2v6a

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Chlamydomonas reinhardtii Rubisco with large- subunit mutations V331A, G344S

Structural highlights

2v6a is a 16 chain structure with sequence from Chlamydomonas reinhardtii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.5Å
Ligands:	, , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RBL_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 in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site.[HAMAP-Rule:MF_01338]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Karkehabadi S, Satagopan S, Taylor TC, Spreitzer RJ, Andersson I. 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. Biochemistry. 2007 Oct 2;46(39):11080-9. Epub 2007 Sep 8. PMID:17824672 doi:http://dx.doi.org/10.1021/bi701063f

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2v6a"

@@ Line 1: / Line 1: @@
-==CRYSTAL STRUCTURE OF CHLAMYDOMONAS REINHARDTII RUBISCO WITH LARGE-SUBUNIT MUTATIONS V331A, G344S==
-<StructureSection load='2v6a' size='340' side='right' caption='[[2v6a]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+==Crystal structure of Chlamydomonas reinhardtii Rubisco with large- subunit mutations V331A, G344S==
+<StructureSection load='2v6a' size='340' side='right'caption='[[2v6a]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2v6a]] is a 16 chain structure with sequence 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=2V6A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V6A FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2v6a]] 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=2V6A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V6A FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=HYP:4-HYDROXYPROLINE'>HYP</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MME:N-METHYL+METHIONINE'>MME</scene>, <scene name='pdbligand=SMC:S-METHYLCYSTEINE'>SMC</scene></td></tr>
+<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>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1gk8|1gk8]], [[1uwa|1uwa]], [[1uw9|1uw9]], [[1uzh|1uzh]], [[1ir2|1ir2]], [[1uzd|1uzd]], [[2v63|2v63]], [[2v67|2v67]], [[2v68|2v68]], [[2v69|2v69]]</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=2v6a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v6a OCA], [https://pdbe.org/2v6a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v6a RCSB], [https://www.ebi.ac.uk/pdbsum/2v6a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v6a ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2v6a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v6a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2v6a RCSB], [http://www.ebi.ac.uk/pdbsum/2v6a PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RBL_CHLRE RBL_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 in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site.[HAMAP-Rule:MF_01338] [[http://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.
+[https://www.uniprot.org/uniprot/RBL_CHLRE RBL_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 in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site.[HAMAP-Rule:MF_01338]
 == 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/v6/2v6a_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v6/2v6a_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2v6a ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 29: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2v6a" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[RuBisCO|RuBisCO]]
+*[[RuBisCO 3D structures|RuBisCO 3D structures]]
 == References ==
 <references/>
@@ Line 37: / Line 37: @@
 </StructureSection>
 [[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: 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: Rubisco]]
-[[Category: Transit peptide]]

2v6a

From Proteopedia

Current revision

Crystal structure of Chlamydomonas reinhardtii Rubisco with large- subunit mutations V331A, G344S

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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