7ndz - Revision history

OCA at 12:33, 1 February 2024

2024-02-01T12:33:23Z

←Older revision		Revision as of 12:33, 1 February 2024
Line 3:		Line 3:
	<StructureSection load='7ndz' size='340' side='right'caption='[[7ndz]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='7ndz' size='340' side='right'caption='[[7ndz]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7ndz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_43589 Atcc 43589~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NDZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ndz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NDZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FDA:DIHYDROFLAVINE-ADENINE+DINUCLEOTIDE'>FDA</scene>, <scene name='pdbligand=HUF:[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl]+hydrogen+phosphate'>HUF</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 2.7Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7ndw\|7ndw]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FDA:DIHYDROFLAVINE-ADENINE+DINUCLEOTIDE'>FDA</scene>, <scene name='pdbligand=HUF:[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl]+hydrogen+phosphate'>HUF</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">thyX, thy1, TM_0449 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Thymidylate_synthase_(FAD) Thymidylate synthase (FAD)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.148 2.1.1.148] </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=7ndz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ndz OCA], [https://pdbe.org/7ndz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ndz RCSB], [https://www.ebi.ac.uk/pdbsum/7ndz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ndz 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=7ndz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ndz OCA], [https://pdbe.org/7ndz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ndz RCSB], [https://www.ebi.ac.uk/pdbsum/7ndz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ndz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/THYX_THEMA THYX_THEMA]] Catalyzes the formation of dTMP and tetrahydrofolate from dUMP and methylenetetrahydrofolate.	+	[https://www.uniprot.org/uniprot/THYX_THEMA THYX_THEMA] Catalyzes the formation of dTMP and tetrahydrofolate from dUMP and methylenetetrahydrofolate.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 7ndz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7ndz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Thymidylate synthase 3D structures\|Thymidylate synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43589]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bou-Nader, C]]	+	[[Category: Thermotoga maritima]]
-	[[Category: Hamdane, D]]	+	[[Category: Bou-Nader C]]
-	[[Category: Pecqueur, L]]	+	[[Category: Hamdane D]]
-	~~[[Category: Flavin-dependent thymidylate synthase]]~~	+	[[Category: Pecqueur L]]
-	~~[[Category: Methylenetetrahydrofolate]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:03, 29 September 2021

2021-09-29T09:03:39Z

←Older revision		Revision as of 09:03, 29 September 2021
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	==ThyX reconstituted with N5-carbinolamine flavin==		==ThyX reconstituted with N5-carbinolamine flavin==
-	<StructureSection load='7ndz' size='340' side='right'caption='[[7ndz]]' scene=''>	+	<StructureSection load='7ndz' size='340' side='right'caption='[[7ndz]], [[Resolution\|resolution]] 2.70Å' 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=7NDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NDZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ndz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NDZ 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=7ndz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ndz OCA], [https://pdbe.org/7ndz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ndz RCSB], [https://www.ebi.ac.uk/pdbsum/7ndz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ndz 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=FDA:DIHYDROFLAVINE-ADENINE+DINUCLEOTIDE'>FDA</scene>, <scene name='pdbligand=HUF:[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl]+hydrogen+phosphate'>HUF</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7ndw\|7ndw]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">thyX, thy1, TM_0449 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Thymidylate_synthase_(FAD) Thymidylate synthase (FAD)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.148 2.1.1.148] </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=7ndz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ndz OCA], [https://pdbe.org/7ndz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ndz RCSB], [https://www.ebi.ac.uk/pdbsum/7ndz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ndz ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/THYX_THEMA THYX_THEMA]] Catalyzes the formation of dTMP and tetrahydrofolate from dUMP and methylenetetrahydrofolate.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Folate enzyme cofactors and their derivatives have the unique ability to provide a single carbon unit at different oxidation levels for the de novo synthesis of amino-acids, purines, or thymidylate, an essential DNA nucleotide. How these cofactors mediate methylene transfer is not fully settled yet, particularly with regard to how the methylene is transferred to the methylene acceptor. Here, we uncovered that the bacterial thymidylate synthase ThyX, which relies on both folate and flavin for activity, can also use a formaldehyde-shunt to directly synthesize thymidylate. Combining biochemical, spectroscopic and anaerobic crystallographic analyses, we showed that formaldehyde reacts with the reduced flavin coenzyme to form a carbinolamine intermediate used by ThyX for dUMP methylation. The crystallographic structure of this intermediate reveals how ThyX activates formaldehyde and uses it, with the assistance of active site residues, to methylate dUMP. Our results reveal that carbinolamine species promote methylene transfer and suggest that the use of a CH2O-shunt may be relevant in several other important folate-dependent reactions.
		+
		+	An enzymatic activation of formaldehyde for nucleotide methylation.,Bou-Nader C, Stull FW, Pecqueur L, Simon P, Guerineau V, Royant A, Fontecave M, Lombard M, Palfey BA, Hamdane D Nat Commun. 2021 Jul 27;12(1):4542. doi: 10.1038/s41467-021-24756-8. PMID:34315871<ref>PMID:34315871</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7ndz" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 43589]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bou-Nader C]]	+	[[Category: Bou-Nader, C]]
-	[[Category: Hamdane D]]	+	[[Category: Hamdane, D]]
-	[[Category: Pecqueur L]]	+	[[Category: Pecqueur, L]]
		+	[[Category: Flavin-dependent thymidylate synthase]]
		+	[[Category: Methylenetetrahydrofolate]]
		+	[[Category: Transferase]]

OCA at 08:59, 21 July 2021

2021-07-21T08:59:02Z

←Older revision		Revision as of 08:59, 21 July 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7ndz is ~~ON HOLD until Paper Publication~~	+	==ThyX reconstituted with N5-carbinolamine flavin==
-		+	<StructureSection load='7ndz' size='340' side='right'caption='[[7ndz]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NDZ FirstGlance]. <br>
-	~~Description~~:	+	</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=7ndz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ndz OCA], [https://pdbe.org/7ndz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ndz RCSB], [https://www.ebi.ac.uk/pdbsum/7ndz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ndz ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Bou-Nader C]]
		+	[[Category: Hamdane D]]
		+	[[Category: Pecqueur L]]

OCA at 08:52, 17 February 2021

2021-02-17T08:52:17Z

←Older revision		Revision as of 08:52, 17 February 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7ndz is ON HOLD	+	The entry 7ndz is ON HOLD until Paper Publication

	Authors:		Authors:

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

2021-02-10T09:25:59Z

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

←Older revision

Revision as of 09:25, 10 February 2021

OCA: New page: '''Unreleased structure''' The entry 7ndz is ON HOLD Authors: Description: Category: Unreleased Structures

2021-02-10T09:25:58Z

New page: '''Unreleased structure''' The entry 7ndz is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7ndz is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]