3o0o: Difference between revisions

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==Thermotoga maritima Ribonucleotide Reductase, NrdJ, in complex with dTTP, GDP and Adenosylcobalamin==
The line below this paragraph, containing "STRUCTURE_3o0o", creates the "Structure Box" on the page.
<StructureSection load='3o0o' size='340' side='right'caption='[[3o0o]], [[Resolution|resolution]] 1.90&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'>[[3o0o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O0O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O0O 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]] 1.9&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <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>
{{STRUCTURE_3o0o|  PDB=3o0o  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3o0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o0o OCA], [https://pdbe.org/3o0o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o0o RCSB], [https://www.ebi.ac.uk/pdbsum/3o0o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o0o ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/O33839_THEMT O33839_THEMT]
== 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/o0/3o0o_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3o0o ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Class II ribonucleotide reductases (RNR) catalyse the formation of an essential thiyl radical by homolytic cleavage of the Co-C bond in their adenosylcobalamin (AdoCbl) cofactor. Several mechanisms for the dramatic acceleration of Co-C bond cleavage in AdoCbl-dependent enzymes have been advanced, but no consensus yet exists. We present the structure of the class II RNR from Thermotoga maritima in three complexes: 1) with allosteric effector dTTP, substrate GDP and AdoCbl; 2) with dTTP and AdoCbl; 3) with dTTP, GDP and adenosine. Comparison of these structures gives the deepest structural insights so far into the mechanism of radical generation and transfer for AdoCbl-dependent RNR. AdoCbl binds to the active site pocket, shielding the substrate, transient 5'-deoxyadenosyl radical and nascent thiyl radical from solution. The e-propionamide side chain of AdoCbl forms hydrogen bonds directly to the alpha-phosphate group of the substrate. This interaction appears to cause a "locking-in" of the cofactor, and it is the first observation of a direct cofactor-substrate interaction in an AdoCbl-dependent enzyme. The structures support an ordered sequential reaction mechanism with release or relaxation of AdoCbl on each catalytic cycle. A conformational change of the AdoCbl adenosyl ribose is required to allow hydrogen transfer to the catalytic thiol group. Previously proposed mechanisms for radical transfer in B12-dependent enzymes cannot fully explain the mechanism in class II RNR, suggesting that it may form a separate class that differs from the well-characterised eliminases and mutases.


===Thermotoga maritima Ribonucleotide Reductase, NrdJ, in complex with dTTP, GDP and Adenosylcobalamin===
Structural basis for adenosylcobalamin activation in AdoCbl-dependent ribonucleotide reductases.,Larsson KM, Logan DT, Nordlund P ACS Chem Biol. 2010 Jul 30. PMID:20672854<ref>PMID:20672854</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3o0o" style="background-color:#fffaf0;"></div>


==About this Structure==
==See Also==
3O0O is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O0O OCA].
*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
[[Category: Ribonucleoside-diphosphate reductase]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermotoga maritima]]
[[Category: Thermotoga maritima]]
[[Category: Larsson, K M.]]
[[Category: Larsson K-M]]
[[Category: Logan, D T.]]
[[Category: Logan DT]]
[[Category: Nordlund, P.]]
[[Category: Nordlund P]]
[[Category: 10 alpha/beta barrel]]
[[Category: Adenosylcobalamin dependent]]
[[Category: Coenzyme b12]]
[[Category: Dttp]]
[[Category: Effector]]
[[Category: Gdp]]
[[Category: Oxidoreductase]]
[[Category: Reduction ribonucleotide 2'-oh position]]
[[Category: Ribonucleotide reductase]]
[[Category: Substrate]]
 
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