5fo5 - Revision history

OCA at 07:01, 19 July 2023

OCA — Wed, 19 Jul 2023 07:01:01 GMT

←Older revision		Revision as of 07:01, 19 July 2023
Line 3:		Line 3:
	<StructureSection load='5fo5' size='340' side='right'caption='[[5fo5]], [[Resolution\|resolution]] 2.16Å' scene=''>		<StructureSection load='5fo5' size='340' side='right'caption='[[5fo5]], [[Resolution\|resolution]] 2.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fo5]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FO5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5FO5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fo5]] 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=5FO5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FO5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 2.16Å</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=5fo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fo5 OCA], [~~http~~://pdbe.org/5fo5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fo5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fo5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fo5 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5fo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fo5 OCA], [https://pdbe.org/5fo5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fo5 RCSB], [https://www.ebi.ac.uk/pdbsum/5fo5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fo5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/METR_ECOLI METR_ECOLI]] Control of the last step in methionine biosynthesis; MetR is a positive activator of the metA, metE and metH genes. MetR is also a negative regulator of its own expression. Binds homocysteine as an inducer.	+	[https://www.uniprot.org/uniprot/METR_ECOLI METR_ECOLI] Control of the last step in methionine biosynthesis; MetR is a positive activator of the metA, metE and metH genes. MetR is also a negative regulator of its own expression. Binds homocysteine as an inducer.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5fo5" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5fo5" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Transcriptional activator 3D structures\|Transcriptional activator 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Carr~~, S B~~]]	+	[[Category: Carr SB]]
-	[[Category: Phillips~~, S E~~]]	+	[[Category: Phillips SE]]
-	[[Category: Porter, J]]	+	[[Category: Porter J]]
-	[[Category: Punekar~~, A S~~]]	+	[[Category: Punekar AS]]
-	[[Category: Stauffer~~, G V~~]]	+	[[Category: Stauffer GV]]
-	[[Category: Urbanowski~~, M L]]~~	+	[[Category: Urbanowski ML]]
-	~~[[Category: Activator]]~~	+
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Hth]]~~	+
-	~~[[Category: Lysr-type transcriptional regulator]]~~	+
-	~~[[Category: Methionine biosynthesis]]~~	+
-	~~[[Category: Repressor]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription regulation~~]]	+

OCA at 07:27, 6 May 2020

OCA — Wed, 06 May 2020 07:27:59 GMT

←Older revision		Revision as of 07:27, 6 May 2020
Line 1:		Line 1:

	==Structure of the DNA-binding domain of Escherichia coli methionine biosynthesis regulator MetR==		==Structure of the DNA-binding domain of Escherichia coli methionine biosynthesis regulator MetR==
-	<StructureSection load='5fo5' size='340' side='right' caption='[[5fo5]], [[Resolution\|resolution]] 2.16Å' scene=''>	+	<StructureSection load='5fo5' size='340' side='right'caption='[[5fo5]], [[Resolution\|resolution]] 2.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fo5]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FO5 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FO5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fo5]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FO5 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FO5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5fo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fo5 OCA], [http://pdbe.org/5fo5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fo5 RCSB], [http://www.ebi.ac.uk/pdbsum/5fo5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fo5 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=5fo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fo5 OCA], [http://pdbe.org/5fo5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fo5 RCSB], [http://www.ebi.ac.uk/pdbsum/5fo5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fo5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Carr, S B]]		[[Category: Carr, S B]]
	[[Category: Phillips, S E]]		[[Category: Phillips, S E]]

OCA at 17:36, 12 July 2016

OCA — Tue, 12 Jul 2016 17:36:45 GMT

←Older revision		Revision as of 17:36, 12 July 2016
Line 5:		Line 5:
	<table><tr><td colspan='2'>[[5fo5]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FO5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FO5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5fo5]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FO5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FO5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5fo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fo5 OCA], [http://pdbe.org/5fo5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fo5 RCSB], [http://www.ebi.ac.uk/pdbsum/5fo5 PDBsum]</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=5fo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fo5 OCA], [http://pdbe.org/5fo5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fo5 RCSB], [http://www.ebi.ac.uk/pdbsum/5fo5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fo5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/METR_ECOLI METR_ECOLI]] Control of the last step in methionine biosynthesis; MetR is a positive activator of the metA, metE and metH genes. MetR is also a negative regulator of its own expression. Binds homocysteine as an inducer.		[[http://www.uniprot.org/uniprot/METR_ECOLI METR_ECOLI]] Control of the last step in methionine biosynthesis; MetR is a positive activator of the metA, metE and metH genes. MetR is also a negative regulator of its own expression. Binds homocysteine as an inducer.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	MetR, a LysR-type transcriptional regulator (LTTR), has been extensively studied owing to its role in the control of methionine biosynthesis in proteobacteria. A MetR homodimer binds to a 24-base-pair operator region of the met genes and specifically recognizes the interrupted palindromic sequence 5'-TGAA-N5-TTCA-3'. Mechanistic details underlying the interaction of MetR with its target DNA at the molecular level remain unknown. In this work, the crystal structure of the DNA-binding domain (DBD) of MetR was determined at 2.16 A resolution. MetR-DBD adopts a winged-helix-turn-helix (wHTH) motif and shares significant fold similarity with the DBD of the LTTR protein BenM. Furthermore, a data-driven macromolecular-docking strategy was used to model the structure of MetR-DBD bound to DNA, which revealed that a bent conformation of DNA is required for the recognition helix alpha3 and the wing loop of the wHTH motif to interact with the major and minor grooves, respectively. Comparison of the MetR-DBD-DNA complex with the crystal structures of other LTTR-DBD-DNA complexes revealed residues that may confer operator-sequence binding specificity for MetR. Taken together, the results show that MetR-DBD uses a combination of direct base-specific interactions and indirect shape recognition of the promoter to regulate the transcription of met genes.
		+
		+	Structural basis for DNA recognition by the transcription regulator MetR.,Punekar AS, Porter J, Carr SB, Phillips SE Acta Crystallogr F Struct Biol Commun. 2016 Jun 1;72(Pt 6):417-26. doi:, 10.1107/S2053230X16006828. Epub 2016 May 23. PMID:27303893<ref>PMID:27303893</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5fo5" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 15:23, 20 June 2016

OCA — Mon, 20 Jun 2016 15:23:23 GMT

←Older revision		Revision as of 15:23, 20 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5fo5 ~~is ON HOLD until Paper Publication~~	+	==Structure of the DNA-binding domain of Escherichia coli methionine biosynthesis regulator MetR==
-		+	<StructureSection load='5fo5' size='340' side='right' caption='[[5fo5]], [[Resolution\|resolution]] 2.16Å' scene=''>
-	~~Authors~~: ~~Punekar, A~~.S.~~, Porter, J~~., ~~Urbanowski~~, M.L., ~~Stauffer, G~~.V., ~~Carr~~, S.B., ~~Phillips, S~~.E.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5fo5]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FO5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FO5 FirstGlance]. <br>
-	~~Description~~: ~~Structure~~ of the ~~DNA-binding domain of Escherichia coli~~ methionine biosynthesis ~~regulator~~ MetR	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5fo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fo5 OCA], [http://pdbe.org/5fo5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fo5 RCSB], [http://www.ebi.ac.uk/pdbsum/5fo5 PDBsum]</span></td></tr>
-	[[Category: ~~Urbanowski~~, ~~M.L~~]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/METR_ECOLI METR_ECOLI]] Control of the last step in methionine biosynthesis; MetR is a positive activator of the metA, metE and metH genes. MetR is also a negative regulator of its own expression. Binds homocysteine as an inducer.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Carr, S B]]
		+	[[Category: Phillips, S E]]
	[[Category: Porter, J]]		[[Category: Porter, J]]
-	[[Category: Punekar, A.S]]	+	[[Category: Punekar, A S]]
-	[[Category: ~~Phillips~~, ~~S.E~~]]	+	[[Category: Stauffer, G V]]
-	[[Category: ~~Stauffer~~, ~~G.V~~]]	+	[[Category: Urbanowski, M L]]
-	[[Category: ~~Carr, S.B~~]]	+	[[Category: Activator]]
		+	[[Category: Dna-binding]]
		+	[[Category: Hth]]
		+	[[Category: Lysr-type transcriptional regulator]]
		+	[[Category: Methionine biosynthesis]]
		+	[[Category: Repressor]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription regulation]]

OCA at 12:01, 2 March 2016

OCA — Wed, 02 Mar 2016 12:01:26 GMT

←Older revision		Revision as of 12:01, 2 March 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5fo5 is ON HOLD	+	The entry 5fo5 is ON HOLD until Paper Publication

	Authors: Punekar, A.S., Porter, J., Urbanowski, M.L., Stauffer, G.V., Carr, S.B., Phillips, S.E.		Authors: Punekar, A.S., Porter, J., Urbanowski, M.L., Stauffer, G.V., Carr, S.B., Phillips, S.E.

OCA: Protected "5fo5" [edit=sysop:move=sysop]

OCA — Tue, 01 Dec 2015 03:43:48 GMT

Protected "5fo5" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:43, 1 December 2015

OCA: New page: '''Unreleased structure''' The entry 5fo5 is ON HOLD Authors: Punekar, A.S., Porter, J., Urbanowski, M.L., Stauffer, G.V., Carr, S.B., Phillips, S.E. Description: Structure of the DNA-...

OCA — Tue, 01 Dec 2015 03:43:47 GMT

New page: '''Unreleased structure''' The entry 5fo5 is ON HOLD Authors: Punekar, A.S., Porter, J., Urbanowski, M.L., Stauffer, G.V., Carr, S.B., Phillips, S.E. Description: Structure of the DNA-...

New page

'''Unreleased structure'''

The entry 5fo5 is ON HOLD

Authors: Punekar, A.S., Porter, J., Urbanowski, M.L., Stauffer, G.V., Carr, S.B., Phillips, S.E.

Description: Structure of the DNA-binding domain of Escherichia coli methionine biosynthesis regulator MetR
[[Category: Unreleased Structures]]
[[Category: Urbanowski, M.L]]
[[Category: Porter, J]]
[[Category: Punekar, A.S]]
[[Category: Phillips, S.E]]
[[Category: Stauffer, G.V]]
[[Category: Carr, S.B]]