2vdi

From Proteopedia

(Difference between revisions)

Revision as of 20:59, 20 October 2021

Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit C192S mutation

Structural highlights

2vdi 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:	2v67, 2v63, 2v68, 1ir2, 1uzh, 2v69, 1uw9, 1uzd, 2vdh, 1uwa, 2v6a, 1gk8
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

Proximal Cys(172) and Cys(192) in the large subunit of the photosynthetic enzyme Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39) are evolutionarily conserved among cyanobacteria, algae and higher plants. Mutation of Cys(172) has been shown to affect the redox properties of Rubisco in vitro and to delay the degradation of the enzyme in vivo under stress conditions. Here, we report the effect of the replacement of Cys(172) and Cys(192) by serine on the catalytic properties, thermostability and three-dimensional structure of Chlamydomonas reinhardtii Rubisco. The most striking effect of the C172S substitution was an 11% increase in the specificity factor when compared with the wild-type enzyme. The specificity factor of C192S Rubisco was not altered. The V(c) (V(max) for carboxylation) was similar to that of wild-type Rubisco in the case of the C172S enzyme, but approx. 30% lower for the C192S Rubisco. In contrast, the K(m) for CO(2) and O(2) was similar for C192S and wild-type enzymes, but distinctly higher (approximately double) for the C172S enzyme. C172S Rubisco showed a critical denaturation temperature approx. 2 degrees C lower than wild-type Rubisco and a distinctly higher denaturation rate at 55 degrees C, whereas C192S Rubisco was only slightly more sensitive to temperature denaturation than the wild-type enzyme. X-ray crystal structures reveal that the C172S mutation causes a shift of the main-chain backbone atoms of beta-strand 1 of the alpha/beta-barrel affecting a number of amino acid side chains. This may cause the exceptional catalytic features of C172S. In contrast, the C192S mutation does not produce similar structural perturbations.

Structural and functional consequences of the replacement of proximal residues Cys(172) and Cys(192) in the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from Chlamydomonas reinhardtii.,Garcia-Murria MJ, Karkehabadi S, Marin-Navarro J, Satagopan S, Andersson I, Spreitzer RJ, Moreno J Biochem J. 2008 Apr 15;411(2):241-7. PMID:18072944^[1]

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

References

↑ Garcia-Murria MJ, Karkehabadi S, Marin-Navarro J, Satagopan S, Andersson I, Spreitzer RJ, Moreno J. Structural and functional consequences of the replacement of proximal residues Cys(172) and Cys(192) in the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from Chlamydomonas reinhardtii. Biochem J. 2008 Apr 15;411(2):241-7. PMID:18072944 doi:10.1042/BJ20071422

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/2vdi"

@@ Line 3: / Line 3: @@
 <StructureSection load='2vdi' size='340' side='right'caption='[[2vdi]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vdi]] 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=2VDI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VDI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vdi]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Chlre Chlre]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VDI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VDI 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">[[2v67|2v67]], [[2v63|2v63]], [[2v68|2v68]], [[1ir2|1ir2]], [[1uzh|1uzh]], [[2v69|2v69]], [[1uw9|1uw9]], [[1uzd|1uzd]], [[2vdh|2vdh]], [[1uwa|1uwa]], [[2v6a|2v6a]], [[1gk8|1gk8]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2v67|2v67]], [[2v63|2v63]], [[2v68|2v68]], [[1ir2|1ir2]], [[1uzh|1uzh]], [[2v69|2v69]], [[1uw9|1uw9]], [[1uzd|1uzd]], [[2vdh|2vdh]], [[1uwa|1uwa]], [[2v6a|2v6a]], [[1gk8|1gk8]]</div></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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribulose-bisphosphate_carboxylase Ribulose-bisphosphate carboxylase], with EC number [https://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=2vdi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vdi OCA], [http://pdbe.org/2vdi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vdi RCSB], [http://www.ebi.ac.uk/pdbsum/2vdi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vdi ProSAT]</span></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=2vdi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vdi OCA], [https://pdbe.org/2vdi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vdi RCSB], [https://www.ebi.ac.uk/pdbsum/2vdi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vdi ProSAT]</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] [[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]]
@@ Line 33: / Line 33: @@
 ==See Also==
-*[[RuBisCO|RuBisCO]]
+*[[RuBisCO 3D structures|RuBisCO 3D structures]]
 == References ==
 <references/>

2vdi

From Proteopedia

Revision as of 20:59, 20 October 2021

Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit C192S mutation

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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