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2v63

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Revision as of 11:21, 17 June 2020

Crystal structure of Rubisco from Chlamydomonas reinhardtii with a large-subunit V331A mutation

Structural highlights

2v63 is a 16 chain structure with sequence from Chlre. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
NonStd Res:	, , ,
Related:	1uw9, 1ir2, 1uzd, 1uzh, 1gk8, 2v67, 2v68, 2v69, 2v6a
Activity:	Ribulose-bisphosphate carboxylase, with EC number 4.1.1.39
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] [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

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/2v63"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Rubisco from Chlamydomonas reinhardtii with a large-subunit V331A mutation==
-<StructureSection load='2v63' size='340' side='right' caption='[[2v63]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='2v63' size='340' side='right'caption='[[2v63]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2v63]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Chlre Chlre]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V63 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V63 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2v63]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Chlre Chlre]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V63 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2V63 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='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=MG:MAGNESIUM+ION'>MG</scene></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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1uw9|1uw9]], [[1ir2|1ir2]], [[1uzd|1uzd]], [[1uzh|1uzh]], [[1gk8|1gk8]], [[2v67|2v67]], [[2v68|2v68]], [[2v69|2v69]], [[2v6a|2v6a]]</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=2v63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v63 OCA], [http://pdbe.org/2v63 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2v63 RCSB], [http://www.ebi.ac.uk/pdbsum/2v63 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2v63 ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2v63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v63 OCA], [http://pdbe.org/2v63 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2v63 RCSB], [http://www.ebi.ac.uk/pdbsum/2v63 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2v63 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 33: / Line 33: @@
 ==See Also==
-*[[RuBisCO|RuBisCO]]
+*[[RuBisCO 3D structures|RuBisCO 3D structures]]
 == References ==
 <references/>
@@ Line 39: / Line 39: @@
 </StructureSection>
 [[Category: Chlre]]
+[[Category: Large Structures]]
 [[Category: Ribulose-bisphosphate carboxylase]]
 [[Category: Andersson, I]]

2v63

From Proteopedia

Revision as of 11:21, 17 June 2020

Crystal structure of Rubisco from Chlamydomonas reinhardtii with a large-subunit V331A mutation

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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