2av8: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2av8.png|left|200px]]
-{{STRUCTURE_2av8|  PDB=2av8  |  SCENE=  }}
+==Y122F MUTANT OF RIBONUCLEOTIDE REDUCTASE FROM ESCHERICHIA COLI==
+<StructureSection load='2av8' size='340' side='right'caption='[[2av8]], [[Resolution|resolution]] 2.46&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2av8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AV8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AV8 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]] 2.46&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</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=2av8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2av8 OCA], [https://pdbe.org/2av8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2av8 RCSB], [https://www.ebi.ac.uk/pdbsum/2av8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2av8 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RIR2_ECOLI RIR2_ECOLI] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2 contains the tyrosyl radical required for catalysis.
+== 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/av/2av8_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=2av8 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Ribonucleotide reductase (RNR) from Escherichia coli catalyzes the conversion of ribonucleotides to deoxyribonucleotides. It is composed of two homodimeric subunits, R1 and R2. R2 contains the diferric-tyrosyl radical cofactor essential for the nucleotide reduction process. The in vitro mechanism of assembly of this cluster starting with apo R2 or with a diferrous form of R2 has been examined by time-resolved physical biochemical methods. An intermediate, Fe3+/Fe4+ cluster (intermediate X), has been identified that is thought to be directly involved in the oxidation of Y122 to the tyrosyl radical (*Y122). An R2 mutant in which phenylalanine has replaced Y122 has been used to accumulate intermediate X at sufficient levels that it can be studied using a variety of spectroscopic methods. The details of the reconstitution of the apo and diferrous forms of Y122F R2 have been examined by stopped-flow UV/vis spectroscopy and by rapid freeze quench electron paramagnetic resonance, and Mossbauer spectroscopies. In addition the structure of this mutant, crystallized at pH 7.6 in the absence of mercury, at 2.46 A resolution has been determined. These studies suggest that Y122F R2 is an appropriate model for the examination of intermediate X in the assembly process. Studies with two mutants, Y356F and double mutant Y356F and Y122F R2, are interpreted in terms of the possible role of Y356 in the putative electron transfer reaction between the R1 and R2 subunits of this RNR.
-===Y122F MUTANT OF RIBONUCLEOTIDE REDUCTASE FROM ESCHERICHIA COLI===
+Characterization of Y122F R2 of Escherichia coli ribonucleotide reductase by time-resolved physical biochemical methods and X-ray crystallography.,Tong W, Burdi D, Riggs-Gelasco P, Chen S, Edmondson D, Huynh BH, Stubbe J, Han S, Arvai A, Tainer J Biochemistry. 1998 Apr 28;37(17):5840-8. PMID:9558317<ref>PMID:9558317</ref>
-{{ABSTRACT_PUBMED_9558317}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2av8" style="background-color:#fffaf0;"></div>
-[[2av8]] is a 2 chain structure of [[Ribonucleotide reductase]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AV8 OCA].
 ==See Also==
-*[[Ribonucleotide reductase|Ribonucleotide reductase]]
+*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:009558317</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Ribonucleoside-diphosphate reductase]]
+[[Category: Large Structures]]
-[[Category: Arvai, A.]]
+[[Category: Arvai A]]
-[[Category: Han, S.]]
+[[Category: Han S]]
-[[Category: Tainer, J A.]]
+[[Category: Tainer JA]]
-[[Category: Dna replication]]
-[[Category: Oxidoreductase]]