5z6f - Revision history

OCA at 08:46, 22 November 2023

OCA — Wed, 22 Nov 2023 08:46:26 GMT

←Older revision		Revision as of 08:46, 22 November 2023
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	<StructureSection load='5z6f' size='340' side='right'caption='[[5z6f]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5z6f' size='340' side='right'caption='[[5z6f]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z6f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z6F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5Z6F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z6f]] 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=5Z6F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z6F FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>~~, ~~<scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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]] 1.801Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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'>[https://proteopedia.org/fgij/fg.htm?mol=5z6f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z6f OCA], [https://pdbe.org/5z6f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z6f RCSB], [https://www.ebi.ac.uk/pdbsum/5z6f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z6f 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=5z6f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z6f OCA], [~~http~~://pdbe.org/5z6f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5z6f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5z6f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5z6f 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 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Dihydrofolate reductase~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Nagae, T]]	+	[[Category: Nagae T]]
-	[[Category: Watanabe, N]]	+	[[Category: Watanabe N]]
-	[[Category: Yamada, H]]	+	[[Category: Yamada H]]
-	~~[[Category: M20 loop closed form]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 21:15, 28 October 2020

OCA — Wed, 28 Oct 2020 21:15:05 GMT

←Older revision		Revision as of 21:15, 28 October 2020
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	==High-pressure Crystal Structure Analysis of DHFR(0.1 MPa)==		==High-pressure Crystal Structure Analysis of DHFR(0.1 MPa)==
-	<StructureSection load='5z6f' size='340' side='right' caption='[[5z6f]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5z6f' size='340' side='right'caption='[[5z6f]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z6f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z6F OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Z6F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z6f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z6F OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5Z6F FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</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=5z6f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z6f OCA], [http://pdbe.org/5z6f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z6f RCSB], [http://www.ebi.ac.uk/pdbsum/5z6f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z6f 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=5z6f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z6f OCA], [http://pdbe.org/5z6f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z6f RCSB], [http://www.ebi.ac.uk/pdbsum/5z6f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z6f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5z6f" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5z6f" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dihydrofolate reductase 3D structures\|Dihydrofolate reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Dihydrofolate reductase]]		[[Category: Dihydrofolate reductase]]
		+	[[Category: Large Structures]]
	[[Category: Nagae, T]]		[[Category: Nagae, T]]
	[[Category: Watanabe, N]]		[[Category: Watanabe, N]]

OCA at 19:40, 19 September 2018

OCA — Wed, 19 Sep 2018 19:40:29 GMT

←Older revision		Revision as of 19:40, 19 September 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5z6f is ~~ON HOLD until Paper~~ Publication	+	==High-pressure Crystal Structure Analysis of DHFR(0.1 MPa)==
		+	<StructureSection load='5z6f' size='340' side='right' caption='[[5z6f]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5z6f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z6F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z6F FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</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=5z6f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z6f OCA], [http://pdbe.org/5z6f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z6f RCSB], [http://www.ebi.ac.uk/pdbsum/5z6f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z6f 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 ==
		+	A high-pressure crystallographic study was conducted on Escherichia coli dihydrofolate reductase (ecDHFR) complexed with folate and NADP(+) in crystal forms containing both the open and closed conformations of the M20 loop under high-pressure conditions of up to 800 MPa. At pressures between 270 and 500 MPa the crystal form containing the open conformation exhibited a phase transition from P21 to C2. Several structural changes in ecDHFR were observed at high pressure that were also accompanied by structural changes in the NADP(+) cofactor and the hydration structure. In the crystal form with the closed conformation the M20 loop moved as the pressure changed, with accompanying conformational changes around the active site, including NADP(+) and folate. These movements were consistent with the suggested hypothesis that movement of the M20 loop was necessary for ecDHFR to catalyze the reaction. In the crystal form with the open conformation the nicotinamide ring of the NADP(+) cofactor undergoes a large flip as an intermediate step in the reaction, despite being in a crystalline state. Furthermore, observation of the water molecules between Arg57 and folate elucidated an early step in the substrate-binding pathway. These results demonstrate the possibility of using high-pressure protein crystallography as a method to capture high-energy substates or transient structures related to the protein reaction cycle.

-	~~Authors: Watanabe, N~~., Nagae, T., Yamada, H.	+	High-pressure protein crystal structure analysis of Escherichia coli dihydrofolate reductase complexed with folate and NADP().,Nagae T, Yamada H, Watanabe N Acta Crystallogr D Struct Biol. 2018 Sep 1;74(Pt 9):895-905. doi:, 10.1107/S2059798318009397. Epub 2018 Sep 3. PMID:30198899<ref>PMID:30198899</ref>

-	~~Description: High-pressure Crystal Structure Analysis~~ of ~~DHFR(0~~.~~1 MPa)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5z6f" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dihydrofolate reductase]]
		+	[[Category: Nagae, T]]
	[[Category: Watanabe, N]]		[[Category: Watanabe, N]]
	[[Category: Yamada, H]]		[[Category: Yamada, H]]
-	[[Category: ~~Nagae, T~~]]	+	[[Category: M20 loop closed form]]
		+	[[Category: Oxidoreductase]]

OCA at 04:57, 14 March 2018

OCA — Wed, 14 Mar 2018 04:57:29 GMT

←Older revision		Revision as of 04:57, 14 March 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5z6f is ON HOLD	+	The entry 5z6f is ON HOLD until Paper Publication

	Authors: Watanabe, N., Nagae, T., Yamada, H.		Authors: Watanabe, N., Nagae, T., Yamada, H.

-	Description: High-pressure Crystal Structure Analysis of DHFR	+	Description: High-pressure Crystal Structure Analysis of DHFR(0.1 MPa)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Watanabe, N]]		[[Category: Watanabe, N]]
	[[Category: Yamada, H]]		[[Category: Yamada, H]]
	[[Category: Nagae, T]]		[[Category: Nagae, T]]

OCA: Protected "5z6f" [edit=sysop:move=sysop]

OCA — Wed, 31 Jan 2018 04:41:08 GMT

Protected "5z6f" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:41, 31 January 2018

OCA: New page: '''Unreleased structure''' The entry 5z6f is ON HOLD Authors: Watanabe, N., Nagae, T., Yamada, H. Description: High-pressure Crystal Structure Analysis of DHFR [[Category: Unreleased S...

OCA — Wed, 31 Jan 2018 04:41:07 GMT

New page: '''Unreleased structure''' The entry 5z6f is ON HOLD Authors: Watanabe, N., Nagae, T., Yamada, H. Description: High-pressure Crystal Structure Analysis of DHFR [[Category: Unreleased S...

New page

'''Unreleased structure'''

The entry 5z6f is ON HOLD

Authors: Watanabe, N., Nagae, T., Yamada, H.

Description: High-pressure Crystal Structure Analysis of DHFR
[[Category: Unreleased Structures]]
[[Category: Watanabe, N]]
[[Category: Yamada, H]]
[[Category: Nagae, T]]