3k8t: Difference between revisions

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[[Image:3k8t.png|left|200px]]


{{STRUCTURE_3k8t| PDB=3k8t | SCENE= }}
==Structure of eukaryotic rnr large subunit R1 complexed with designed adp analog compound==
<StructureSection load='3k8t' size='340' side='right'caption='[[3k8t]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3k8t]] 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=3K8T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K8T 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]] 2.1&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2A5:2-DEOXY-2-(2-HYDROXYETHYL)ADENOSINE+5-(TRIHYDROGEN+DIPHOSPHATE)'>2A5</scene>, <scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=3k8t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k8t OCA], [https://pdbe.org/3k8t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k8t RCSB], [https://www.ebi.ac.uk/pdbsum/3k8t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k8t 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/k8/3k8t_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=3k8t ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Analysis of the recently solved X-ray crystal structures of Saccharomyces cerevisiae ribonucleotide reductase I (ScRnr1) in complex with effectors and substrates led to the discovery of a conserved water molecule located at the active site that interacted with the 2'-hydroxy group of the nucleoside ribose. In this study 2'-(2-hydroxyethyl)-2'-deoxyadenosine 1 and the 5'-diphosphate derivative 2 were designed and synthesized to see if the conserved water molecule could be displaced by a hydroxymethylene group, to generate novel RNR inhibitors as potential antitumor agents. Herein we report the synthesis of analogues 1 and 2, and the co-crystal structure of adenosine diphosphate analogue 2 bound to ScRnr1, which shows the conserved water molecule is displaced as hypothesized.


===Structure of eukaryotic rnr large subunit R1 complexed with designed adp analog compound===
Structure-Based Design, Synthesis, and Evaluation of 2'-(2-Hydroxyethyl)-2'-deoxyadenosine and the 5'-Diphosphate Derivative as Ribonucleotide Reductase Inhibitors.,Sun D, Xu H, Wijerathna SR, Dealwis C, Lee RE ChemMedChem. 2009 Oct;4(10):1649-56. PMID:19681093<ref>PMID:19681093</ref>


{{ABSTRACT_PUBMED_19681093}}
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
==About this Structure==
<div class="pdbe-citations 3k8t" style="background-color:#fffaf0;"></div>
[[3k8t]] 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=3K8T OCA].


==See Also==
==See Also==
*[[Ribonucleotide reductase|Ribonucleotide reductase]]
*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:019681093</ref><references group="xtra"/>
__TOC__
[[Category: Ribonucleoside-diphosphate reductase]]
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Dealwis, C.]]
[[Category: Dealwis C]]
[[Category: Lee, R E.]]
[[Category: Lee RE]]
[[Category: Sun, D.]]
[[Category: Sun D]]
[[Category: Xu, H.]]
[[Category: Xu H]]
[[Category: Allosteric enzyme]]
[[Category: Allosteric enzyme atp-binding]]
[[Category: Atp-binding]]
[[Category: Dna replication]]
[[Category: Eukaryotic ribonucleotide reductase]]
[[Category: Nucleotide analog]]
[[Category: Nucleotide-binding]]
[[Category: Nucleotide-binding oxidoreductase]]
[[Category: Oxidoreductase]]
[[Category: Phosphoprotein]]
Retrieved from "https://proteopedia.org/3k8t"