2cvv - Revision history

OCA at 13:43, 13 March 2024

2024-03-13T13:43:57Z

←Older revision		Revision as of 13:43, 13 March 2024
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	<StructureSection load='2cvv' size='340' side='right'caption='[[2cvv]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='2cvv' size='340' side='right'caption='[[2cvv]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2cvv]] 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=2CVV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CVV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2cvv]] 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=2CVV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CVV 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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]] 2.9Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1zyz\|1zyz]], [[2cvs\|2cvs]], [[2cvt\|2cvt]], [[2cvu\|2cvu]], [[2cvw\|2cvw]], [[2cvx\|2cvx]], [[2cvy\|2cvy]]~~</~~div~~><~~/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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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=2cvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cvv OCA], [https://pdbe.org/2cvv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cvv RCSB], [https://www.ebi.ac.uk/pdbsum/2cvv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cvv 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=2cvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cvv OCA], [https://pdbe.org/2cvv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cvv RCSB], [https://www.ebi.ac.uk/pdbsum/2cvv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cvv 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=2cvv 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=2cvv ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Ribonucleotide reductase catalyzes a crucial step in de novo DNA synthesis and is allosterically controlled by relative levels of dNTPs to maintain a balanced pool of deoxynucleoside triphosphates in the cell. In eukaryotes, the enzyme comprises a heterooligomer of alpha(2) and beta(2) subunits. The alpha subunit, Rnr1, contains catalytic and regulatory sites. Here, we report the only x-ray structures of the eukaryotic alpha subunit of ribonucleotide reductase from Saccharomyces cerevisiae. The structures of the apo-, AMPPNP only-, AMPPNP-CDP-, AMPPNP-UDP-, dGTP-ADP- and TTP-GDP-bound complexes give insight into substrate and effector binding and specificity cross-talk. These are Class I structures with the only fully ordered catalytic sites, including loop 2, a stretch of polypeptide that spans specificity and catalytic sites, conferring specificity. Binding of specificity effector rearranges loop 2; in our structures, this rearrangement moves P294, a residue unique to eukaryotes, out of the catalytic site, accommodating substrate binding. Substrate binding further rearranges loop 2. Cross-talk, by which effector binding regulates substrate preference, occurs largely through R293 and Q288 of loop 2, which are analogous to residues in Thermotoga maritima that mediate cross-talk. However loop-2 conformations and residue-substrate interactions differ substantially between yeast and T. maritima. In most effector-substrate complexes, water molecules help mediate substrate-loop 2 interactions. Finally, the substrate ribose binds with its 3' hydroxyl closer than its 2' hydroxyl to C218 of the catalytic redox pair. We also see a conserved water molecule at the catalytic site in all our structures, near the ribose 2' hydroxyl.
-
-	Structures of eukaryotic ribonucleotide reductase I provide insights into dNTP regulation.,Xu H, Faber C, Uchiki T, Fairman JW, Racca J, Dealwis C Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4022-7. Epub 2006 Mar 6. PMID:16537479<ref>PMID:16537479</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2cvv" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 27:
	__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: Dntp regulation]]~~	+
-	~~[[Category: Eukaryotic]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Ribonucleotide reductase~~]]	+

OCA at 07:01, 1 December 2021

2021-12-01T07:01:39Z

←Older revision		Revision as of 07:01, 1 December 2021
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	<StructureSection load='2cvv' size='340' side='right'caption='[[2cvv]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='2cvv' size='340' side='right'caption='[[2cvv]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2cvv]] 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=2CVV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2CVV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2cvv]] 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=2CVV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CVV 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zyz\|1zyz]], [[2cvs\|2cvs]], [[2cvt\|2cvt]], [[2cvu\|2cvu]], [[2cvw\|2cvw]], [[2cvx\|2cvx]], [[2cvy\|2cvy]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1zyz\|1zyz]], [[2cvs\|2cvs]], [[2cvt\|2cvt]], [[2cvu\|2cvu]], [[2cvw\|2cvw]], [[2cvx\|2cvx]], [[2cvy\|2cvy]]</div></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=2cvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cvv OCA], [~~http~~://pdbe.org/2cvv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2cvv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2cvv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2cvv 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=2cvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cvv OCA], [https://pdbe.org/2cvv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cvv RCSB], [https://www.ebi.ac.uk/pdbsum/2cvv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cvv 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]]

OCA at 11:08, 26 February 2020

2020-02-26T11:08:36Z

←Older revision		Revision as of 11:08, 26 February 2020
Line 1:		Line 1:

	==Structures of Yeast Ribonucleotide Reductase I==		==Structures of Yeast Ribonucleotide Reductase I==
-	<StructureSection load='2cvv' size='340' side='right' caption='[[2cvv]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='2cvv' size='340' side='right'caption='[[2cvv]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2cvv]] 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=2CVV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CVV FirstGlance]. <br>		<table><tr><td colspan='2'>[[2cvv]] 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=2CVV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CVV FirstGlance]. <br>
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 08:38, 23 May 2018

2018-05-23T08:38:03Z

←Older revision		Revision as of 08:38, 23 May 2018
Line 1:		Line 1:
		+
	==Structures of Yeast Ribonucleotide Reductase I==		==Structures of Yeast Ribonucleotide Reductase I==
	<StructureSection load='2cvv' size='340' side='right' caption='[[2cvv]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='2cvv' size='340' side='right' caption='[[2cvv]], [[Resolution\|resolution]] 2.90Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zyz\|1zyz]], [[2cvs\|2cvs]], [[2cvt\|2cvt]], [[2cvu\|2cvu]], [[2cvw\|2cvw]], [[2cvx\|2cvx]], [[2cvy\|2cvy]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zyz\|1zyz]], [[2cvs\|2cvs]], [[2cvt\|2cvt]], [[2cvu\|2cvu]], [[2cvw\|2cvw]], [[2cvx\|2cvx]], [[2cvy\|2cvy]]</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=2cvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cvv OCA], [http://pdbe.org/2cvv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2cvv RCSB], [http://www.ebi.ac.uk/pdbsum/2cvv 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=2cvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cvv OCA], [http://pdbe.org/2cvv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2cvv RCSB], [http://www.ebi.ac.uk/pdbsum/2cvv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2cvv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cv/2cvv_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cv/2cvv_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>
	</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=2cvv ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:13, 11 September 2015

2015-09-11T10:13:42Z

←Older revision		Revision as of 10:13, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2cvv' size='340' side='right' caption='[[2cvv]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='2cvv' size='340' side='right' caption='[[2cvv]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2cvv]] 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=2CVV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CVV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2cvv]] 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=2CVV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CVV 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zyz\|1zyz]], [[2cvs\|2cvs]], [[2cvt\|2cvt]], [[2cvu\|2cvu]], [[2cvw\|2cvw]], [[2cvx\|2cvx]], [[2cvy\|2cvy]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zyz\|1zyz]], [[2cvs\|2cvs]], [[2cvt\|2cvt]], [[2cvu\|2cvu]], [[2cvw\|2cvw]], [[2cvx\|2cvx]], [[2cvy\|2cvy]]</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=2cvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cvv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2cvv RCSB], [http://www.ebi.ac.uk/pdbsum/2cvv 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=2cvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cvv OCA], [http://pdbe.org/2cvv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2cvv RCSB], [http://www.ebi.ac.uk/pdbsum/2cvv 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 2cvv" 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 14:59, 25 December 2014

2014-12-25T14:59:57Z

←Older revision		Revision as of 14:59, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2cvv]] 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=2CVV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CVV FirstGlance]. <br>		<table><tr><td colspan='2'>[[2cvv]] 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=2CVV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CVV 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zyz\|1zyz]], [[2cvs\|2cvs]], [[2cvt\|2cvt]], [[2cvu\|2cvu]], [[2cvw\|2cvw]], [[2cvx\|2cvx]], [[2cvy\|2cvy]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zyz\|1zyz]], [[2cvs\|2cvs]], [[2cvt\|2cvt]], [[2cvu\|2cvu]], [[2cvw\|2cvw]], [[2cvx\|2cvx]], [[2cvy\|2cvy]]</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=2cvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cvv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2cvv RCSB], [http://www.ebi.ac.uk/pdbsum/2cvv 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=2cvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cvv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2cvv RCSB], [http://www.ebi.ac.uk/pdbsum/2cvv 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 W.]]	+	[[Category: Fairman, J W]]
-	[[Category: Racca, J.]]	+	[[Category: Racca, J]]
-	[[Category: Uchiki, T.]]	+	[[Category: Uchiki, T]]
-	[[Category: Xu, H.]]	+	[[Category: Xu, H]]
	[[Category: Dntp regulation]]		[[Category: Dntp regulation]]
	[[Category: Eukaryotic]]		[[Category: Eukaryotic]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Ribonucleotide reductase]]		[[Category: Ribonucleotide reductase]]

OCA at 10:20, 29 September 2014

2014-09-29T10:20:20Z

←Older revision		Revision as of 10:20, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2cvv.~~png~~\|~~left~~\|200px]]	+	==Structures of Yeast Ribonucleotide Reductase I==
		+	<StructureSection load='2cvv' size='340' side='right' caption='[[2cvv]], [[Resolution\|resolution]] 2.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2cvv]] 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=2CVV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CVV 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zyz\|1zyz]], [[2cvs\|2cvs]], [[2cvt\|2cvt]], [[2cvu\|2cvu]], [[2cvw\|2cvw]], [[2cvx\|2cvx]], [[2cvy\|2cvy]]</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=2cvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cvv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2cvv RCSB], [http://www.ebi.ac.uk/pdbsum/2cvv 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/cv/2cvv_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 catalyzes a crucial step in de novo DNA synthesis and is allosterically controlled by relative levels of dNTPs to maintain a balanced pool of deoxynucleoside triphosphates in the cell. In eukaryotes, the enzyme comprises a heterooligomer of alpha(2) and beta(2) subunits. The alpha subunit, Rnr1, contains catalytic and regulatory sites. Here, we report the only x-ray structures of the eukaryotic alpha subunit of ribonucleotide reductase from Saccharomyces cerevisiae. The structures of the apo-, AMPPNP only-, AMPPNP-CDP-, AMPPNP-UDP-, dGTP-ADP- and TTP-GDP-bound complexes give insight into substrate and effector binding and specificity cross-talk. These are Class I structures with the only fully ordered catalytic sites, including loop 2, a stretch of polypeptide that spans specificity and catalytic sites, conferring specificity. Binding of specificity effector rearranges loop 2; in our structures, this rearrangement moves P294, a residue unique to eukaryotes, out of the catalytic site, accommodating substrate binding. Substrate binding further rearranges loop 2. Cross-talk, by which effector binding regulates substrate preference, occurs largely through R293 and Q288 of loop 2, which are analogous to residues in Thermotoga maritima that mediate cross-talk. However loop-2 conformations and residue-substrate interactions differ substantially between yeast and T. maritima. In most effector-substrate complexes, water molecules help mediate substrate-loop 2 interactions. Finally, the substrate ribose binds with its 3' hydroxyl closer than its 2' hydroxyl to C218 of the catalytic redox pair. We also see a conserved water molecule at the catalytic site in all our structures, near the ribose 2' hydroxyl.

-	~~{{STRUCTURE_2cvv\| PDB=2cvv \| SCENE= }}~~	+	Structures of eukaryotic ribonucleotide reductase I provide insights into dNTP regulation.,Xu H, Faber C, Uchiki T, Fairman JW, Racca J, Dealwis C Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4022-7. Epub 2006 Mar 6. PMID:16537479<ref>PMID:16537479</ref>

-	~~===Structures~~ of ~~Yeast Ribonucleotide Reductase I===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16537479}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2cvv]] 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=2CVV OCA].~~	+

	==See Also==		==See Also==
	*[[Ribonucleotide reductase\|Ribonucleotide reductase]]		*[[Ribonucleotide reductase\|Ribonucleotide reductase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:016537479<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]

OCA at 18:05, 20 October 2012

2012-10-20T18:05:34Z

←Older revision		Revision as of 18:05, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2cvv]] 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=2CVV OCA].	+	[[2cvv]] 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=2CVV OCA].

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

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

2012-07-27T02:59:48Z

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

←Older revision

Revision as of 02:59, 27 July 2012

OCA at 02:59, 27 July 2012

2012-07-27T02:59:45Z

←Older revision		Revision as of 02:59, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2cvv.png\|left\|200px]]		[[Image:2cvv.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2cvv", 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_2cvv\| PDB=2cvv \| SCENE= }}		{{STRUCTURE_2cvv\| PDB=2cvv \| SCENE= }}

	===Structures of Yeast Ribonucleotide Reductase I===		===Structures of Yeast Ribonucleotide Reductase I===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16537479}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16537479 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16537479}}		{{ABSTRACT_PUBMED_16537479}}

	==About this Structure==		==About this Structure==
-	~~2CVV~~ 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=2CVV OCA].	+	[[2cvv]] 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=2CVV OCA].
		+
		+	==See Also==
		+	*[[Ribonucleotide reductase\|Ribonucleotide reductase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16537479~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016537479</ref><references group="xtra"/>
	[[Category: Ribonucleoside-diphosphate reductase]]		[[Category: Ribonucleoside-diphosphate reductase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
Line 34:		Line 25:
	[[Category: Dntp regulation]]		[[Category: Dntp regulation]]
	[[Category: Eukaryotic]]		[[Category: Eukaryotic]]
		+	[[Category: Oxidoreductase]]
	[[Category: Ribonucleotide reductase]]		[[Category: Ribonucleotide reductase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 19:40:09 2009''