5im3 - Revision history

OCA at 14:01, 30 August 2023

OCA — Wed, 30 Aug 2023 14:01:04 GMT

←Older revision		Revision as of 14:01, 30 August 2023
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	<StructureSection load='5im3' size='340' side='right'caption='[[5im3]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5im3' size='340' side='right'caption='[[5im3]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5im3]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pseae Pseae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IM3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5IM3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5im3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IM3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IM3 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=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]] 2.298Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>nrdA, PA1156 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~208964 PSEAE])</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=MG:MAGNESIUM+ION'>MG</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=5im3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5im3 OCA], [https://pdbe.org/5im3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5im3 RCSB], [https://www.ebi.ac.uk/pdbsum/5im3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5im3 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=5im3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5im3 OCA], [~~http~~://pdbe.org/5im3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5im3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5im3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5im3 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/Q9I4I1_PSEAE Q9I4I1_PSEAE]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.[RuleBase:RU003410]	+	[https://www.uniprot.org/uniprot/Q9I4I1_PSEAE Q9I4I1_PSEAE] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.[RuleBase:RU003410]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pseae]]~~	+	[[Category: Pseudomonas aeruginosa PAO1]]
-	~~[[Category: Ribonucleoside-diphosphate reductase~~]]	+	[[Category: Johansson R]]
-	[[Category: Johansson, R]]	+	[[Category: Logan DT]]
-	[[Category: Logan~~, D T]]~~	+
-	~~[[Category: Allosteric regulation]]~~	+
-	~~[[Category: Atp cone]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Ten-stranded alpha-beta barrel~~]]	+

OCA at 07:23, 3 June 2020

OCA — Wed, 03 Jun 2020 07:23:49 GMT

←Older revision		Revision as of 07:23, 3 June 2020
Line 1:		Line 1:

	==Crystal structure of the class I ribonucleotide reductase from Pseudomonas aeruginosa in complex with dATP==		==Crystal structure of the class I ribonucleotide reductase from Pseudomonas aeruginosa in complex with dATP==
-	<StructureSection load='5im3' size='340' side='right' caption='[[5im3]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5im3' size='340' side='right'caption='[[5im3]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5im3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IM3 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5IM3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5im3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IM3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5IM3 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=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=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</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">nrdA, PA1156 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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=5im3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5im3 OCA], [http://pdbe.org/5im3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5im3 RCSB], [http://www.ebi.ac.uk/pdbsum/5im3 PDBsum]</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=5im3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5im3 OCA], [http://pdbe.org/5im3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5im3 RCSB], [http://www.ebi.ac.uk/pdbsum/5im3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5im3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5im3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5im3" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonucleotide reductase 3D structures\|Ribonucleotide reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Pseae]]
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]
	[[Category: Johansson, R]]		[[Category: Johansson, R]]

OCA: Protected "5im3" [edit=sysop:move=sysop]

OCA — Wed, 11 May 2016 05:50:54 GMT

Protected "5im3" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:50, 11 May 2016

OCA: New page: ==Crystal structure of the class I ribonucleotide reductase from Pseudomonas aeruginosa in complex with dATP== == Structural highlights ==
<table><tr><td colspan='2'>[[5im3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IM3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IM3 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=MG:MAGNESIUM+ION'>MG</scene></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=5im3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5im3 OCA], [http://pdbe.org/5im3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5im3 RCSB], [http://www.ebi.ac.uk/pdbsum/5im3 PDBsum]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/Q9I4I1_PSEAE Q9I4I1_PSEAE]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.[RuleBase:RU003410]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Ribonucleotide reductases (RNRs) reduce ribonucleotides to deoxyribonucleotides. Their overall activity is stimulated by ATP and downregulated by dATP via a genetically mobile ATP cone domain mediating the formation of oligomeric complexes with varying quaternary structures. The crystal structure and solution X-ray scattering data of a novel dATP-induced homotetramer of the Pseudomonas aeruginosa class I RNR reveal the structural bases for its unique properties, namely one ATP cone that binds two dATP molecules and a second one that is non-functional, binding no nucleotides. Mutations in the observed tetramer interface ablate oligomerization and dATP-induced inhibition but not the ability to bind dATP. Sequence analysis shows that the novel type of ATP cone may be widespread in RNRs. The present study supports a scenario in which diverse mechanisms for allosteric activity regulation are gained and lost through acquisition and evolutionary erosion of different types of ATP cone.

Structural Mechanism of Allosteric Activity Regulation in a Ribonucleotide Reductase with Double ATP Cones.,Johansson R, Jonna VR, Kumar R, Nayeri N, Lundin D, Sjoberg BM, Hofer A, Logan DT Structure. 2016 Apr 27. pii: S0969-2126(16)30036-3. doi:, 10.1016/j.str.2016.03.025. PMID:27133024<ref>PMID:27133024</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5im3" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Ribonucleoside-diphosphate reductase]]
[[Category: Johansson, R]]
[[Category: Logan, D T]]
[[Category: Allosteric regulation]]
[[Category: Atp cone]]
[[Category: Oxidoreductase]]
[[Category: Ten-stranded alpha-beta barrel]]