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| | ==Hexameric Form II RuBisCO from Rhodopseudomonas palustris, activated and complexed with sulfate and magnesium== | | ==Hexameric Form II RuBisCO from Rhodopseudomonas palustris, activated and complexed with sulfate and magnesium== |
| - | <StructureSection load='4lf2' size='340' side='right' caption='[[4lf2]], [[Resolution|resolution]] 2.38Å' scene=''> | + | <StructureSection load='4lf2' size='340' side='right'caption='[[4lf2]], [[Resolution|resolution]] 2.38Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4lf2]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LF2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LF2 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4lf2]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodopseudomonas_palustris_CGA009 Rhodopseudomonas palustris CGA009]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LF2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LF2 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.38Å</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=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4lf1|4lf1]]</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=4lf2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lf2 OCA], [https://pdbe.org/4lf2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lf2 RCSB], [https://www.ebi.ac.uk/pdbsum/4lf2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lf2 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=4lf2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lf2 OCA], [http://pdbe.org/4lf2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4lf2 RCSB], [http://www.ebi.ac.uk/pdbsum/4lf2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4lf2 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RBL2_RHOPA RBL2_RHOPA]] 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 (By similarity). | + | [https://www.uniprot.org/uniprot/RBL2_RHOPA RBL2_RHOPA] 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 (By similarity). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[RuBisCO|RuBisCO]] | + | *[[RuBisCO 3D structures|RuBisCO 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ribulose-bisphosphate carboxylase]] | + | [[Category: Large Structures]] |
| - | [[Category: Chan, S]] | + | [[Category: Rhodopseudomonas palustris CGA009]] |
| - | [[Category: Eisenberg, D]] | + | [[Category: Chan S]] |
| - | [[Category: Perry, L J]] | + | [[Category: Eisenberg D]] |
| - | [[Category: Satagopan, S]] | + | [[Category: Perry LJ]] |
| - | [[Category: Sawaya, M R]] | + | [[Category: Satagopan S]] |
| - | [[Category: Tabita, F R]] | + | [[Category: Sawaya MR]] |
| - | [[Category: Cbbm 2-cabp]]
| + | [[Category: Tabita FR]] |
| - | [[Category: Form ii]]
| + | |
| - | [[Category: Lyase]]
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| - | [[Category: Oxidoreductase]]
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| - | [[Category: Photosynthesis]]
| + | |
| - | [[Category: Photosynthetic carbon fixation]]
| + | |
| - | [[Category: Reaction intermediate analogue]]
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| - | [[Category: Transition-state analog]]
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| Structural highlights
Function
RBL2_RHOPA 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 (By similarity).
Publication Abstract from PubMed
The first x-ray crystal structure has been solved for an activated transition-state analog-bound form II ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). This enzyme, from Rhodopseudomonas palustris, assembles as a unique hexamer with three pairs of catalytic large subunit homodimers around a central 3-fold symmetry axis. This oligomer arrangement is unique among all known Rubisco structures, including the form II homolog from Rhodospirillum rubrum. The presence of a transition-state analog in the active site locked the activated enzyme in a "closed" conformation and revealed the positions of critical active site residues during catalysis. Functional roles of two form II-specific residues (Ile(165) and Met(331)) near the active site were examined via site-directed mutagenesis. Substitutions at these residues affect function but not the ability of the enzyme to assemble. Random mutagenesis and suppressor selection in a Rubisco deletion strain of Rhodobacter capsulatus identified a residue in the amino terminus of one subunit (Ala(47)) that compensated for a negative change near the active site of a neighboring subunit. In addition, substitution of the native carboxyl-terminal sequence with the last few dissimilar residues from the related R. rubrum homolog increased the enzyme's kcat for carboxylation. However, replacement of a longer carboxyl-terminal sequence with termini from either a form III or a form I enzyme, which varied both in length and sequence, resulted in complete loss of function. From these studies, it is evident that a number of subtle interactions near the active site and the carboxyl terminus account for functional differences between the different forms of Rubiscos found in nature.
Structure-function studies with the unique hexameric form II ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Rhodopseudomonas palustris.,Satagopan S, Chan S, Perry LJ, Tabita FR J Biol Chem. 2014 Aug 1;289(31):21433-50. doi: 10.1074/jbc.M114.578625. Epub 2014, Jun 18. PMID:24942737[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Satagopan S, Chan S, Perry LJ, Tabita FR. Structure-function studies with the unique hexameric form II ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Rhodopseudomonas palustris. J Biol Chem. 2014 Aug 1;289(31):21433-50. doi: 10.1074/jbc.M114.578625. Epub 2014, Jun 18. PMID:24942737 doi:http://dx.doi.org/10.1074/jbc.M114.578625
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