2v69: Difference between revisions

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{{Seed}}
[[Image:2v69.png|left|200px]]


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==Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit mutation D473E==
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<StructureSection load='2v69' size='340' side='right'caption='[[2v69]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2v69]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Chlamydomonas_reinhardtii Chlamydomonas reinhardtii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V69 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V69 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#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=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HYP:4-HYDROXYPROLINE'>HYP</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MME:N-METHYL+METHIONINE'>MME</scene>, <scene name='pdbligand=SMC:S-METHYLCYSTEINE'>SMC</scene></td></tr>
{{STRUCTURE_2v69|  PDB=2v69  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2v69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v69 OCA], [https://pdbe.org/2v69 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v69 RCSB], [https://www.ebi.ac.uk/pdbsum/2v69 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v69 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RBS1_CHLRE RBS1_CHLRE] RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.
== 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/v6/2v69_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=2v69 ConSurf].
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<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The loop between alpha-helix 6 and beta-strand 6 in the alpha/beta-barrel of ribulose-1,5-bisphosphate carboxylase/oxygenase plays a key role in discriminating between CO2 and O2. Genetic screening in Chlamydomonas reinhardtii previously identified a loop-6 V331A substitution that decreases carboxylation and CO2/O2 specificity. Revertant selection identified T342I and G344S substitutions that restore photosynthetic growth by increasing carboxylation and specificity of the V331A enzyme. In numerous X-ray crystal structures, loop 6 is closed or open depending on the activation state of the enzyme and the presence or absence of ligands. The carboxy terminus folds over loop 6 in the closed state. To study the molecular basis for catalysis, directed mutagenesis and chloroplast transformation were used to create T342I and G344S substitutions alone. X-ray crystal structures were then solved for the V331A, V331A/T342I, T342I, and V331A/G344S enzymes, as well as for a D473E enzyme created to assess the role of the carboxy terminus in loop-6 closure. V331A disturbs a hydrophobic pocket, abolishing several van der Waals interactions. These changes are complemented by T342I and G344S, both of which alone cause decreases in CO2/O2 specificity. In the V331A/T342I revertant enzyme, Arg339 main-chain atoms are displaced. In V331A/G344S, alpha-helix 6 is shifted. D473E causes disorder of the carboxy terminus, but loop 6 remains closed. Interactions between a transition-state analogue and several residues are altered in the mutant enzymes. However, active-site Lys334 at the apex of loop 6 has a normal conformation. A variety of subtle interactions must be responsible for catalytic efficiency and CO2/O2 specificity.


===CRYSTAL STRUCTURE OF CHLAMYDOMONAS REINHARDTII RUBISCO WITH A LARGE-SUBUNIT MUTATION D473E===
Structural analysis of altered large-subunit loop-6/carboxy-terminus interactions that influence catalytic efficiency and CO2/O2 specificity of ribulose-1,5-bisphosphate carboxylase/oxygenase.,Karkehabadi S, Satagopan S, Taylor TC, Spreitzer RJ, Andersson I Biochemistry. 2007 Oct 2;46(39):11080-9. Epub 2007 Sep 8. PMID:17824672<ref>PMID:17824672</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 2v69" style="background-color:#fffaf0;"></div>


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==See Also==
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*[[RuBisCO 3D structures|RuBisCO 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 17824672 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_17824672}}
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</StructureSection>
==About this Structure==
2V69 is a 16 chains structure of sequences from [http://en.wikipedia.org/wiki/Chlamydomonas_reinhardtii Chlamydomonas reinhardtii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V69 OCA].
 
==Reference==
<ref group="xtra">PMID:17824672</ref><references group="xtra"/>
[[Category: Chlamydomonas reinhardtii]]
[[Category: Chlamydomonas reinhardtii]]
[[Category: Ribulose-bisphosphate carboxylase]]
[[Category: Large Structures]]
[[Category: Andersson, I.]]
[[Category: Andersson I]]
[[Category: Karkehabadi, S.]]
[[Category: Karkehabadi S]]
[[Category: Satagopan, S.]]
[[Category: Satagopan S]]
[[Category: Spreitzer, R J.]]
[[Category: Spreitzer RJ]]
[[Category: Taylor, T C.]]
[[Category: Taylor TC]]
[[Category: Acetylation]]
[[Category: Calvin cycle]]
[[Category: Carbon dioxide fixation]]
[[Category: Chloroplast]]
[[Category: Co2/o2 specificity]]
[[Category: Hydroxylation]]
[[Category: Large subunit loop 6 mutation]]
[[Category: Lyase]]
[[Category: Magnesium]]
[[Category: Metal-binding]]
[[Category: Methylation]]
[[Category: Monooxygenase]]
[[Category: Oxidoreductase]]
[[Category: Photorespiration]]
[[Category: Photosynthesis]]
[[Category: Plastid]]
[[Category: Rubisco]]
[[Category: Transit peptide]]
 
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