5w3q - Revision history

OCA at 14:06, 4 October 2023

OCA — Wed, 04 Oct 2023 14:06:23 GMT

←Older revision		Revision as of 14:06, 4 October 2023
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	<StructureSection load='5w3q' size='340' side='right'caption='[[5w3q]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='5w3q' size='340' side='right'caption='[[5w3q]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w3q]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W3Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5W3Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w3q]] 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=5W3Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5W3Q FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>~~, ~~<scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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]] 1.401Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>folA, tmrA, b0048, JW0047 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~83333 ECOLI])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Dihydrofolate_reductase Dihydrofolate reductase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=5w3q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w3q OCA], [https://pdbe.org/5w3q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5w3q RCSB], [https://www.ebi.ac.uk/pdbsum/5w3q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5w3q 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=5w3q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w3q OCA], [https://pdbe.org/5w3q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5w3q RCSB], [https://www.ebi.ac.uk/pdbsum/5w3q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5w3q ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[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.	+	[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 ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Dihydrofolate reductase]]~~	+	[[Category: Escherichia coli K-12]]
-	~~[[Category: Ecoli~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Oyen, D]]	+	[[Category: Oyen D]]
-	[[Category: Wilson~~, I A~~]]	+	[[Category: Wilson IA]]
-	[[Category: Wright~~, P E]]~~	+	[[Category: Wright PE]]
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 11:32, 23 March 2022

OCA — Wed, 23 Mar 2022 11:32:12 GMT

←Older revision		Revision as of 11:32, 23 March 2022
Line 3:		Line 3:
	<StructureSection load='5w3q' size='340' side='right'caption='[[5w3q]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='5w3q' size='340' side='right'caption='[[5w3q]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w3q]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W3Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5W3Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w3q]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W3Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5W3Q FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">folA, tmrA, b0048, JW0047 ([https://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'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5w3q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w3q OCA], [~~http~~://pdbe.org/5w3q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5w3q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5w3q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5w3q ProSAT]</span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Dihydrofolate_reductase Dihydrofolate reductase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=5w3q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w3q OCA], [https://pdbe.org/5w3q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5w3q RCSB], [https://www.ebi.ac.uk/pdbsum/5w3q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5w3q 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 ==
Line 27:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Dihydrofolate reductase]]		[[Category: Dihydrofolate reductase]]
		+	[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Oyen, D]]		[[Category: Oyen, D]]

OCA at 08:47, 30 September 2020

OCA — Wed, 30 Sep 2020 08:47:53 GMT

←Older revision		Revision as of 08:47, 30 September 2020
Line 1:		Line 1:

	==L28F E.coli DHFR in complex with NADPH==		==L28F E.coli DHFR in complex with NADPH==
-	<StructureSection load='5w3q' size='340' side='right' caption='[[5w3q]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='5w3q' size='340' side='right'caption='[[5w3q]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w3q]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W3Q OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5W3Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w3q]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W3Q OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5W3Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></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=5w3q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w3q OCA], [http://pdbe.org/5w3q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w3q RCSB], [http://www.ebi.ac.uk/pdbsum/5w3q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w3q ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5w3q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w3q OCA], [http://pdbe.org/5w3q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w3q RCSB], [http://www.ebi.ac.uk/pdbsum/5w3q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w3q ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5w3q" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5w3q" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dihydrofolate reductase 3D structures\|Dihydrofolate reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Dihydrofolate reductase]]		[[Category: Dihydrofolate reductase]]
		+	[[Category: Large Structures]]
	[[Category: Oyen, D]]		[[Category: Oyen, D]]
	[[Category: Wilson, I A]]		[[Category: Wilson, I A]]
	[[Category: Wright, P E]]		[[Category: Wright, P E]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA: Protected "5w3q" [edit=sysop:move=sysop]

OCA — Wed, 09 Aug 2017 09:03:34 GMT

Protected "5w3q" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:03, 9 August 2017

OCA: New page: ==L28F E.coli DHFR in complex with NADPH== == Structural highligh...

OCA — Wed, 09 Aug 2017 09:03:31 GMT

New page: ==L28F E.coli DHFR in complex with NADPH== <StructureSection load='5w3q' size='340' side='right' caption='5w3q, resolution 1.40Å' scene=''> == Structural highligh...

New page

==L28F E.coli DHFR in complex with NADPH==
<StructureSection load='5w3q' size='340' side='right' caption='[[5w3q]], [[Resolution|resolution]] 1.40Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5w3q]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W3Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W3Q FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></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=5w3q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w3q OCA], [http://pdbe.org/5w3q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w3q RCSB], [http://www.ebi.ac.uk/pdbsum/5w3q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w3q 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 ==
The rate-determining step in the catalytic cycle of E. coli dihydrofolate reductase is tetrahydrofolate (THF) product release, which can occur via an allosteric or an intrinsic pathway. The allosteric pathway, which becomes accessible when the reduced cofactor NADPH is bound, involves transient sampling of a higher energy conformational state, greatly increasing the product dissociation rate as compared to the intrinsic pathway that obtains when NADPH is absent. Although the kinetics of this process are known, the enzyme structure and the THF product conformation in the transiently formed excited state remain elusive. Here, we use side-chain proton NMR relaxation dispersion measurements, X-ray crystallography, and structure-based chemical shift predictions to explore the structural basis of allosteric product release. In the excited state of the E:THF:NADPH product release complex, the reduced nicotinamide ring of the cofactor transiently enters the active site where it displaces the pterin ring of the THF product. The p-aminobenzoyl-l-glutamate tail of THF remains weakly bound in a widened binding cleft. Thus, through transient entry of the nicotinamide ring into the active site, the NADPH cofactor remodels the enzyme structure and the conformation of the THF to form a weakly populated excited state that is poised for rapid product release.

Defining the Structural Basis for Allosteric Product Release from E. coli Dihydrofolate Reductase Using NMR Relaxation Dispersion.,Oyen D, Fenwick RB, Aoto PC, Stanfield RL, Wilson IA, Dyson HJ, Wright PE J Am Chem Soc. 2017 Aug 3. doi: 10.1021/jacs.7b05958. PMID:28737940<ref>PMID:28737940</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5w3q" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Dihydrofolate reductase]]
[[Category: Oyen, D]]
[[Category: Wilson, I A]]
[[Category: Wright, P E]]
[[Category: Oxidoreductase]]