2v69

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[[Image:2v69.jpg|left|200px]]
 
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{{Structure
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==Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit mutation D473E==
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|PDB= 2v69 |SIZE=350|CAPTION= <scene name='initialview01'>2v69</scene>, resolution 2.80&Aring;
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<StructureSection load='2v69' size='340' side='right'caption='[[2v69]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:Mg+Binding+Site+For+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Cap+Binding+Site+For+Chain+A'>AC2</scene>, <scene name='pdbsite=AC3:Mg+Binding+Site+For+Chain+B'>AC3</scene>, <scene name='pdbsite=AC4:Cap+Binding+Site+For+Chain+B'>AC4</scene>, <scene name='pdbsite=AC5:Mg+Binding+Site+For+Chain+C'>AC5</scene>, <scene name='pdbsite=AC6:Cap+Binding+Site+For+Chain+C'>AC6</scene>, <scene name='pdbsite=AC7:Mg+Binding+Site+For+Chain+D'>AC7</scene>, <scene name='pdbsite=AC8:Cap+Binding+Site+For+Chain+D'>AC8</scene>, <scene name='pdbsite=AC9:Mg+Binding+Site+For+Chain+E'>AC9</scene>, <scene name='pdbsite=BC1:Cap+Binding+Site+For+Chain+E'>BC1</scene>, <scene name='pdbsite=BC2:Mg+Binding+Site+For+Chain+F'>BC2</scene>, <scene name='pdbsite=BC3:Cap+Binding+Site+For+Chain+F'>BC3</scene>, <scene name='pdbsite=BC4:Mg+Binding+Site+For+Chain+G'>BC4</scene>, <scene name='pdbsite=BC5:Cap+Binding+Site+For+Chain+G'>BC5</scene>, <scene name='pdbsite=BC6:Mg+Binding+Site+For+Chain+H'>BC6</scene>, <scene name='pdbsite=BC7:Cap+Binding+Site+For+Chain+H'>BC7</scene>, <scene name='pdbsite=BC8:Edo+Binding+Site+For+Chain+A'>BC8</scene>, <scene name='pdbsite=BC9:Edo+Binding+Site+For+Chain+A'>BC9</scene>, <scene name='pdbsite=CC1:Edo+Binding+Site+For+Chain+C'>CC1</scene>, <scene name='pdbsite=CC2:Edo+Binding+Site+For+Chain+C'>CC2</scene>, <scene name='pdbsite=CC3:Edo+Binding+Site+For+Chain+C'>CC3</scene>, <scene name='pdbsite=CC4:Edo+Binding+Site+For+Chain+E'>CC4</scene>, <scene name='pdbsite=CC5:Edo+Binding+Site+For+Chain+E'>CC5</scene>, <scene name='pdbsite=CC7:Edo+Binding+Site+For+Chain+G'>CC7</scene>, <scene name='pdbsite=CC8:Edo+Binding+Site+For+Chain+G'>CC8</scene>, <scene name='pdbsite=CC9:Edo+Binding+Site+For+Chain+E'>CC9</scene>, <scene name='pdbsite=DC1:Edo+Binding+Site+For+Chain+A'>DC1</scene>, <scene name='pdbsite=DC2:Edo+Binding+Site+For+Chain+H'>DC2</scene>, <scene name='pdbsite=DC3:Edo+Binding+Site+For+Chain+B'>DC3</scene>, <scene name='pdbsite=DC4:Edo+Binding+Site+For+Chain+B'>DC4</scene>, <scene name='pdbsite=DC5:Edo+Binding+Site+For+Chain+H'>DC5</scene>, <scene name='pdbsite=DC6:Edo+Binding+Site+For+Chain+H'>DC6</scene>, <scene name='pdbsite=DC7:Edo+Binding+Site+For+Chain+H'>DC7</scene>, <scene name='pdbsite=DC8:Edo+Binding+Site+For+Chain+F'>DC8</scene>, <scene name='pdbsite=DC9:Edo+Binding+Site+For+Chain+F'>DC9</scene>, <scene name='pdbsite=EC1:Edo+Binding+Site+For+Chain+D'>EC1</scene>, <scene name='pdbsite=EC2:Edo+Binding+Site+For+Chain+D'>EC2</scene>, <scene name='pdbsite=EC3:Edo+Binding+Site+For+Chain+D'>EC3</scene> and <scene name='pdbsite=EC4:Edo+Binding+Site+For+Chain+G'>EC4</scene>
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== Structural highlights ==
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|LIGAND= <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>
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<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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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribulose-bisphosphate_carboxylase Ribulose-bisphosphate carboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.39 4.1.1.39] </span>
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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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|GENE=
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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>
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|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=CHL00040 rbcL], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam00016 RuBisCO_large], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam02788 RuBisCO_large_N], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd03527 RuBisCO_small]</span>
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<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>
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|RELATEDENTRY=[[1uw9|1UW9]], [[1uzh|1UZH]], [[1gk8|1GK8]], [[1ir2|1IR2]], [[1uwa|1UWA]], [[1uzd|1UZD]], [[2v63|2V63]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2v69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v69 OCA], [http://www.ebi.ac.uk/pdbsum/2v69 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2v69 RCSB]</span>
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== Function ==
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}}
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[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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v6/2v69_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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'''CRYSTAL STRUCTURE OF CHLAMYDOMONAS REINHARDTII RUBISCO WITH A LARGE-SUBUNIT MUTATION D473E'''
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2v69" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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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.
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*[[RuBisCO 3D structures|RuBisCO 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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2V69 is a [[Protein complex]] 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].
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__TOC__
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</StructureSection>
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==Reference==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/17824672 17824672]
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[[Category: Chlamydomonas reinhardtii]]
[[Category: Chlamydomonas reinhardtii]]
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[[Category: Protein complex]]
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[[Category: Large Structures]]
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[[Category: Ribulose-bisphosphate carboxylase]]
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[[Category: Andersson I]]
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[[Category: Andersson, I.]]
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[[Category: Karkehabadi S]]
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[[Category: Karkehabadi, S.]]
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[[Category: Satagopan S]]
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[[Category: Satagopan, S.]]
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[[Category: Spreitzer RJ]]
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[[Category: Spreitzer, R J.]]
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[[Category: Taylor TC]]
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[[Category: Taylor, T C.]]
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[[Category: acetylation]]
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[[Category: calvin cycle]]
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[[Category: carbon dioxide fixation]]
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[[Category: chloroplast]]
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[[Category: co2/o2 specificity]]
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[[Category: hydroxylation]]
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[[Category: large subunit loop 6 mutation]]
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[[Category: lyase]]
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[[Category: magnesium]]
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[[Category: metal-binding]]
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[[Category: methylation]]
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[[Category: monooxygenase]]
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[[Category: oxidoreductase]]
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[[Category: photorespiration]]
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[[Category: photosynthesis]]
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[[Category: plastid]]
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[[Category: rubisco]]
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[[Category: transit peptide]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 2 11:32:21 2008''
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Current revision

Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit mutation D473E

PDB ID 2v69

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