6cxk - Revision history

OCA at 15:13, 4 October 2023

2023-10-04T15:13:23Z

←Older revision		Revision as of 15:13, 4 October 2023
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	<StructureSection load='6cxk' size='340' side='right'caption='[[6cxk]], [[Resolution\|resolution]] 1.11Å' scene=''>		<StructureSection load='6cxk' size='340' side='right'caption='[[6cxk]], [[Resolution\|resolution]] 1.11Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cxk]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecol6 Ecol6~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CXK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6CXK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cxk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_CFT073 Escherichia coli CFT073]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CXK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CXK 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></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]] 1.108Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6cw7\|6cw7]]~~, [[~~6cqa~~\|~~6cqa~~]]</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></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~folA, c0058 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=199310 ECOL6])</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=6cxk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cxk OCA], [https://pdbe.org/6cxk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cxk RCSB], [https://www.ebi.ac.uk/pdbsum/6cxk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cxk 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=6cxk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cxk OCA], [~~http~~://pdbe.org/6cxk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6cxk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6cxk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6cxk ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~DYR_ECOL6 DYR_ECOL6]~~] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis ~~(By similarity)~~.	+	[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 CFT073]]
-	~~[[Category: Ecol6~~]]	+
	[[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: Dhfr]]~~	+
-	~~[[Category: Dihydrofolate]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 10:52, 1 January 2020

2020-01-01T10:52:50Z

←Older revision		Revision as of 10:52, 1 January 2020
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	==E. coli DHFR substrate complex with Dihydrofolate==		==E. coli DHFR substrate complex with Dihydrofolate==
-	<StructureSection load='6cxk' size='340' side='right' caption='[[6cxk]], [[Resolution\|resolution]] 1.11Å' scene=''>	+	<StructureSection load='6cxk' size='340' side='right'caption='[[6cxk]], [[Resolution\|resolution]] 1.11Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cxk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CXK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CXK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cxk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecol6 Ecol6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CXK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CXK 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></td></tr>		</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></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6cw7\|6cw7]], [[6cqa\|6cqa]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6cw7\|6cw7]], [[6cqa\|6cqa]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">folA, c0058 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=199310 ECOL6])</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='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=6cxk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cxk OCA], [http://pdbe.org/6cxk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cxk RCSB], [http://www.ebi.ac.uk/pdbsum/6cxk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cxk 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=6cxk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cxk OCA], [http://pdbe.org/6cxk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cxk RCSB], [http://www.ebi.ac.uk/pdbsum/6cxk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cxk ProSAT]</span></td></tr>
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	</div>		</div>
	<div class="pdbe-citations 6cxk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6cxk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dihydrofolate reductase 3D structures\|Dihydrofolate reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Dihydrofolate reductase]]		[[Category: Dihydrofolate reductase]]
		+	[[Category: Ecol6]]
		+	[[Category: Large Structures]]
	[[Category: Benach, J]]		[[Category: Benach, J]]
	[[Category: Cao, H]]		[[Category: Cao, H]]

OCA at 06:34, 9 January 2019

2019-01-09T06:34:29Z

←Older revision		Revision as of 06:34, 9 January 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6cxk is ~~ON HOLD until Paper~~ Publication	+	==E. coli DHFR substrate complex with Dihydrofolate==
		+	<StructureSection load='6cxk' size='340' side='right' caption='[[6cxk]], [[Resolution\|resolution]] 1.11Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6cxk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CXK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CXK 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></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6cw7\|6cw7]], [[6cqa\|6cqa]]</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=6cxk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cxk OCA], [http://pdbe.org/6cxk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cxk RCSB], [http://www.ebi.ac.uk/pdbsum/6cxk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cxk ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DYR_ECOL6 DYR_ECOL6]] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Dihydrofolate reductase (DHFR) catalyzes the stereospecific reduction of 7,8-dihydrofolate (FH2) to (6s)-5,6,7,8-tetrahydrofolate (FH4) via hydride transfer from NADPH. The consensus Escherichia coli DHFR mechanism involves conformational changes between closed and occluded states occurring during the rate-limiting product release step. Although the Protein Data Bank (PDB) contains over 250 DHFR structures, the FH4 complex structure responsible for rate-limiting product release is unknown. We report to our knowledge the first crystal structure of an E. coli. DHFR:FH4 complex at 1.03 A resolution showing distinct stabilizing interactions absent in FH2 or related (6R)-5,10-dideaza-FH4 complexes. We discover the time course of decay of the co-purified endogenous FH4 during crystal growth, with conversion from FH4 to FH2 occurring in 2-3 days. We also determine another occluded complex structure of E. coli DHFR with a slow-onset nanomolar inhibitor that contrasts with the methotrexate complex, suggesting a plausible strategy for designing DHFR antibiotics by targeting FH4 product conformations.

-	~~Authors:~~ Cao, H., ~~Rodrigues~~, ~~J., Benach~~, J.~~, Frommelt, A~~.~~, Morisco, L~~.~~, Koss, J~~.~~, Shakhnovich, E., Skolnick, J~~.	+	The crystal structure of a tetrahydrofolate-bound dihydrofolate reductase reveals the origin of slow product release.,Cao H, Gao M, Zhou H, Skolnick J Commun Biol. 2018 Dec 12;1:226. doi: 10.1038/s42003-018-0236-y. eCollection 2018. PMID:30564747<ref>PMID:30564747</ref>

-	~~Description: E~~. ~~coli DHFR substrate complex with~~ Dihydrofolate	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6cxk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dihydrofolate reductase]]
		+	[[Category: Benach, J]]
		+	[[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: ~~Benach~~, J]]	+	[[Category: Shakhnovich, E]]
	[[Category: Skolnick, J]]		[[Category: Skolnick, J]]
-	[[Category: ~~Cao, H~~]]	+	[[Category: Complex]]
		+	[[Category: Dhfr]]
		+	[[Category: Dihydrofolate]]
		+	[[Category: Oxidoreductase]]

OCA at 04:12, 18 April 2018

2018-04-18T04:12:17Z

←Older revision		Revision as of 04:12, 18 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6cxk is ON HOLD	+	The entry 6cxk is ON HOLD until Paper Publication

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

-	Description: E. coli DHFR ~~product~~ complex with Dihydrofolate	+	Description: E. coli DHFR substrate complex with Dihydrofolate
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Koss, J]]		[[Category: Koss, J]]

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

2018-04-11T12:32:30Z

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

←Older revision

Revision as of 12:32, 11 April 2018

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

2018-04-11T12:32:28Z

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

New page

'''Unreleased structure'''

The entry 6cxk is ON HOLD

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

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