1rxo: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1rxo]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RXO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RXO FirstGlance]. <br>
<table><tr><td colspan='2'>[[1rxo]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RXO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RXO FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=RUB:RIBULOSE-1,5-DIPHOSPHATE'>RUB</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]] 2.2&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=RUB:RIBULOSE-1,5-DIPHOSPHATE'>RUB</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=1rxo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rxo OCA], [https://pdbe.org/1rxo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rxo RCSB], [https://www.ebi.ac.uk/pdbsum/1rxo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rxo 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=1rxo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rxo OCA], [https://pdbe.org/1rxo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rxo RCSB], [https://www.ebi.ac.uk/pdbsum/1rxo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rxo ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/RBL_SPIOL RBL_SPIOL]] 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_SPIOL RBS1_SPIOL]] 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_SPIOL RBL_SPIOL] 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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=1rxo 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=1rxo ConSurf].
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<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The three-dimensional structure of the complex of ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco; EC 4.1.1.39) from spinach with its natural substrate ribulose 1,5-bisphosphate (RuBP) has been determined both under activating and non-activating conditions by X-ray crystallography to a resolution of 2.1 A and 2.4 A, respectively. Under activating conditions, the use of calcium instead of magnesium as the activator metal ion enabled us to trap the substrate in a stable complex for crystallographic analysis. Comparison of the structure of the activated and the non-activated RuBP complexes shows a tighter binding for the substrate in the non-activated form of the enzyme, in line with previous solution studies. In the non-activated complex, the substrate triggers isolation of the active site by inducing movements of flexible loop regions of the catalytic subunits. In contrast, in the activated complex the active site remains partly open, probably awaiting the binding of the gaseous substrate. By inspection of the structures and by comparison with other complexes of the enzyme we were able to identify a network of hydrogen bonds that stabilise a closed active site structure during crucial steps in the reaction. The present structure underlines the central role of the carbamylated lysine 201 in both activation and catalysis, and completes available structural information for our proposal on the mechanism of the enzyme.
The structure of the complex between rubisco and its natural substrate ribulose 1,5-bisphosphate.,Taylor TC, Andersson I J Mol Biol. 1997 Jan 31;265(4):432-44. PMID:9034362<ref>PMID:9034362</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1rxo" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[RuBisCO 3D structures|RuBisCO 3D structures]]
*[[RuBisCO 3D structures|RuBisCO 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Ribulose-bisphosphate carboxylase]]
[[Category: Spinacia oleracea]]
[[Category: Spinacia oleracea]]
[[Category: Andersson, I]]
[[Category: Andersson I]]
[[Category: Taylor, T C]]
[[Category: Taylor TC]]

Revision as of 11:27, 1 May 2024

ACTIVATED SPINACH RUBISCO IN COMPLEX WITH ITS SUBSTRATE RIBULOSE-1,5-BISPHOSPHATE AND CALCIUMACTIVATED SPINACH RUBISCO IN COMPLEX WITH ITS SUBSTRATE RIBULOSE-1,5-BISPHOSPHATE AND CALCIUM

Structural highlights

1rxo is a 8 chain structure with sequence from Spinacia oleracea. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RBL_SPIOL 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.

See Also

1rxo, resolution 2.20Å

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