3c8f - Revision history

OCA at 09:00, 13 August 2026

2026-08-13T09:00:14Z

← Older revision		Revision as of 09:00, 13 August 2026
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	<table><tr><td colspan='2'>[[3c8f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C8F FirstGlance]. <br>		<table><tr><td colspan='2'>[[3c8f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C8F FirstGlance]. <br>
	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.25Å</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]] 2.25Å</td></tr>
	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MT2:[(3S)-3-AMINO-3-CARBOXYPROPYL](ETHYL)METHYLSULFONIUM'>MT2</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE~~</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4~~</scene></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MT2:[(3S)-3-AMINO-3-CARBOXYPROPYL](ETHYL)METHYLSULFONIUM'>MT2</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=3c8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8f OCA], [https://pdbe.org/3c8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c8f RCSB], [https://www.ebi.ac.uk/pdbsum/3c8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c8f 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=3c8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8f OCA], [https://pdbe.org/3c8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c8f RCSB], [https://www.ebi.ac.uk/pdbsum/3c8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c8f ProSAT]</span></td></tr>
	</table>		</table>
Line 15:		Line 15:
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c8/3c8f_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c8/3c8f_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3c8f ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3c8f ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Pyruvate formate-lyase activating enzyme generates a stable and catalytically essential glycyl radical on G(734) of pyruvate formate-lyase via the direct, stereospecific abstraction of a hydrogen atom from pyruvate formate-lyase. The activase performs this remarkable feat by using an iron-sulfur cluster and S-adenosylmethionine (AdoMet), thus placing it among the AdoMet radical superfamily of enzymes. We report here structures of the substrate-free and substrate-bound forms of pyruvate formate-lyase-activating enzyme, the first structures of an AdoMet radical activase. To obtain the substrate-bound structure, we have used a peptide substrate, the 7-mer RVSGYAV, which contains the sequence surrounding G(734). Our structures provide fundamental insights into the interactions between the activase and the G(734) loop of pyruvate formate-lyase and provide a structural basis for direct and stereospecific H atom abstraction from the buried G(734) of pyruvate formate-lyase.

			Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme.,Vey JL, Yang J, Li M, Broderick WE, Broderick JB, Drennan CL Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16137-41. Epub 2008 Oct 13. PMID:18852451<ref>PMID:18852451</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 3c8f" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 09:33, 21 February 2024

2024-02-21T09:33:37Z

← Older revision		Revision as of 09:33, 21 February 2024
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	<StructureSection load='3c8f' size='340' side='right'caption='[[3c8f]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='3c8f' size='340' side='right'caption='[[3c8f]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3c8f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C8F FirstGlance]. <br>		<table><tr><td colspan='2'>[[3c8f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C8F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MT2:[(3S)-3-AMINO-3-CARBOXYPROPYL](ETHYL)METHYLSULFONIUM'>MT2</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 2.25Å</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/[Formate-C-acetyltransferase]-activating_enzyme [Formate-C-acetyltransferase]-activating enzyme], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.97.1.4 1.97.1.4] </span></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MT2:[(3S)-3-AMINO-3-CARBOXYPROPYL](ETHYL)METHYLSULFONIUM'>MT2</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=3c8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8f OCA], [https://pdbe.org/3c8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c8f RCSB], [https://www.ebi.ac.uk/pdbsum/3c8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c8f 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=3c8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8f OCA], [https://pdbe.org/3c8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c8f RCSB], [https://www.ebi.ac.uk/pdbsum/3c8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c8f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/PFLA_ECOLI PFLA_ECOLI]] Activation of pyruvate formate-lyase 1 under anaerobic conditions by generation of an organic free radical, using S-adenosylmethionine and reduced flavodoxin as cosubstrates to produce 5'-deoxy-adenosine.		[https://www.uniprot.org/uniprot/PFLA_ECOLI PFLA_ECOLI] Activation of pyruvate formate-lyase 1 under anaerobic conditions by generation of an organic free radical, using S-adenosylmethionine and reduced flavodoxin as cosubstrates to produce 5'-deoxy-adenosine.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3c8f ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3c8f ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Pyruvate formate-lyase activating enzyme generates a stable and catalytically essential glycyl radical on G(734) of pyruvate formate-lyase via the direct, stereospecific abstraction of a hydrogen atom from pyruvate formate-lyase. The activase performs this remarkable feat by using an iron-sulfur cluster and S-adenosylmethionine (AdoMet), thus placing it among the AdoMet radical superfamily of enzymes. We report here structures of the substrate-free and substrate-bound forms of pyruvate formate-lyase-activating enzyme, the first structures of an AdoMet radical activase. To obtain the substrate-bound structure, we have used a peptide substrate, the 7-mer RVSGYAV, which contains the sequence surrounding G(734). Our structures provide fundamental insights into the interactions between the activase and the G(734) loop of pyruvate formate-lyase and provide a structural basis for direct and stereospecific H atom abstraction from the buried G(734) of pyruvate formate-lyase.

	Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme.,Vey JL, Yang J, Li M, Broderick WE, Broderick JB, Drennan CL Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16137-41. Epub 2008 Oct 13. PMID:18852451<ref>PMID:18852451</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 3c8f" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Drennan~~, C L~~]]		[[Category: Drennan CL]]
	[[Category: Vey~~, J L]]~~		[[Category: Vey JL]]
	~~[[Category: Activase]]~~
	~~[[Category: Adomet radical]]~~
	~~[[Category: Carbohydrate metabolism]]~~
	~~[[Category: Glucose metabolism]]~~
	~~[[Category: Glycyl radical]]~~
	~~[[Category: Iron]]~~
	~~[[Category: Iron-sulfur]]~~
	~~[[Category: Metal-binding]]~~
	~~[[Category: Oxidoreductase]]~~
	~~[[Category: S-adenosyl-l-methionine]]~~
	~~[[Category: Sam radical~~]]

OCA at 07:47, 27 January 2022

2022-01-27T07:47:07Z

← Older revision		Revision as of 07:47, 27 January 2022
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	<StructureSection load='3c8f' size='340' side='right'caption='[[3c8f]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='3c8f' size='340' side='right'caption='[[3c8f]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3c8f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C8F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3C8F FirstGlance]. <br>		<table><tr><td colspan='2'>[[3c8f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C8F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MT2:[(3S)-3-AMINO-3-CARBOXYPROPYL](ETHYL)METHYLSULFONIUM'>MT2</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=MT2:[(3S)-3-AMINO-3-CARBOXYPROPYL](ETHYL)METHYLSULFONIUM'>MT2</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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'>[~~http~~://en.wikipedia.org/wiki/[Formate-C-acetyltransferase]-activating_enzyme [Formate-C-acetyltransferase]-activating enzyme], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.97.1.4 1.97.1.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/[Formate-C-acetyltransferase]-activating_enzyme [Formate-C-acetyltransferase]-activating enzyme], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.97.1.4 1.97.1.4] </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=3c8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8f OCA], [~~http~~://pdbe.org/3c8f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3c8f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3c8f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3c8f 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=3c8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8f OCA], [https://pdbe.org/3c8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c8f RCSB], [https://www.ebi.ac.uk/pdbsum/3c8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c8f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/PFLA_ECOLI PFLA_ECOLI]] Activation of pyruvate formate-lyase 1 under anaerobic conditions by generation of an organic free radical, using S-adenosylmethionine and reduced flavodoxin as cosubstrates to produce 5'-deoxy-adenosine.		[[https://www.uniprot.org/uniprot/PFLA_ECOLI PFLA_ECOLI]] Activation of pyruvate formate-lyase 1 under anaerobic conditions by generation of an organic free radical, using S-adenosylmethionine and reduced flavodoxin as cosubstrates to produce 5'-deoxy-adenosine.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:57, 31 July 2019

2019-07-31T07:57:57Z

← Older revision		Revision as of 07:57, 31 July 2019
Line 1:		Line 1:

	==4Fe-4S-Pyruvate formate-lyase Activating Enzyme with partially disordered AdoMet==		==4Fe-4S-Pyruvate formate-lyase Activating Enzyme with partially disordered AdoMet==
	<StructureSection load='3c8f' size='340' side='right' caption='[[3c8f]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='3c8f' size='340' side='right'caption='[[3c8f]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3c8f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C8F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3C8F FirstGlance]. <br>		<table><tr><td colspan='2'>[[3c8f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C8F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3C8F FirstGlance]. <br>
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c8/3c8f_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c8/3c8f_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 33:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Drennan, C L]]		[[Category: Drennan, C L]]
	[[Category: Vey, J L]]		[[Category: Vey, J L]]

OCA at 08:20, 25 October 2017

2017-10-25T08:20:13Z

← Older revision		Revision as of 08:20, 25 October 2017
Line 1:		Line 1:

	==4Fe-4S-Pyruvate formate-lyase Activating Enzyme with partially disordered AdoMet==		==4Fe-4S-Pyruvate formate-lyase Activating Enzyme with partially disordered AdoMet==
	<StructureSection load='3c8f' size='340' side='right' caption='[[3c8f]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='3c8f' size='340' side='right' caption='[[3c8f]], [[Resolution\|resolution]] 2.25Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MT2:[(3S)-3-AMINO-3-CARBOXYPROPYL](ETHYL)METHYLSULFONIUM'>MT2</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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"><scene name='pdbligand=MT2:[(3S)-3-AMINO-3-CARBOXYPROPYL](ETHYL)METHYLSULFONIUM'>MT2</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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'>[http://en.wikipedia.org/wiki/[Formate-C-acetyltransferase]-activating_enzyme [Formate-C-acetyltransferase]-activating enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.97.1.4 1.97.1.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Formate-C-acetyltransferase]-activating_enzyme [Formate-C-acetyltransferase]-activating enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.97.1.4 1.97.1.4] </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=3c8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8f OCA], [http://pdbe.org/3c8f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3c8f RCSB], [http://www.ebi.ac.uk/pdbsum/3c8f PDBsum]</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=3c8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8f OCA], [http://pdbe.org/3c8f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3c8f RCSB], [http://www.ebi.ac.uk/pdbsum/3c8f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3c8f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 01:49, 9 February 2016

2016-02-09T01:49:32Z

← Older revision		Revision as of 01:49, 9 February 2016
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MT2:[(3S)-3-AMINO-3-CARBOXYPROPYL](ETHYL)METHYLSULFONIUM'>MT2</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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"><scene name='pdbligand=MT2:[(3S)-3-AMINO-3-CARBOXYPROPYL](ETHYL)METHYLSULFONIUM'>MT2</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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'>[http://en.wikipedia.org/wiki/[Formate-C-acetyltransferase]-activating_enzyme [Formate-C-acetyltransferase]-activating enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.97.1.4 1.97.1.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Formate-C-acetyltransferase]-activating_enzyme [Formate-C-acetyltransferase]-activating enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.97.1.4 1.97.1.4] </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=3c8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3c8f RCSB], [http://www.ebi.ac.uk/pdbsum/3c8f PDBsum]</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=3c8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8f OCA], [http://pdbe.org/3c8f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3c8f RCSB], [http://www.ebi.ac.uk/pdbsum/3c8f PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3c8f ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 3c8f" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 03:35, 25 December 2014

2014-12-25T03:35:34Z

← Older revision		Revision as of 03:35, 25 December 2014
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	<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=3c8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3c8f RCSB], [http://www.ebi.ac.uk/pdbsum/3c8f PDBsum]</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=3c8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3c8f RCSB], [http://www.ebi.ac.uk/pdbsum/3c8f PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/PFLA_ECOLI PFLA_ECOLI]] Activation of pyruvate formate-lyase 1 under anaerobic conditions by generation of an organic free radical, using S-adenosylmethionine and reduced flavodoxin as cosubstrates to produce 5'-deoxy-adenosine.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Drennan, C L.]]		[[Category: Drennan, C L]]
	[[Category: Vey, J L.]]		[[Category: Vey, J L]]
	[[Category: Activase]]		[[Category: Activase]]
	[[Category: Adomet radical]]		[[Category: Adomet radical]]

OCA at 06:52, 10 October 2014

2014-10-10T06:52:48Z

← Older revision		Revision as of 06:52, 10 October 2014
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	<StructureSection load='3c8f' size='340' side='right' caption='[[3c8f]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='3c8f' size='340' side='right' caption='[[3c8f]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3c8f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C8F OCA]. <br>		<table><tr><td colspan='2'>[[3c8f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C8F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3C8F FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MT2:[(3S)-3-AMINO-3-CARBOXYPROPYL](ETHYL)METHYLSULFONIUM'>MT2</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MT2:[(3S)-3-AMINO-3-CARBOXYPROPYL](ETHYL)METHYLSULFONIUM'>MT2</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~Glucokinase Glucokinase~~], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.~~2 2~~.7.1.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Formate-C-acetyltransferase]-activating_enzyme [Formate-C-acetyltransferase]-activating enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.97.1.4 1.97.1.4] </span></td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3c8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3c8f RCSB], [http://www.ebi.ac.uk/pdbsum/3c8f PDBsum]</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=3c8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3c8f RCSB], [http://www.ebi.ac.uk/pdbsum/3c8f PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme.,Vey JL, Yang J, Li M, Broderick WE, Broderick JB, Drennan CL Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16137-41. Epub 2008 Oct 13. PMID:18852451<ref>PMID:18852451</ref>		Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme.,Vey JL, Yang J, Li M, Broderick WE, Broderick JB, Drennan CL Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16137-41. Epub 2008 Oct 13. PMID:18852451<ref>PMID:18852451</ref>

	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	== References ==		== References ==

OCA at 06:51, 14 May 2014

2014-05-14T06:51:25Z

← Older revision		Revision as of 06:51, 14 May 2014
Line 1:		Line 1:
	[[Image:~~3c8f~~.~~png~~\|~~left~~\|~~200px~~]]		==4Fe-4S-Pyruvate formate-lyase Activating Enzyme with partially disordered AdoMet==
			<StructureSection load='3c8f' size='340' side='right' caption='[[3c8f]], [[Resolution\|resolution]] 2.25Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[3c8f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C8F OCA]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MT2:[(3S)-3-AMINO-3-CARBOXYPROPYL](ETHYL)METHYLSULFONIUM'>MT2</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene><br>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3c8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3c8f RCSB], [http://www.ebi.ac.uk/pdbsum/3c8f PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c8/3c8f_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Pyruvate formate-lyase activating enzyme generates a stable and catalytically essential glycyl radical on G(734) of pyruvate formate-lyase via the direct, stereospecific abstraction of a hydrogen atom from pyruvate formate-lyase. The activase performs this remarkable feat by using an iron-sulfur cluster and S-adenosylmethionine (AdoMet), thus placing it among the AdoMet radical superfamily of enzymes. We report here structures of the substrate-free and substrate-bound forms of pyruvate formate-lyase-activating enzyme, the first structures of an AdoMet radical activase. To obtain the substrate-bound structure, we have used a peptide substrate, the 7-mer RVSGYAV, which contains the sequence surrounding G(734). Our structures provide fundamental insights into the interactions between the activase and the G(734) loop of pyruvate formate-lyase and provide a structural basis for direct and stereospecific H atom abstraction from the buried G(734) of pyruvate formate-lyase.

	~~{{STRUCTURE_3c8f\| PDB=3c8f \| SCENE= }}~~		Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme.,Vey JL, Yang J, Li M, Broderick WE, Broderick JB, Drennan CL Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16137-41. Epub 2008 Oct 13. PMID:18852451<ref>PMID:18852451</ref>

	~~===4Fe-4S-Pyruvate formate-lyase Activating Enzyme with partially disordered AdoMet===~~		From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_18852451}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[3c8f]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3C8F OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:018852451<~~/~~ref~~><~~references group="xtra"~~/>
	~~[[Category: Escherichia coli]]~~
	[[Category: Drennan, C L.]]		[[Category: Drennan, C L.]]
	[[Category: Vey, J L.]]		[[Category: Vey, J L.]]

OCA: Protected "3c8f" [edit=sysop:move=sysop]

2013-01-07T19:03:41Z

Protected "3c8f" [edit=sysop:move=sysop]

← Older revision	Revision as of 19:03, 7 January 2013
(No difference)