit, which are conserved in pyruvate:ferredoxin oxidoreductase from Desulfovbrio africanus (DaPFOR). In the structure of StOFOR1 co-crystallized with 2-oxobutyrate, electron density corresponding to a 1-hydroxypropyl group (post-decarboxylation state) was observed at the thiazole ring of TPP. The binding pockets of the StOFORs surrounding the methyl or propyl group of the ligands are wider than that of DaPFOR. Mutational analyses indicated that several residues were responsible for the broad 2-oxoacid specificity of StOFORs. We also constructed a possible complex structural model by placing a Zn(2+)-containing dicluster ferredoxin of S. tokodaii into the large pocket of StOFOR2, providing insight into the electron transfer between the two redox proteins.

-	~~Authors~~:	+	Crystal structures of archaeal 2-oxoacid:ferredoxin oxidoreductases from Sulfolobus tokodaii.,Yan Z, Maruyama A, Arakawa T, Fushinobu S, Wakagi T Sci Rep. 2016 Sep 13;6:33061. doi: 10.1038/srep33061. PMID:27619895<ref>PMID:27619895</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5b48" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arakawa, T]]
		+	[[Category: Fushinobu, S]]
		+	[[Category: Maruyama, A]]
		+	[[Category: Wakagi, T]]
		+	[[Category: Yan, Z]]
		+	[[Category: Ferredoxin]]
		+	[[Category: Iron-sulfur cluster]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Thiamin pyrophosphate]]

OCA at 11:07, 15 May 2016

OCA — Sun, 15 May 2016 11:07:59 GMT

←Older revision		Revision as of 11:07, 15 May 2016
Line 3:		Line 3:
	The entry 5b48 is ON HOLD until Paper Publication		The entry 5b48 is ON HOLD until Paper Publication

-	Authors: ~~Yan, Z., Maruyama, A., Arakawa, T., Fushinobu, S., Wakagi, T.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Arakawa, T]]
-	[[Category: Fushinobu, S]]
-	[[Category: Maruyama, A]]
-	[[Category: Wakagi, T]]
-	[[Category: Yan, Z]]

OCA: Protected "5b48" [edit=sysop:move=sysop]

OCA — Tue, 10 May 2016 20:57:37 GMT

Protected "5b48" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:57, 10 May 2016

OCA: New page: '''Unreleased structure''' The entry 5b48 is ON HOLD until Paper Publication Authors: Yan, Z., Maruyama, A., Arakawa, T., Fushinobu, S., Wakagi, T. Description: [[Category: Unreleased...

OCA — Tue, 10 May 2016 20:57:36 GMT

New page: '''Unreleased structure''' The entry 5b48 is ON HOLD until Paper Publication Authors: Yan, Z., Maruyama, A., Arakawa, T., Fushinobu, S., Wakagi, T. Description: [[Category: Unreleased...

New page

'''Unreleased structure'''

The entry 5b48 is ON HOLD until Paper Publication

Authors: Yan, Z., Maruyama, A., Arakawa, T., Fushinobu, S., Wakagi, T.

Description:
[[Category: Unreleased Structures]]
[[Category: Arakawa, T]]
[[Category: Fushinobu, S]]
[[Category: Maruyama, A]]
[[Category: Wakagi, T]]
[[Category: Yan, Z]]