2cvw: Difference between revisions

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-[[Image:2cvw.gif|left|200px]]<br /><applet load="2cvw" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2cvw, resolution 2.40&Aring;" />
-'''Structures of Yeast Ribonucleotide Reductase I'''<br />
-==Overview==
+==Structures of Yeast Ribonucleotide Reductase I==
-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.
+<StructureSection load='2cvw' size='340' side='right'caption='[[2cvw]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2cvw]] 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=2CVW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CVW FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></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=2cvw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cvw OCA], [https://pdbe.org/2cvw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cvw RCSB], [https://www.ebi.ac.uk/pdbsum/2cvw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cvw ProSAT]</span></td></tr>
+</table>
+== 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/2cvw_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=2cvw ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-CVW is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with MG, TTP and GDP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2CVW OCA].
+*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
+== References ==
-==Reference==
+<references/>
-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://ispc.weizmann.ac.il//pmbin/getpm?pmid=16537479 16537479]
+__TOC__
-[[Category: Ribonucleoside-diphosphate reductase]]
+</StructureSection>
+[[Category: Large Structures]]
 [[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: GDP]]
-[[Category: MG]]
-[[Category: TTP]]
-[[Category: dntp regulation]]
-[[Category: eukaryotic]]
-[[Category: ribonucleotide reductase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 09:17:49 2007''