1mxr: 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: @@
-{{Seed}}
-[[Image:1mxr.png|left|200px]]
-<!--
+==High resolution structure of Ribonucleotide reductase R2 from E. coli in its oxidised (Met) form==
-The line below this paragraph, containing "STRUCTURE_1mxr", creates the "Structure Box" on the page.
+<StructureSection load='1mxr' size='340' side='right'caption='[[1mxr]], [[Resolution|resolution]] 1.42&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1mxr]] 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=1MXR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MXR FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.42&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></td></tr>
-{{STRUCTURE_1mxr|  PDB=1mxr  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1mxr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mxr OCA], [https://pdbe.org/1mxr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mxr RCSB], [https://www.ebi.ac.uk/pdbsum/1mxr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mxr 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/mx/1mxr_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=1mxr ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The R2 protein of class I ribonucleotide reductase generates and stores a tyrosyl radical essential for ribonucleotide reduction and, thus, DNA synthesis. X-ray structures of the protein have enabled detailed mechanistic suggestions, but no structural information has been available for the active radical-containing state of the protein. Here we report on methods to generate the functional tyrosyl radical in single crystals of R2 from Escherichia coli (Y122(*)). We further report on subsequent high-field EPR experiments on the radical-containing crystals. A full rotational pattern of the spectra was collected and the orientation of the g-tensor axes were determined, which directly reflect the orientation of the radical in the crystal frame. The EPR data are discussed in comparison with a 1.42-A x-ray structure of the met (oxidized) form of the protein, also presented in this paper. Comparison of the orientation of the radical Y122(*) obtained from high-field EPR with that of the reduced tyrosine Y122-OH reveals a significant rotation of the tyrosyl side chain, away from the diiron center, in the active radical state. Implications for the radical transfer connecting the diiron site in R2 with the substrate-binding site in R1 are discussed. In addition, the present study demonstrates that structural and functional information about active radical states can be obtained by combined x-ray and high-field EPR crystallography.
-===High resolution structure of Ribonucleotide reductase R2 from E. coli in its oxidised (Met) form===
+Displacement of the tyrosyl radical cofactor in ribonucleotide reductase obtained by single-crystal high-field EPR and 1.4-A x-ray data.,Hogbom M, Galander M, Andersson M, Kolberg M, Hofbauer W, Lassmann G, Nordlund P, Lendzian F Proc Natl Acad Sci U S A. 2003 Mar 18;100(6):3209-14. Epub 2003 Mar 6. PMID:12624184<ref>PMID:12624184</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1mxr" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12624184}}, adds the Publication Abstract to the page
+*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12624184 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12624184}}
+__TOC__
+</StructureSection>
-==About this Structure==
-MXR is a [[Single protein]] structure of 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=1MXR OCA].
-==Reference==
-Displacement of the tyrosyl radical cofactor in ribonucleotide reductase obtained by single-crystal high-field EPR and 1.4-A x-ray data., Hogbom M, Galander M, Andersson M, Kolberg M, Hofbauer W, Lassmann G, Nordlund P, Lendzian F, Proc Natl Acad Sci U S A. 2003 Mar 18;100(6):3209-14. Epub 2003 Mar 6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12624184 12624184]
 [[Category: Escherichia coli]]
-[[Category: Ribonucleoside-diphosphate reductase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Andersson MA]]
-[[Category: Andersson, M A.]]
+[[Category: Hogbom M]]
-[[Category: Hogbom, M.]]
+[[Category: Nordlund P]]
-[[Category: Nordlund, P.]]
-[[Category: Di iron]]
-[[Category: Radical protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 01:46:43 2008''