3tba - Revision history

OCA at 10:07, 1 March 2024

OCA — Fri, 01 Mar 2024 10:07:22 GMT

←Older revision		Revision as of 10:07, 1 March 2024
Line 3:		Line 3:
	<StructureSection load='3tba' size='340' side='right'caption='[[3tba]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3tba' size='340' side='right'caption='[[3tba]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tba]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TBA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TBA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tba]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TBA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TBA FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ADP:ADENOSINE~~-~~5-DIPHOSPHATE'>ADP</scene>~~, ~~<scene name='pdbligand=DGT:~~2~~-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</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]] 2.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[2cvu\|2cvu]], [[3tb9\|3tb9]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</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">RNR1, CRT7, RIR1, SDS12, YER070W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5~~&id=559292 Baker~~'~~s yeast])</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=3tba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tba OCA], [https://pdbe.org/3tba PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tba RCSB], [https://www.ebi.ac.uk/pdbsum/3tba PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tba 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=3tba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tba OCA], [https://pdbe.org/3tba PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tba RCSB], [https://www.ebi.ac.uk/pdbsum/3tba PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tba ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RIR1_YEAST RIR1_YEAST]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.<ref>PMID:11893751</ref>	+	[https://www.uniprot.org/uniprot/RIR1_YEAST RIR1_YEAST] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.<ref>PMID:11893751</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Ribonucleotide reductases (RRs) catalyze the rate-limiting step of de novo deoxynucleotide (dNTP) synthesis. Eukaryotic RRs consist of two proteins, RR1 (alpha) that contains the catalytic site and RR2 (beta) that houses a diferric-tyrosyl radical essential for ribonucleoside diphosphate reduction. Biochemical analysis has been combined with isothermal titration calorimetry (ITC), X-ray crystallography and yeast genetics to elucidate the roles of two loop 2 mutations R293A and Q288A in Saccharomyces cerevisiae RR1 (ScRR1). These mutations, R293A and Q288A, cause lethality and severe S phase defects, respectively, in cells that use ScRR1 as the sole source of RR1 activity. Compared to the wild-type enzyme activity, R293A and Q288A mutants show 4% and 15%, respectively, for ADP reduction, whereas they are 20% and 23%, respectively, for CDP reduction. ITC data showed that R293A ScRR1 is unable to bind ADP and binds CDP with 2-fold lower affinity compared to wild-type ScRR1. With the Q288A ScRR1 mutant, there is a 6-fold loss of affinity for ADP binding and a 2-fold loss of affinity for CDP compared to the wild type. X-ray structures of R293A ScRR1 complexed with dGTP and AMPPNP-CDP [AMPPNP, adenosine 5-(beta,gamma-imido)triphosphate tetralithium salt] reveal that ADP is not bound at the catalytic site, and CDP binds farther from the catalytic site compared to wild type. Our in vivo functional analyses demonstrated that R293A cannot support mitotic growth, whereas Q288A can, albeit with a severe S phase defect. Taken together, our structure, activity, ITC and in vivo data reveal that the arginine 293 and glutamine 288 residues of ScRR1 are crucial in facilitating ADP and CDP substrate selection.	+
-		+
-	Role of Arginine 293 and Glutamine 288 in Communication between Catalytic and Allosteric Sites in Yeast Ribonucleotide Reductase.,Ahmad MF, Kaushal PS, Wan Q, Wijerathna SR, An X, Huang M, Dealwis CG J Mol Biol. 2012 Mar 29. PMID:22465672<ref>PMID:22465672</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3tba" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 28:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ribonucleoside-diphosphate reductase~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: Ahmad~~, M F~~]]	+	[[Category: Ahmad MF]]
-	[[Category: Dealwis, C]]	+	[[Category: Dealwis C]]
-	[[Category: Huang, M]]	+	[[Category: Huang M]]
-	[[Category: Kaushal~~, P S~~]]	+	[[Category: Kaushal PS]]
-	[[Category: Wan, Q]]	+	[[Category: Wan Q]]
-	[[Category: Wijeratna~~, S R]]~~	+	[[Category: Wijeratna SR]]
-	~~[[Category: Dntp regulation]]~~	+
-	~~[[Category: Eukaryotic]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Ribonucleotide reductase~~]]	+

OCA at 16:50, 6 July 2022

OCA — Wed, 06 Jul 2022 16:50:51 GMT

←Older revision		Revision as of 16:50, 6 July 2022
Line 1:		Line 1:

	==Structure of Yeast Ribonucleotide Reductase 1 Q288A with dGTP and ADP==		==Structure of Yeast Ribonucleotide Reductase 1 Q288A with dGTP and ADP==
-	<StructureSection load='3tba' size='340' side='right' caption='[[3tba]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='3tba' size='340' side='right'caption='[[3tba]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tba]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TBA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3TBA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tba]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TBA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TBA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2cvu\|2cvu]], [[3tb9\|3tb9]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2cvu\|2cvu]], [[3tb9\|3tb9]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNR1, CRT7, RIR1, SDS12, YER070W ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNR1, CRT7, RIR1, SDS12, YER070W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=3tba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tba OCA], [~~http~~://pdbe.org/3tba PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3tba RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3tba PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3tba 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=3tba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tba OCA], [https://pdbe.org/3tba PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tba RCSB], [https://www.ebi.ac.uk/pdbsum/3tba PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tba ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RIR1_YEAST RIR1_YEAST]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.<ref>PMID:11893751</ref>	+	[[https://www.uniprot.org/uniprot/RIR1_YEAST RIR1_YEAST]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.<ref>PMID:11893751</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 3tba" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3tba" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonucleotide reductase 3D structures\|Ribonucleotide reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 26:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Baker's yeast]]		[[Category: Baker's yeast]]
		+	[[Category: Large Structures]]
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]
	[[Category: Ahmad, M F]]		[[Category: Ahmad, M F]]

OCA at 09:49, 8 November 2017

OCA — Wed, 08 Nov 2017 09:49:57 GMT

←Older revision		Revision as of 09:49, 8 November 2017
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 3tba" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3tba" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Ribonucleotide reductase\|Ribonucleotide reductase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:21, 5 August 2016

OCA — Fri, 05 Aug 2016 21:21:28 GMT

←Older revision		Revision as of 21:21, 5 August 2016
Line 1:		Line 1:
		+
	==Structure of Yeast Ribonucleotide Reductase 1 Q288A with dGTP and ADP==		==Structure of Yeast Ribonucleotide Reductase 1 Q288A with dGTP and ADP==
	<StructureSection load='3tba' size='340' side='right' caption='[[3tba]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3tba' size='340' side='right' caption='[[3tba]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tba]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TBA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TBA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tba]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TBA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TBA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2cvu\|2cvu]], [[3tb9\|3tb9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2cvu\|2cvu]], [[3tb9\|3tb9]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNR1, CRT7, RIR1, SDS12, YER070W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~4932 Saccharomyces cerevisiae~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNR1, CRT7, RIR1, SDS12, YER070W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=3tba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tba OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tba RCSB], [http://www.ebi.ac.uk/pdbsum/3tba 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=3tba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tba OCA], [http://pdbe.org/3tba PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3tba RCSB], [http://www.ebi.ac.uk/pdbsum/3tba PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3tba ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 3tba" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 26:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]
-	[[Category: Saccharomyces cerevisiae]]
	[[Category: Ahmad, M F]]		[[Category: Ahmad, M F]]
	[[Category: Dealwis, C]]		[[Category: Dealwis, C]]

OCA at 21:59, 25 December 2014

OCA — Thu, 25 Dec 2014 21:59:50 GMT

←Older revision		Revision as of 21:59, 25 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3tba.~~png~~\|~~left~~\|~~200px~~]]	+	==Structure of Yeast Ribonucleotide Reductase 1 Q288A with dGTP and ADP==
		+	<StructureSection load='3tba' size='340' side='right' caption='[[3tba]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3tba]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TBA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TBA FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2cvu\|2cvu]], [[3tb9\|3tb9]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNR1, CRT7, RIR1, SDS12, YER070W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=3tba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tba OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tba RCSB], [http://www.ebi.ac.uk/pdbsum/3tba PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RIR1_YEAST RIR1_YEAST]] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.<ref>PMID:11893751</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ribonucleotide reductases (RRs) catalyze the rate-limiting step of de novo deoxynucleotide (dNTP) synthesis. Eukaryotic RRs consist of two proteins, RR1 (alpha) that contains the catalytic site and RR2 (beta) that houses a diferric-tyrosyl radical essential for ribonucleoside diphosphate reduction. Biochemical analysis has been combined with isothermal titration calorimetry (ITC), X-ray crystallography and yeast genetics to elucidate the roles of two loop 2 mutations R293A and Q288A in Saccharomyces cerevisiae RR1 (ScRR1). These mutations, R293A and Q288A, cause lethality and severe S phase defects, respectively, in cells that use ScRR1 as the sole source of RR1 activity. Compared to the wild-type enzyme activity, R293A and Q288A mutants show 4% and 15%, respectively, for ADP reduction, whereas they are 20% and 23%, respectively, for CDP reduction. ITC data showed that R293A ScRR1 is unable to bind ADP and binds CDP with 2-fold lower affinity compared to wild-type ScRR1. With the Q288A ScRR1 mutant, there is a 6-fold loss of affinity for ADP binding and a 2-fold loss of affinity for CDP compared to the wild type. X-ray structures of R293A ScRR1 complexed with dGTP and AMPPNP-CDP [AMPPNP, adenosine 5-(beta,gamma-imido)triphosphate tetralithium salt] reveal that ADP is not bound at the catalytic site, and CDP binds farther from the catalytic site compared to wild type. Our in vivo functional analyses demonstrated that R293A cannot support mitotic growth, whereas Q288A can, albeit with a severe S phase defect. Taken together, our structure, activity, ITC and in vivo data reveal that the arginine 293 and glutamine 288 residues of ScRR1 are crucial in facilitating ADP and CDP substrate selection.

-	~~<!--~~	+	Role of Arginine 293 and Glutamine 288 in Communication between Catalytic and Allosteric Sites in Yeast Ribonucleotide Reductase.,Ahmad MF, Kaushal PS, Wan Q, Wijerathna SR, An X, Huang M, Dealwis CG J Mol Biol. 2012 Mar 29. PMID:22465672<ref>PMID:22465672</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3tba"~~, ~~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_3tba\| PDB=3tba \| SCENE= }}~~	+

-	~~===Structure~~ of ~~Yeast Ribonucleotide Reductase 1 Q288A with dGTP and ADP===~~	+	From MEDLINE®/PubMed®, 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_22465672}}, adds the Publication Abstract to the page~~	+	== References ==
-	~~(as it appears on PubMed at http://www.pubmed.gov), where 22465672 is the PubMed ID number.~~	+	<references/>
-	~~-->~~	+	__TOC__
-	~~{{ABSTRACT_PUBMED_22465672}}~~	+	</StructureSection>
-		+
-	==~~About this Structure~~==	+
-	[[~~3tba~~]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TBA OCA].	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022465672<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Ahmad, M F.]]	+	[[Category: Ahmad, M F]]
	[[Category: Dealwis, C]]		[[Category: Dealwis, C]]
-	[[Category: Huang, M.]]	+	[[Category: Huang, M]]
-	[[Category: Kaushal, P S.]]	+	[[Category: Kaushal, P S]]
-	[[Category: Wan, Q.]]	+	[[Category: Wan, Q]]
-	[[Category: Wijeratna, S R.]]	+	[[Category: Wijeratna, S R]]
	[[Category: Dntp regulation]]		[[Category: Dntp regulation]]
	[[Category: Eukaryotic]]		[[Category: Eukaryotic]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Ribonucleotide reductase]]		[[Category: Ribonucleotide reductase]]

OCA at 08:06, 25 April 2012

OCA — Wed, 25 Apr 2012 08:06:23 GMT

←Older revision		Revision as of 08:06, 25 April 2012
Line 1:		Line 1:
-	[[Image:3tba.~~jpg~~\|left\|200px]]	+	[[Image:3tba.png\|left\|200px]]

	<!--		<!--
Line 11:		Line 11:
	===Structure of Yeast Ribonucleotide Reductase 1 Q288A with dGTP and ADP===		===Structure of Yeast Ribonucleotide Reductase 1 Q288A with dGTP and ADP===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22465672}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22465672 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22465672}}

	==About this Structure==		==About this Structure==
	[[3tba]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TBA OCA].		[[3tba]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TBA OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022465672</ref><references group="xtra"/>
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]

OCA at 06:13, 4 April 2012

OCA — Wed, 04 Apr 2012 06:13:15 GMT

←Older revision		Revision as of 06:13, 4 April 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3tba.jpg\|left\|200px]]

-	The ~~entry 3tba~~ is ~~ON HOLD~~ ~~until Apr 04 2013~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3tba", 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_3tba\| PDB=3tba \| SCENE= }}

-	~~Authors: Ahmad, M.F., Kaushal, P.S., Wan, Q., Wijeratna, S.R., Huang, M., Dealwis, C~~	+	===Structure of Yeast Ribonucleotide Reductase 1 Q288A with dGTP and ADP===

-	~~Description:~~ Structure ~~of Yeast Ribonucleotide Reductase~~ 1 ~~Q288A~~ with ~~dGTP and ADP~~	+
		+	==About this Structure==
		+	[[3tba]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TBA OCA].
		+	[[Category: Ribonucleoside-diphosphate reductase]]
		+	[[Category: Saccharomyces cerevisiae]]
		+	[[Category: Ahmad, M F.]]
		+	[[Category: Dealwis, C]]
		+	[[Category: Huang, M.]]
		+	[[Category: Kaushal, P S.]]
		+	[[Category: Wan, Q.]]
		+	[[Category: Wijeratna, S R.]]
		+	[[Category: Dntp regulation]]
		+	[[Category: Eukaryotic]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Ribonucleotide reductase]]

OCA at 07:09, 28 March 2012

OCA — Wed, 28 Mar 2012 07:09:56 GMT

←Older revision		Revision as of 07:09, 28 March 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3tba is ON HOLD until ~~Paper Publication~~	+	The entry 3tba is ON HOLD until Apr 04 2013

	Authors: Ahmad, M.F., Kaushal, P.S., Wan, Q., Wijeratna, S.R., Huang, M., Dealwis, C		Authors: Ahmad, M.F., Kaushal, P.S., Wan, Q., Wijeratna, S.R., Huang, M., Dealwis, C

	Description: Structure of Yeast Ribonucleotide Reductase 1 Q288A with dGTP and ADP		Description: Structure of Yeast Ribonucleotide Reductase 1 Q288A with dGTP and ADP

OCA at 06:22, 31 August 2011

OCA — Wed, 31 Aug 2011 06:22:18 GMT

←Older revision		Revision as of 06:22, 31 August 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Ahmad, M.F., Kaushal, P.S., Wan, Q., Wijeratna, S.R., Huang, M., Dealwis, C		Authors: Ahmad, M.F., Kaushal, P.S., Wan, Q., Wijeratna, S.R., Huang, M., Dealwis, C

	Description: Structure of Yeast Ribonucleotide Reductase 1 Q288A with dGTP and ADP		Description: Structure of Yeast Ribonucleotide Reductase 1 Q288A with dGTP and ADP

OCA at 07:09, 24 August 2011

OCA — Wed, 24 Aug 2011 07:09:58 GMT

←Older revision		Revision as of 07:09, 24 August 2011
Line 3:		Line 3:
	The entry 3tba is ON HOLD		The entry 3tba is ON HOLD

-	Authors: Ahmad, M.F, Kaushal, P.S., Wan, Q., Wijeratna, S.R., Huang, M., Dealwis, C	+	Authors: Ahmad, M.F., Kaushal, P.S., Wan, Q., Wijeratna, S.R., Huang, M., Dealwis, C

	Description: Structure of Yeast Ribonucleotide Reductase 1 Q288A with dGTP and ADP		Description: Structure of Yeast Ribonucleotide Reductase 1 Q288A with dGTP and ADP