6mth - Revision history

OCA at 06:38, 11 October 2023

2023-10-11T06:38:27Z

←Older revision		Revision as of 06:38, 11 October 2023
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	<StructureSection load='6mth' size='340' side='right'caption='[[6mth]], [[Resolution\|resolution]] 1.35Å' scene=''>		<StructureSection load='6mth' size='340' side='right'caption='[[6mth]], [[Resolution\|resolution]] 1.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mth]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MTH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6MTH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mth]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MTH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MTH FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DHF:DIHYDROFOLIC+ACID'>DHF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=THG:(6S)-5,6,7,8-TETRAHYDROFOLATE'>THG</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]] 1.35Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6mr9\|6mr9]], [[6mt8\|6mt8]]</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=DHF:DIHYDROFOLIC+ACID'>DHF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=THG:(6S)-5,6,7,8-TETRAHYDROFOLATE'>THG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">folA, tmrA, b0048, JW0047 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=6mth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mth OCA], [https://pdbe.org/6mth PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mth RCSB], [https://www.ebi.ac.uk/pdbsum/6mth PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mth ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydrofolate_reductase Dihydrofolate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.3 1.5.1.3] </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=6mth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mth OCA], [~~http~~://pdbe.org/6mth PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6mth RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6mth PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6mth ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DYR_ECOLI DYR_ECOLI]] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.	+	[https://www.uniprot.org/uniprot/DYR_ECOLI DYR_ECOLI] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Dihydrofolate reductase]]~~	+	[[Category: Escherichia coli K-12]]
-	~~[[Category: Ecoli~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Benach, J]]	+	[[Category: Benach J]]
-	[[Category: Cao, H]]	+	[[Category: Cao H]]
-	[[Category: Frommelt, A]]	+	[[Category: Frommelt A]]
-	[[Category: Koss, J]]	+	[[Category: Koss J]]
-	[[Category: Morisco, L]]	+	[[Category: Morisco L]]
-	[[Category: Rodrigues, J]]	+	[[Category: Rodrigues J]]
-	[[Category: Shakhnovich, E]]	+	[[Category: Shakhnovich E]]
-	[[Category: Skolnick, J]]	+	[[Category: Skolnick J]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 11:29, 1 January 2020

2020-01-01T11:29:18Z

←Older revision		Revision as of 11:29, 1 January 2020
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	</div>		</div>
	<div class="pdbe-citations 6mth" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6mth" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dihydrofolate reductase 3D structures\|Dihydrofolate reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:32, 21 May 2019

2019-05-21T07:32:27Z

←Older revision		Revision as of 07:32, 21 May 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6mth is ~~ON HOLD until Paper~~ Publication	+	==E. coli DHFR complex modeled with three ligand states==
		+	<StructureSection load='6mth' size='340' side='right'caption='[[6mth]], [[Resolution\|resolution]] 1.35Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6mth]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MTH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MTH FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DHF:DIHYDROFOLIC+ACID'>DHF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=THG:(6S)-5,6,7,8-TETRAHYDROFOLATE'>THG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6mr9\|6mr9]], [[6mt8\|6mt8]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">folA, tmrA, b0048, JW0047 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydrofolate_reductase Dihydrofolate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.3 1.5.1.3] </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=6mth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mth OCA], [http://pdbe.org/6mth PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mth RCSB], [http://www.ebi.ac.uk/pdbsum/6mth PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mth ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DYR_ECOLI DYR_ECOLI]] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Time-resolved crystallography is a powerful technique to elucidate molecular mechanisms at both spatial (angstroms) and temporal (picoseconds to seconds) resolutions. We recently discovered an unusually slow reaction at room temperature that occurs on the order of days: the in crystalline reverse oxidative decay of the chemically labile (6S)-5,6,7,8-tetrahydrofolate in complex with its producing enzyme Escherichia coli dihydrofolate reductase. Here, we report the critical analysis of a representative dataset at an intermediate reaction time point. A quinonoid-like intermediate state lying between tetrahydrofolate and dihydrofolate features a near coplanar geometry of the bicyclic pterin moiety, and a tetrahedral sp (3) C6 geometry is proposed based on the apparent mFo-DFc omit electron densities of the ligand. The presence of this intermediate is strongly supported by Bayesian difference refinement. Isomorphous Fo-Fo difference map and multi-state refinement analyses suggest the presence of end-state ligand populations as well, although the putative intermediate state is likely the most populated. A similar quinonoid intermediate previously proposed to transiently exist during the oxidation of tetrahydrofolate was confirmed by polarography and UV-vis spectroscopy to be relatively stable in the oxidation of its close analog tetrahydropterin. We postulate that the constraints on the ligand imposed by the interactions with the protein environment might be the origin of the slow reaction observed by time-resolved crystallography.

-	~~Authors:~~ Cao, H~~., Rodrigues~~, J.~~, Benach, J~~.~~, Frommelt, A~~.~~, Morisco, L~~.~~, Koss, J~~.~~, Shakhnovich, E., Skolnick, J~~.	+	Time-resolved x-ray crystallography capture of a slow reaction tetrahydrofolate intermediate.,Cao H, Skolnick J Struct Dyn. 2019 Mar 1;6(2):024701. doi: 10.1063/1.5086436. eCollection 2019 Mar. PMID:30868089<ref>PMID:30868089</ref>

-	~~Description: E~~. ~~coli DHFR complex modeled with three ligand states~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6mth" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dihydrofolate reductase]]
		+	[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Benach, J]]		[[Category: Benach, J]]
	[[Category: Cao, H]]		[[Category: Cao, H]]
		+	[[Category: Frommelt, A]]
	[[Category: Koss, J]]		[[Category: Koss, J]]
	[[Category: Morisco, L]]		[[Category: Morisco, L]]
-	[[Category: Frommelt, A]]
-	[[Category: Shakhnovich, E]]
	[[Category: Rodrigues, J]]		[[Category: Rodrigues, J]]
		+	[[Category: Shakhnovich, E]]
	[[Category: Skolnick, J]]		[[Category: Skolnick, J]]
		+	[[Category: Complex]]
		+	[[Category: Oxidoreductase]]

OCA: Protected "6mth" [edit=sysop:move=sysop]

2018-10-31T05:30:56Z

Protected "6mth" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:30, 31 October 2018

OCA: New page: '''Unreleased structure''' The entry 6mth is ON HOLD until Paper Publication Authors: Cao, H., Rodrigues, J., Benach, J., Frommelt, A., Morisco, L., Koss, J., Shakhnovich, E., Skolnick,...

2018-10-31T05:30:55Z

New page: '''Unreleased structure''' The entry 6mth is ON HOLD until Paper Publication Authors: Cao, H., Rodrigues, J., Benach, J., Frommelt, A., Morisco, L., Koss, J., Shakhnovich, E., Skolnick,...

New page

'''Unreleased structure'''

The entry 6mth is ON HOLD until Paper Publication

Authors: Cao, H., Rodrigues, J., Benach, J., Frommelt, A., Morisco, L., Koss, J., Shakhnovich, E., Skolnick, J.

Description: E. coli DHFR complex modeled with three ligand states
[[Category: Unreleased Structures]]
[[Category: Benach, J]]
[[Category: Cao, H]]
[[Category: Koss, J]]
[[Category: Morisco, L]]
[[Category: Frommelt, A]]
[[Category: Shakhnovich, E]]
[[Category: Rodrigues, J]]
[[Category: Skolnick, J]]