3uus - Revision history

OCA at 14:08, 14 March 2024

OCA — Thu, 14 Mar 2024 14:08:50 GMT

←Older revision		Revision as of 14:08, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3uus' size='340' side='right'caption='[[3uus]], [[Resolution\|resolution]] 5.65Å' scene=''>		<StructureSection load='3uus' size='340' side='right'caption='[[3uus]], [[Resolution\|resolution]] 5.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3uus]] is a 8 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=3UUS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UUS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3uus]] is a 8 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=3UUS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UUS FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DTP:2~~-~~DEOXYADENOSINE+~~5~~-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</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]] 5.65Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>b2234, dnaF, JW2228, nrdA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~83333 ECOLI]), b2235, ftsB, JW2229, nrdB ([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=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1]~~ </~~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=3uus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uus OCA], [https://pdbe.org/3uus PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uus RCSB], [https://www.ebi.ac.uk/pdbsum/3uus PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uus 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=3uus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uus OCA], [https://pdbe.org/3uus PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uus RCSB], [https://www.ebi.ac.uk/pdbsum/3uus PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uus ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RIR1_ECOLI RIR1_ECOLI]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R1 contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide. It also provides redox-active cysteines. [[https://www.uniprot.org/uniprot/RIR2_ECOLI RIR2_ECOLI]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2 contains the tyrosyl radical required for catalysis.	+	[https://www.uniprot.org/uniprot/RIR1_ECOLI RIR1_ECOLI] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R1 contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide. It also provides redox-active cysteines.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Essential for DNA biosynthesis and repair, ribonucleotide reductases (RNRs) convert ribonucleotides to deoxyribonucleotides via radical-based chemistry. Although long known that allosteric regulation of RNR activity is vital for cell health, the molecular basis of this regulation has been enigmatic, largely due to a lack of structural information about how the catalytic subunit (alpha(2)) and the radical-generation subunit (beta(2)) interact. Here we present the first structure of a complex between alpha(2) and beta(2) subunits for the prototypic RNR from Escherichia coli. Using four techniques (small-angle X-ray scattering, X-ray crystallography, electron microscopy, and analytical ultracentrifugation), we describe an unprecedented alpha(4)beta(4) ring-like structure in the presence of the negative activity effector dATP and provide structural support for an active alpha(2)beta(2) configuration. We demonstrate that, under physiological conditions, E. coli RNR exists as a mixture of transient alpha(2)beta(2) and alpha(4)beta(4) species whose distributions are modulated by allosteric effectors. We further show that this interconversion between alpha(2)beta(2) and alpha(4)beta(4) entails dramatic subunit rearrangements, providing a stunning molecular explanation for the allosteric regulation of RNR activity in E. coli.	+
-		+
-	Structural interconversions modulate activity of Escherichia coli ribonucleotide reductase.,Ando N, Brignole EJ, Zimanyi CM, Funk MA, Yokoyama K, Asturias FJ, Stubbe J, Drennan CL Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):21046-51. Epub 2011 Dec 12. PMID:22160671<ref>PMID:22160671</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3uus" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[Ribonucleotide reductase 3D structures\|Ribonucleotide reductase 3D structures]]		*[[Ribonucleotide reductase 3D structures\|Ribonucleotide reductase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Ribonucleoside-diphosphate reductase]]~~	+	[[Category: Drennan CL]]
-	[[Category: Drennan~~, C L~~]]	+	[[Category: Zimanyi CM]]
-	[[Category: Zimanyi~~, C M]]~~	+
-	~~[[Category: 10 stranded alpha/beta barrel]]~~	+
-	~~[[Category: Datp bound]]~~	+
-	~~[[Category: Di-iron]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 08:08, 20 July 2022

OCA — Wed, 20 Jul 2022 08:08:33 GMT

←Older revision		Revision as of 08:08, 20 July 2022
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	==Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex==		==Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex==
-	<StructureSection load='3uus' size='340' side='right' caption='[[3uus]], [[Resolution\|resolution]] 5.65Å' scene=''>	+	<StructureSection load='3uus' size='340' side='right'caption='[[3uus]], [[Resolution\|resolution]] 5.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3uus]] is a 8 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=3UUS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3UUS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3uus]] is a 8 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=3UUS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UUS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2234, dnaF, JW2228, nrdA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), b2235, ftsB, JW2229, nrdB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2234, dnaF, JW2228, nrdA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), b2235, ftsB, JW2229, nrdB ([https://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/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </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=3uus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uus OCA], [~~http~~://pdbe.org/3uus PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3uus RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3uus PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3uus 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=3uus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uus OCA], [https://pdbe.org/3uus PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uus RCSB], [https://www.ebi.ac.uk/pdbsum/3uus PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uus ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RIR1_ECOLI RIR1_ECOLI]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R1 contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide. It also provides redox-active cysteines. [[~~http~~://www.uniprot.org/uniprot/RIR2_ECOLI RIR2_ECOLI]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2 contains the tyrosyl radical required for catalysis.	+	[[https://www.uniprot.org/uniprot/RIR1_ECOLI RIR1_ECOLI]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R1 contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide. It also provides redox-active cysteines. [[https://www.uniprot.org/uniprot/RIR2_ECOLI RIR2_ECOLI]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2 contains the tyrosyl radical required for catalysis.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:

	==See Also==		==See Also==
-	*[[Ribonucleotide reductase\|Ribonucleotide reductase]]	+	*[[Ribonucleotide reductase 3D structures\|Ribonucleotide reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 28:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]
	[[Category: Drennan, C L]]		[[Category: Drennan, C L]]

OCA at 04:19, 5 August 2016

OCA — Fri, 05 Aug 2016 04:19:33 GMT

←Older revision		Revision as of 04:19, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex==		==Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex==
	<StructureSection load='3uus' size='340' side='right' caption='[[3uus]], [[Resolution\|resolution]] 5.65Å' scene=''>		<StructureSection load='3uus' size='340' side='right' caption='[[3uus]], [[Resolution\|resolution]] 5.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3uus]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia coli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UUS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UUS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3uus]] is a 8 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=3UUS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UUS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2234, dnaF, JW2228, nrdA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~562 Escherichia coli~~]), b2235, ftsB, JW2229, nrdB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~562 Escherichia coli~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2234, dnaF, JW2228, nrdA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), b2235, ftsB, JW2229, nrdB ([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/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </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=3uus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uus OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3uus RCSB], [http://www.ebi.ac.uk/pdbsum/3uus 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=3uus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uus OCA], [http://pdbe.org/3uus PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3uus RCSB], [http://www.ebi.ac.uk/pdbsum/3uus PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3uus ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3uus" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 25:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia coli~~]]	+	[[Category: Ecoli]]
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]
	[[Category: Drennan, C L]]		[[Category: Drennan, C L]]

OCA at 22:54, 24 December 2014

OCA — Wed, 24 Dec 2014 22:54:08 GMT

←Older revision		Revision as of 22:54, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3uus]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UUS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UUS FirstGlance]. <br>		<table><tr><td colspan='2'>[[3uus]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UUS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UUS FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2234, dnaF, JW2228, nrdA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), b2235, ftsB, JW2229, nrdB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2234, dnaF, JW2228, nrdA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), b2235, ftsB, JW2229, nrdB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3uus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uus OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3uus RCSB], [http://www.ebi.ac.uk/pdbsum/3uus 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=3uus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uus OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3uus RCSB], [http://www.ebi.ac.uk/pdbsum/3uus PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RIR1_ECOLI RIR1_ECOLI]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R1 contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide. It also provides redox-active cysteines. [[http://www.uniprot.org/uniprot/RIR2_ECOLI RIR2_ECOLI]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2 contains the tyrosyl radical required for catalysis.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 16:
	Structural interconversions modulate activity of Escherichia coli ribonucleotide reductase.,Ando N, Brignole EJ, Zimanyi CM, Funk MA, Yokoyama K, Asturias FJ, Stubbe J, Drennan CL Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):21046-51. Epub 2011 Dec 12. PMID:22160671<ref>PMID:22160671</ref>		Structural interconversions modulate activity of Escherichia coli ribonucleotide reductase.,Ando N, Brignole EJ, Zimanyi CM, Funk MA, Yokoyama K, Asturias FJ, Stubbe J, Drennan CL Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):21046-51. Epub 2011 Dec 12. PMID:22160671<ref>PMID:22160671</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>

Line 25:		Line 27:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]
-	[[Category: Drennan, C L.]]	+	[[Category: Drennan, C L]]
-	[[Category: Zimanyi, C M.]]	+	[[Category: Zimanyi, C M]]
	[[Category: 10 stranded alpha/beta barrel]]		[[Category: 10 stranded alpha/beta barrel]]
	[[Category: Datp bound]]		[[Category: Datp bound]]
	[[Category: Di-iron]]		[[Category: Di-iron]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 06:04, 5 June 2014

OCA — Thu, 05 Jun 2014 06:04:55 GMT

←Older revision		Revision as of 06:04, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3uus.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex==
		+	<StructureSection load='3uus' size='340' side='right' caption='[[3uus]], [[Resolution\|resolution]] 5.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3uus]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UUS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UUS FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2234, dnaF, JW2228, nrdA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), b2235, ftsB, JW2229, nrdB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3uus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uus OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3uus RCSB], [http://www.ebi.ac.uk/pdbsum/3uus PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Essential for DNA biosynthesis and repair, ribonucleotide reductases (RNRs) convert ribonucleotides to deoxyribonucleotides via radical-based chemistry. Although long known that allosteric regulation of RNR activity is vital for cell health, the molecular basis of this regulation has been enigmatic, largely due to a lack of structural information about how the catalytic subunit (alpha(2)) and the radical-generation subunit (beta(2)) interact. Here we present the first structure of a complex between alpha(2) and beta(2) subunits for the prototypic RNR from Escherichia coli. Using four techniques (small-angle X-ray scattering, X-ray crystallography, electron microscopy, and analytical ultracentrifugation), we describe an unprecedented alpha(4)beta(4) ring-like structure in the presence of the negative activity effector dATP and provide structural support for an active alpha(2)beta(2) configuration. We demonstrate that, under physiological conditions, E. coli RNR exists as a mixture of transient alpha(2)beta(2) and alpha(4)beta(4) species whose distributions are modulated by allosteric effectors. We further show that this interconversion between alpha(2)beta(2) and alpha(4)beta(4) entails dramatic subunit rearrangements, providing a stunning molecular explanation for the allosteric regulation of RNR activity in E. coli.

-	~~<!--~~	+	Structural interconversions modulate activity of Escherichia coli ribonucleotide reductase.,Ando N, Brignole EJ, Zimanyi CM, Funk MA, Yokoyama K, Asturias FJ, Stubbe J, Drennan CL Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):21046-51. Epub 2011 Dec 12. PMID:22160671<ref>PMID:22160671</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3uus"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+
-	~~or leave the SCENE parameter empty for the default display.~~	+
-	-->	+
-	~~{{STRUCTURE_3uus\| PDB=3uus \| SCENE= }}~~	+

-	~~===Crystal structure~~ of the ~~dATP inhibited E~~. ~~coli class Ia ribonucleotide reductase complex===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-		+	==See Also==
-	~~<!--~~	+	*[[Ribonucleotide reductase\|Ribonucleotide reductase]]
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_22160671}}, adds the Publication Abstract to the page~~	+	== References ==
-	~~(as it appears on PubMed at http://www.pubmed.gov), where 22160671 is the PubMed ID number.~~	+	<references/>
-	~~-->~~	+	__TOC__
-	~~{{ABSTRACT_PUBMED_22160671}}~~	+	</StructureSection>
-		+
-	==~~About this Structure~~==	+
-	[[~~3uus~~]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UUS OCA].	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022160671<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]

OCA at 05:36, 11 January 2012

OCA — Wed, 11 Jan 2012 05:36:50 GMT

←Older revision		Revision as of 05:36, 11 January 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3uus.png\|left\|200px]]

-	The ~~entry 3uus~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3uus", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3uus\| PDB=3uus \| SCENE= }}

-	~~Authors: Zimanyi, C.M., Drennan, C.L~~.	+	===Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex===

-	~~Description~~: ~~Crystal structure of~~ the ~~dATP inhibited E~~. coli ~~class Ia ribonucleotide~~ reductase ~~complex~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22160671}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22160671 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22160671}}
		+
		+	==About this Structure==
		+	[[3uus]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UUS OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022160671</ref><references group="xtra"/>
		+	[[Category: Escherichia coli]]
		+	[[Category: Ribonucleoside-diphosphate reductase]]
		+	[[Category: Drennan, C L.]]
		+	[[Category: Zimanyi, C M.]]
		+	[[Category: 10 stranded alpha/beta barrel]]
		+	[[Category: Datp bound]]
		+	[[Category: Di-iron]]
		+	[[Category: Oxidoreductase]]

OCA at 11:12, 14 December 2011

OCA — Wed, 14 Dec 2011 11:12:35 GMT

←Older revision		Revision as of 11:12, 14 December 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3uus is ON HOLD	+	The entry 3uus is ON HOLD until Paper Publication

	Authors: Zimanyi, C.M., Drennan, C.L.		Authors: Zimanyi, C.M., Drennan, C.L.

	Description: Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex		Description: Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex

OCA: Protected "3uus" [edit=sysop:move=sysop]

OCA — Wed, 07 Dec 2011 07:39:45 GMT

Protected "3uus" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:39, 7 December 2011

OCA: New page: '''Unreleased structure''' The entry 3uus is ON HOLD Authors: Zimanyi, C.M., Drennan, C.L. Description: Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductas...

OCA — Wed, 07 Dec 2011 07:39:44 GMT

New page: '''Unreleased structure''' The entry 3uus is ON HOLD Authors: Zimanyi, C.M., Drennan, C.L. Description: Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductas...

New page

'''Unreleased structure'''

The entry 3uus is ON HOLD

Authors: Zimanyi, C.M., Drennan, C.L.

Description: Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex