2eud - Revision history

OCA at 09:19, 14 February 2024

2024-02-14T09:19:45Z

←Older revision		Revision as of 09:19, 14 February 2024
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	<StructureSection load='2eud' size='340' side='right'caption='[[2eud]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2eud' size='340' side='right'caption='[[2eud]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2eud]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EUD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EUD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2eud]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EUD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EUD FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID~~-~~ADENYLATE+ESTER'>ANP</scene>~~, ~~<scene name='pdbligand=GCQ:GEMCITABINE+DIPHOSPHATE'>GCQ</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]] 2.3Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~RNR1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=4932 ATCC 18824])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=GCQ:GEMCITABINE+DIPHOSPHATE'>GCQ</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~~'>~~[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=2eud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eud OCA], [https://pdbe.org/2eud PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2eud RCSB], [https://www.ebi.ac.uk/pdbsum/2eud PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2eud 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=2eud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eud OCA], [https://pdbe.org/2eud PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2eud RCSB], [https://www.ebi.ac.uk/pdbsum/2eud PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2eud 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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2eud ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2eud ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Ribonucleotide reductase (RNR) catalyzes the conversion of nucleoside diphosphates to deoxynucleoside diphosphates. Crucial for rapidly dividing cells, RNR is a target for cancer therapy. In eukaryotes, RNR comprises a heterooligomer of alpha(2) and beta(2) subunits. Rnr1, the alpha subunit, contains regulatory and catalytic sites; Rnr2, the beta subunit (in yeast, a heterodimer of Rnr2 and Rnr4), houses the diferric-tyrosyl radical crucial for catalysis. Here, we present three x-ray structures of eukaryotic Rnr1 from Saccharomyces cerevisiae: one bound to gemcitabine diphosphate (GemdP), the active metabolite of the mechanism-based chemotherapeutic agent gemcitabine; one with an Rnr2-derived peptide, and one with an Rnr4-derived peptide. Our structures reveal that GemdP binds differently from its analogue, cytidine diphosphate; because of unusual interactions of the geminal fluorines, the ribose and base of GemdP shift substantially, and loop 2, which mediates substrate specificity, adopts different conformations when binding to GemdP and cytidine diphosphate. The Rnr2 and Rnr4 peptides, which block RNR assembly, bind differently from each other but have unique modes of binding not seen in prokaryotic RNR. The Rnr2 peptide adopts a conformation similar to that previously reported from an NMR study for a mouse Rnr2-based peptide. In yeast, the Rnr2 peptide binds at subsites consisting of residues that are highly conserved among yeast, mouse, and human Rnr1s, suggesting that the mode of Rnr1-Rnr2 binding is conserved among eukaryotes. These structures provide new insights into subunit assembly and a framework for structure-based drug design targeting RNR.
-
-	Structures of eukaryotic ribonucleotide reductase I define gemcitabine diphosphate binding and subunit assembly.,Xu H, Faber C, Uchiki T, Racca J, Dealwis C Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4028-33. Epub 2006 Mar 6. PMID:16537480<ref>PMID:16537480</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2eud" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ribonucleoside-diphosphate reductase~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: Dealwis, C]]	+	[[Category: Dealwis C]]
-	[[Category: Faber, C]]	+	[[Category: Faber C]]
-	[[Category: Fairman~~, J W~~]]	+	[[Category: Fairman JW]]
-	[[Category: Racca, J]]	+	[[Category: Racca J]]
-	[[Category: Uchiki, T]]	+	[[Category: Uchiki T]]
-	[[Category: Xu, H]]	+	[[Category: Xu H]]
-	~~[[Category: Ligand interaction]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Ribonucleotide reductase]]~~	+
-	~~[[Category: Subunit assembly~~]]	+

OCA at 12:29, 10 February 2021

2021-02-10T12:29:52Z

←Older revision		Revision as of 12:29, 10 February 2021
Line 1:		Line 1:

	==Structures of Yeast Ribonucleotide Reductase I complexed with Ligands and Subunit Peptides==		==Structures of Yeast Ribonucleotide Reductase I complexed with Ligands and Subunit Peptides==
-	<StructureSection load='2eud' size='340' side='right' caption='[[2eud]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='2eud' size='340' side='right'caption='[[2eud]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2eud]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EUD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2EUD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2eud]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EUD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EUD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=GCQ:GEMCITABINE+DIPHOSPHATE'>GCQ</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=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=GCQ:GEMCITABINE+DIPHOSPHATE'>GCQ</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 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNR1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=2eud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eud OCA], [~~http~~://pdbe.org/2eud PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2eud RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2eud PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2eud 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=2eud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eud OCA], [https://pdbe.org/2eud PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2eud RCSB], [https://www.ebi.ac.uk/pdbsum/2eud PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2eud 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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[Ribonucleotide reductase\|Ribonucleotide reductase]]	+	*[[Ribonucleotide reductase 3D structures\|Ribonucleotide reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
		+	[[Category: Large Structures]]
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]
	[[Category: Dealwis, C]]		[[Category: Dealwis, C]]

OCA at 08:46, 14 June 2018

2018-06-14T08:46:13Z

←Older revision		Revision as of 08:46, 14 June 2018
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNR1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNR1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=2eud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eud OCA], [http://pdbe.org/2eud PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2eud RCSB], [http://www.ebi.ac.uk/pdbsum/2eud 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=2eud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eud OCA], [http://pdbe.org/2eud PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2eud RCSB], [http://www.ebi.ac.uk/pdbsum/2eud PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2eud ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eu/2eud_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eu/2eud_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 19:03, 20 February 2016

2016-02-20T19:03:52Z

←Older revision		Revision as of 19:03, 20 February 2016
Line 1:		Line 1:
		+
	==Structures of Yeast Ribonucleotide Reductase I complexed with Ligands and Subunit Peptides==		==Structures of Yeast Ribonucleotide Reductase I complexed with Ligands and Subunit Peptides==
	<StructureSection load='2eud' size='340' side='right' caption='[[2eud]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2eud' size='340' side='right' caption='[[2eud]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 18:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2eud ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 40:		Line 41:
	[[Category: Dealwis, C]]		[[Category: Dealwis, C]]
	[[Category: Faber, C]]		[[Category: Faber, C]]
-	[[Category: Fairman, J]]	+	[[Category: Fairman, J W]]
	[[Category: Racca, J]]		[[Category: Racca, J]]
	[[Category: Uchiki, T]]		[[Category: Uchiki, T]]

OCA at 02:14, 12 September 2015

2015-09-12T02:14:03Z

←Older revision		Revision as of 02:14, 12 September 2015
Line 2:		Line 2:
	<StructureSection load='2eud' size='340' side='right' caption='[[2eud]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2eud' size='340' side='right' caption='[[2eud]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2eud]] 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=2EUD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EUD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2eud]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EUD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EUD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=GCQ:GEMCITABINE+DIPHOSPHATE'>GCQ</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=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=GCQ:GEMCITABINE+DIPHOSPHATE'>GCQ</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 ([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 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=2eud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eud OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2eud RCSB], [http://www.ebi.ac.uk/pdbsum/2eud 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=2eud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eud OCA], [http://pdbe.org/2eud PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2eud RCSB], [http://www.ebi.ac.uk/pdbsum/2eud PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 2eud" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 18824]]
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]
-	[[Category: Saccharomyces cerevisiae]]
	[[Category: Dealwis, C]]		[[Category: Dealwis, C]]
	[[Category: Faber, C]]		[[Category: Faber, C]]

OCA at 22:32, 25 December 2014

2014-12-25T22:32:54Z

←Older revision		Revision as of 22:32, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2eud]] 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=2EUD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EUD FirstGlance]. <br>		<table><tr><td colspan='2'>[[2eud]] 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=2EUD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EUD FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=GCQ:GEMCITABINE+DIPHOSPHATE'>GCQ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=GCQ:GEMCITABINE+DIPHOSPHATE'>GCQ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNR1 ([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 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=2eud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eud OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2eud RCSB], [http://www.ebi.ac.uk/pdbsum/2eud 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=2eud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eud OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2eud RCSB], [http://www.ebi.ac.uk/pdbsum/2eud PDBsum]</span></td></tr>
-	<table>	+	</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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Dealwis, C.]]	+	[[Category: Dealwis, C]]
-	[[Category: Faber, C.]]	+	[[Category: Faber, C]]
-	[[Category: Fairman, J.]]	+	[[Category: Fairman, J]]
-	[[Category: Racca, J.]]	+	[[Category: Racca, J]]
-	[[Category: Uchiki, T.]]	+	[[Category: Uchiki, T]]
-	[[Category: Xu, H.]]	+	[[Category: Xu, H]]
	[[Category: Ligand interaction]]		[[Category: Ligand interaction]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Ribonucleotide reductase]]		[[Category: Ribonucleotide reductase]]
	[[Category: Subunit assembly]]		[[Category: Subunit assembly]]

OCA at 09:48, 29 September 2014

2014-09-29T09:48:10Z

←Older revision		Revision as of 09:48, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2eud.~~png~~\|~~left~~\|200px]]	+	==Structures of Yeast Ribonucleotide Reductase I complexed with Ligands and Subunit Peptides==
		+	<StructureSection load='2eud' size='340' side='right' caption='[[2eud]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2eud]] 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=2EUD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EUD FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=GCQ:GEMCITABINE+DIPHOSPHATE'>GCQ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNR1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=2eud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eud OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2eud RCSB], [http://www.ebi.ac.uk/pdbsum/2eud PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eu/2eud_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ribonucleotide reductase (RNR) catalyzes the conversion of nucleoside diphosphates to deoxynucleoside diphosphates. Crucial for rapidly dividing cells, RNR is a target for cancer therapy. In eukaryotes, RNR comprises a heterooligomer of alpha(2) and beta(2) subunits. Rnr1, the alpha subunit, contains regulatory and catalytic sites; Rnr2, the beta subunit (in yeast, a heterodimer of Rnr2 and Rnr4), houses the diferric-tyrosyl radical crucial for catalysis. Here, we present three x-ray structures of eukaryotic Rnr1 from Saccharomyces cerevisiae: one bound to gemcitabine diphosphate (GemdP), the active metabolite of the mechanism-based chemotherapeutic agent gemcitabine; one with an Rnr2-derived peptide, and one with an Rnr4-derived peptide. Our structures reveal that GemdP binds differently from its analogue, cytidine diphosphate; because of unusual interactions of the geminal fluorines, the ribose and base of GemdP shift substantially, and loop 2, which mediates substrate specificity, adopts different conformations when binding to GemdP and cytidine diphosphate. The Rnr2 and Rnr4 peptides, which block RNR assembly, bind differently from each other but have unique modes of binding not seen in prokaryotic RNR. The Rnr2 peptide adopts a conformation similar to that previously reported from an NMR study for a mouse Rnr2-based peptide. In yeast, the Rnr2 peptide binds at subsites consisting of residues that are highly conserved among yeast, mouse, and human Rnr1s, suggesting that the mode of Rnr1-Rnr2 binding is conserved among eukaryotes. These structures provide new insights into subunit assembly and a framework for structure-based drug design targeting RNR.

-	~~{{STRUCTURE_2eud\| PDB=2eud \| SCENE= }}~~	+	Structures of eukaryotic ribonucleotide reductase I define gemcitabine diphosphate binding and subunit assembly.,Xu H, Faber C, Uchiki T, Racca J, Dealwis C Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4028-33. Epub 2006 Mar 6. PMID:16537480<ref>PMID:16537480</ref>

-	~~===Structures~~ of ~~Yeast Ribonucleotide Reductase I complexed with Ligands and Subunit Peptides===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16537480}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2eud]] 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=2EUD OCA].~~	+

	==See Also==		==See Also==
	*[[Ribonucleotide reductase\|Ribonucleotide reductase]]		*[[Ribonucleotide reductase\|Ribonucleotide reductase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:016537480<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]

OCA at 22:25, 20 October 2012

2012-10-20T22:25:45Z

←Older revision		Revision as of 22:25, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2eud]] is a 1 chain structure ~~of [[Ribonucleotide reductase]]~~ 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=2EUD OCA].	+	[[2eud]] 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=2EUD OCA].

	==See Also==		==See Also==

OCA: Protected "2eud" [edit=sysop:move=sysop]

2012-07-27T16:16:05Z

Protected "2eud" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:16, 27 July 2012

OCA at 16:16, 27 July 2012

2012-07-27T16:16:03Z

←Older revision		Revision as of 16:16, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2eud.png\|left\|200px]]		[[Image:2eud.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2eud", 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.
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	{{STRUCTURE_2eud\| PDB=2eud \| SCENE= }}		{{STRUCTURE_2eud\| PDB=2eud \| SCENE= }}

	===Structures of Yeast Ribonucleotide Reductase I complexed with Ligands and Subunit Peptides===		===Structures of Yeast Ribonucleotide Reductase I complexed with Ligands and Subunit Peptides===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16537480}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16537480 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16537480}}		{{ABSTRACT_PUBMED_16537480}}

	==About this Structure==		==About this Structure==
-	~~2EUD~~ is a 1 chain structure of 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=2EUD OCA].	+	[[2eud]] is a 1 chain structure of [[Ribonucleotide reductase]] 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=2EUD OCA].
		+
		+	==See Also==
		+	*[[Ribonucleotide reductase\|Ribonucleotide reductase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16537480~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016537480</ref><references group="xtra"/>
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
Line 33:		Line 24:
	[[Category: Xu, H.]]		[[Category: Xu, H.]]
	[[Category: Ligand interaction]]		[[Category: Ligand interaction]]
		+	[[Category: Oxidoreductase]]
	[[Category: Ribonucleotide reductase]]		[[Category: Ribonucleotide reductase]]
	[[Category: Subunit assembly]]		[[Category: Subunit assembly]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:49:50 2009''