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2cvx

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Structures of Yeast Ribonucleotide Reductase I

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Retrieved from "http://52.214.119.220/wiki/index.php/2cvx"

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-[[Image:2cvx.gif|left|200px]]
- {{Structure
+==Structures of Yeast Ribonucleotide Reductase I==
-|PDB= 2cvx |SIZE=350|CAPTION= <scene name='initialview01'>2cvx</scene>, resolution 2.20&Aring;
+<StructureSection load='2cvx' size='340' side='right'caption='[[2cvx]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ADP:ADENOSINE-5&#39;-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=DGT:2&#39;-DEOXYGUANOSINE-5&#39;-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
+<table><tr><td colspan='2'>[[2cvx]] 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=2CVX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CVX FirstGlance]. <br>
-|ACTIVITY= <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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-|GENE=
+<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>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2cvx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cvx OCA], [https://pdbe.org/2cvx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cvx RCSB], [https://www.ebi.ac.uk/pdbsum/2cvx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cvx ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1zyz|1ZYZ]], [[2cvs|2CVS]], [[2cvt|2CVT]], [[2cvu|2CVU]], [[2cvv|2CVV]], [[2cvw|2CVW]], [[2cvy|2CVY]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2cvx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cvx OCA], [http://www.ebi.ac.uk/pdbsum/2cvx PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2cvx RCSB]</span>
+== 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>
+== 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/2cvx_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/main_output.php?pdb_ID=2cvx ConSurf].
+<div style="clear:both"></div>
-'''Structures of Yeast Ribonucleotide Reductase I'''
+==See Also==
+*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
+== References ==
-==Overview==
+<references/>
-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.
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-CVX is a [[Single protein]] 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=2CVX OCA].
-==Reference==
-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:[http://www.ncbi.nlm.nih.gov/pubmed/16537479 16537479]
-[[Category: Ribonucleoside-diphosphate reductase]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Dealwis C]]
-[[Category: Dealwis, C.]]
+[[Category: Faber C]]
-[[Category: Faber, C.]]
+[[Category: Fairman JW]]
-[[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: eukaryotic]]
-[[Category: ribonucleotide reductase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:27:06 2008''

2cvx

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Structures of Yeast Ribonucleotide Reductase I

Structural highlights

Function

Evolutionary Conservation

See Also

References

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