4fhe - Revision history

OCA at 11:16, 1 March 2024

OCA — Fri, 01 Mar 2024 11:16:36 GMT

←Older revision		Revision as of 11:16, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4fhe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_thermodenitrificans_NG80-2 Geobacillus thermodenitrificans NG80-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FHE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FHE FirstGlance]. <br>		<table><tr><td colspan='2'>[[4fhe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_thermodenitrificans_NG80-2 Geobacillus thermodenitrificans NG80-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FHE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FHE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EEM:[(3S)-3-AMINO-4-HYDROXY-4-OXO-BUTYL]-[[(2S,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL]-METHYL-SELANIUM'>EEM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EEM:[(3S)-3-AMINO-4-HYDROXY-4-OXO-BUTYL]-[[(2S,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL]-METHYL-SELANIUM'>EEM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4fhe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fhe OCA], [https://pdbe.org/4fhe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fhe RCSB], [https://www.ebi.ac.uk/pdbsum/4fhe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fhe 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=4fhe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fhe OCA], [https://pdbe.org/4fhe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fhe RCSB], [https://www.ebi.ac.uk/pdbsum/4fhe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fhe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/A4IQU1_GEOTN A4IQU1_GEOTN]		[https://www.uniprot.org/uniprot/A4IQU1_GEOTN A4IQU1_GEOTN]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Bacterial spores possess an enormous resistance to ultraviolet (UV) radiation. This is largely due to a unique DNA repair enzyme, Spore Photoproduct Lyase (SP lyase) that repairs a specific UV-induced DNA lesion, the spore photoproduct (SP), through an unprecedented radical-based mechanism. Unlike DNA photolyases, SP lyase belongs to the emerging superfamily of radical S-adenosyl-l-methionine (SAM) enzymes and uses a [4Fe-4S](1+) cluster and SAM to initiate the repair reaction. We report here the first crystal structure of this enigmatic enzyme in complex with its [4Fe-4S] cluster and its SAM cofactor, in the absence and presence of a DNA lesion, the dinucleoside SP. The high resolution structures provide fundamental insights into the active site, the DNA lesion recognition and binding which involve a beta-hairpin structure. We show that SAM and a conserved cysteine residue are perfectly positioned in the active site for hydrogen atom abstraction from the dihydrothymine residue of the lesion and donation to the alpha-thyminyl radical moiety, respectively. Based on structural and biochemical characterizations of mutant proteins, we substantiate the role of this cysteine in the enzymatic mechanism. Our structure reveals how SP lyase combines specific features of radical SAM and DNA repair enzymes to enable a complex radical-based repair reaction to take place.
-
-	Structural insights into recognition and repair of UV-DNA damage by Spore Photoproduct Lyase, a radical SAM enzyme.,Benjdia A, Heil K, Barends TR, Carell T, Schlichting I Nucleic Acids Res. 2012 Jul 2. PMID:22761404<ref>PMID:22761404</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4fhe" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 19:48, 19 October 2022

OCA — Wed, 19 Oct 2022 19:48:52 GMT

←Older revision		Revision as of 19:48, 19 October 2022
Line 1:		Line 1:

	==Spore photoproduct lyase C140A mutant==		==Spore photoproduct lyase C140A mutant==
-	<StructureSection load='4fhe' size='340' side='right' caption='[[4fhe]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='4fhe' size='340' side='right'caption='[[4fhe]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4fhe]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Geotn Geotn~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FHE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4FHE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4fhe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_thermodenitrificans_NG80-2 Geobacillus thermodenitrificans NG80-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FHE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FHE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EEM:[(3S)-3-AMINO-4-HYDROXY-4-OXO-BUTYL]-[[(2S,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL]-METHYL-SELANIUM'>EEM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EEM:[(3S)-3-AMINO-4-HYDROXY-4-OXO-BUTYL]-[[(2S,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL]-METHYL-SELANIUM'>EEM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4fhc\|4fhc]], [[4fhd\|4fhd]], [[4fhf\|4fhf]], [[4fhg\|4fhg]]</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=4fhe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fhe OCA], [https://pdbe.org/4fhe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fhe RCSB], [https://www.ebi.ac.uk/pdbsum/4fhe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fhe ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GTNG_2348 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=420246 GEOTN])~~</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=4fhe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fhe OCA], [~~http~~://pdbe.org/4fhe PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4fhe RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4fhe PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4fhe ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A4IQU1_GEOTN A4IQU1_GEOTN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Geotn~~]]	+	[[Category: Geobacillus thermodenitrificans NG80-2]]
-	[[Category: Barends~~, T R.M~~]]	+	[[Category: Large Structures]]
-	[[Category: Benjdia, A]]	+	[[Category: Barends TRM]]
-	[[Category: Carell, T]]	+	[[Category: Benjdia A]]
-	[[Category: Heil, K]]	+	[[Category: Carell T]]
-	[[Category: Schlichting, I]]	+	[[Category: Heil K]]
-	~~[[Category: Damaged dna]]~~	+	[[Category: Schlichting I]]
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Partial tim-barrel~~]]	+

OCA at 10:03, 5 August 2016

OCA — Fri, 05 Aug 2016 10:03:45 GMT

←Older revision		Revision as of 10:03, 5 August 2016
Line 1:		Line 1:
-	[[Image:4fhe.png\|left\|200px]]

-	~~{{STRUCTURE_4fhe~~\| ~~PDB~~=4fhe \| ~~SCENE~~= }}	+	==Spore photoproduct lyase C140A mutant==
		+	<StructureSection load='4fhe' size='340' side='right' caption='[[4fhe]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4fhe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Geotn Geotn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FHE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FHE FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EEM:[(3S)-3-AMINO-4-HYDROXY-4-OXO-BUTYL]-[[(2S,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL]-METHYL-SELANIUM'>EEM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4fhc\|4fhc]], [[4fhd\|4fhd]], [[4fhf\|4fhf]], [[4fhg\|4fhg]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GTNG_2348 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=420246 GEOTN])</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=4fhe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fhe OCA], [http://pdbe.org/4fhe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fhe RCSB], [http://www.ebi.ac.uk/pdbsum/4fhe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fhe ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacterial spores possess an enormous resistance to ultraviolet (UV) radiation. This is largely due to a unique DNA repair enzyme, Spore Photoproduct Lyase (SP lyase) that repairs a specific UV-induced DNA lesion, the spore photoproduct (SP), through an unprecedented radical-based mechanism. Unlike DNA photolyases, SP lyase belongs to the emerging superfamily of radical S-adenosyl-l-methionine (SAM) enzymes and uses a [4Fe-4S](1+) cluster and SAM to initiate the repair reaction. We report here the first crystal structure of this enigmatic enzyme in complex with its [4Fe-4S] cluster and its SAM cofactor, in the absence and presence of a DNA lesion, the dinucleoside SP. The high resolution structures provide fundamental insights into the active site, the DNA lesion recognition and binding which involve a beta-hairpin structure. We show that SAM and a conserved cysteine residue are perfectly positioned in the active site for hydrogen atom abstraction from the dihydrothymine residue of the lesion and donation to the alpha-thyminyl radical moiety, respectively. Based on structural and biochemical characterizations of mutant proteins, we substantiate the role of this cysteine in the enzymatic mechanism. Our structure reveals how SP lyase combines specific features of radical SAM and DNA repair enzymes to enable a complex radical-based repair reaction to take place.

-	~~===~~Spore ~~photoproduct lyase C140A mutant===~~	+	Structural insights into recognition and repair of UV-DNA damage by Spore Photoproduct Lyase, a radical SAM enzyme.,Benjdia A, Heil K, Barends TR, Carell T, Schlichting I Nucleic Acids Res. 2012 Jul 2. PMID:22761404<ref>PMID:22761404</ref>

-	~~{{ABSTRACT_PUBMED_22761404}}~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~==About this Structure==~~	+	<div class="pdbe-citations 4fhe" style="background-color:#fffaf0;"></div>
-	~~[[4fhe]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Geobacillus_thermodenitrificans_ng80~~-~~2 Geobacillus thermodenitrificans ng80~~-~~2]. Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4FHE OCA].~~	+	== References ==
-		+	<references/>
-	==~~Reference~~==	+	__TOC__
-	<~~ref group="xtra">PMID:022761404<~~/~~ref~~><~~references group="xtra"~~/>	+	</StructureSection>
-	[[Category: ~~Geobacillus thermodenitrificans ng80-2~~]]	+	[[Category: Geotn]]
-	[[Category: Barends, T R.M.]]	+	[[Category: Barends, T R.M]]
-	[[Category: Benjdia, A.]]	+	[[Category: Benjdia, A]]
-	[[Category: Carell, T.]]	+	[[Category: Carell, T]]
-	[[Category: Heil, K.]]	+	[[Category: Heil, K]]
-	[[Category: Schlichting, I.]]	+	[[Category: Schlichting, I]]
	[[Category: Damaged dna]]		[[Category: Damaged dna]]
	[[Category: Dna repair]]		[[Category: Dna repair]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Partial tim-barrel]]		[[Category: Partial tim-barrel]]

OCA at 09:36, 31 October 2012

OCA — Wed, 31 Oct 2012 09:36:12 GMT

←Older revision		Revision as of 09:36, 31 October 2012
Line 1:		Line 1:
-	[[Image:4fhe.~~jpg~~\|left\|200px]]	+	[[Image:4fhe.png\|left\|200px]]

	{{STRUCTURE_4fhe\| PDB=4fhe \| SCENE= }}		{{STRUCTURE_4fhe\| PDB=4fhe \| SCENE= }}
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[4fhe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Geobacillus_thermodenitrificans~~ Geobacillus thermodenitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FHE OCA].	+	[[4fhe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_thermodenitrificans_ng80-2 Geobacillus thermodenitrificans ng80-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FHE OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:022761404</ref><references group="xtra"/>		<ref group="xtra">PMID:022761404</ref><references group="xtra"/>
-	[[Category: Geobacillus thermodenitrificans]]	+	[[Category: Geobacillus thermodenitrificans ng80-2]]
	[[Category: Barends, T R.M.]]		[[Category: Barends, T R.M.]]
	[[Category: Benjdia, A.]]		[[Category: Benjdia, A.]]

OCA at 05:24, 18 July 2012

OCA — Wed, 18 Jul 2012 05:24:42 GMT

←Older revision		Revision as of 05:24, 18 July 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4fhe.jpg\|left\|200px]]

-	~~The entry~~ 4fhe ~~is ON HOLD~~	+	{{STRUCTURE_4fhe\| PDB=4fhe \| SCENE= }}

-	~~Authors: Benjdia, A., Heil, K., Barends, T.R.M., Carell, T., Schlichting, I.~~	+	===Spore photoproduct lyase C140A mutant===

-	~~Description~~: ~~Spore photoproduct lyase C140A mutant~~	+	{{ABSTRACT_PUBMED_22761404}}
		+
		+	==About this Structure==
		+	[[4fhe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_thermodenitrificans Geobacillus thermodenitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FHE OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022761404</ref><references group="xtra"/>
		+	[[Category: Geobacillus thermodenitrificans]]
		+	[[Category: Barends, T R.M.]]
		+	[[Category: Benjdia, A.]]
		+	[[Category: Carell, T.]]
		+	[[Category: Heil, K.]]
		+	[[Category: Schlichting, I.]]
		+	[[Category: Damaged dna]]
		+	[[Category: Dna repair]]
		+	[[Category: Lyase]]
		+	[[Category: Partial tim-barrel]]

OCA at 07:25, 20 June 2012

OCA — Wed, 20 Jun 2012 07:25:56 GMT

←Older revision		Revision as of 07:25, 20 June 2012
Line 5:		Line 5:
	Authors: Benjdia, A., Heil, K., Barends, T.R.M., Carell, T., Schlichting, I.		Authors: Benjdia, A., Heil, K., Barends, T.R.M., Carell, T., Schlichting, I.

-	Description: ~~spore~~ photoproduct lyase C140A mutant	+	Description: Spore photoproduct lyase C140A mutant

OCA: Protected "4fhe" [edit=sysop:move=sysop]

OCA — Wed, 13 Jun 2012 05:52:41 GMT

Protected "4fhe" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:52, 13 June 2012

OCA: New page: '''Unreleased structure''' The entry 4fhe is ON HOLD Authors: Benjdia, A., Heil, K., Barends, T.R.M., Carell, T., Schlichting, I. Description: spore photoproduct lyase C140A mutant

OCA — Wed, 13 Jun 2012 05:52:40 GMT

New page: '''Unreleased structure''' The entry 4fhe is ON HOLD Authors: Benjdia, A., Heil, K., Barends, T.R.M., Carell, T., Schlichting, I. Description: spore photoproduct lyase C140A mutant

New page

'''Unreleased structure'''

The entry 4fhe is ON HOLD

Authors: Benjdia, A., Heil, K., Barends, T.R.M., Carell, T., Schlichting, I.

Description: spore photoproduct lyase C140A mutant