RuBisCO: Difference between revisions
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The structure of spinach Rubisco bound to the naturally occurring inhibitor 2-carboxylarabinitol-1,5-bisphosphate (CAP) and Mg<sup>2+</sup> ([[8ruc]]<ref>PMID:8648644</ref>), implicates residues that are involved in the catalytic mechanism [[Image:RubiscoMechanism.pdf]]. [[Image:CAP.jpg|left|]] The structure of CAP (left figure) is similar to the hydrated reaction intermediate that is formed following the addition of CO<sub>2</sub> to RUBP. Here is an <scene name='46/463261/8ruc_active-site/1'>isolated α-β barrel</scene> (cartoon and colored for secondary structure) with CAP and and Mg<sup>2+</sup> in CPK spacefill. This <scene name='46/463261/8ruc_active-site/5'> overview of the active site</scene> in which the helices have been removed, shows that CAP sits at one end of the α-β barrel, and only residues from the beta strands (gold ball & stick) and loops that link them to helices (white ball & stick) are involved in binding RUBP and Mg<sup>2+</sup> (the RUBP-bidning residue contributed by the N-terminal lobe of the adjacent subunit is not shown). The <scene name='46/463261/8ruc_active-site/6'>types of residues</scene> involved are <font color='red'>acidic</font> residues that interact with Mg<sup>2+</sup>, <font color='blue'>basic</font> residues and <font color='lightblue'>histidines</font> that interact with phosphate and hydroxyl groups, <font color='orchid'>polar</font> residues that interact with hydroxyl groups, one <font color='slategray'>hydrophobic</font> residue, and backbone atoms (white ball & stick) of several residues. | The structure of spinach Rubisco bound to the naturally occurring inhibitor 2-carboxylarabinitol-1,5-bisphosphate (CAP) and Mg<sup>2+</sup> ([[8ruc]]<ref>PMID:8648644</ref>), implicates residues that are involved in the catalytic mechanism [[Image:RubiscoMechanism.pdf]]. [[Image:CAP.jpg|left|]] The structure of CAP (left figure) is similar to the hydrated reaction intermediate that is formed following the addition of CO<sub>2</sub> to RUBP. Here is an <scene name='46/463261/8ruc_active-site/1'>isolated α-β barrel</scene> (cartoon and colored for secondary structure) with CAP and and Mg<sup>2+</sup> in CPK spacefill. This <scene name='46/463261/8ruc_active-site/5'> overview of the active site</scene> in which the helices have been removed, shows that CAP sits at one end of the α-β barrel, and only residues from the beta strands (gold ball & stick) and loops that link them to helices (white ball & stick) are involved in binding RUBP and Mg<sup>2+</sup> (the RUBP-bidning residue contributed by the N-terminal lobe of the adjacent subunit is not shown). The <scene name='46/463261/8ruc_active-site/6'>types of residues</scene> involved are <font color='red'>acidic</font> residues that interact with Mg<sup>2+</sup>, <font color='blue'>basic</font> residues and <font color='lightblue'>histidines</font> that interact with phosphate and hydroxyl groups, <font color='orchid'>polar</font> residues that interact with hydroxyl groups, one <font color='slategray'>hydrophobic</font> residue, and backbone atoms (white ball & stick) of several residues. | ||
<scene name='46/463261/8ruc_active-site/10'>Residues that are involved in catalysis</scene> are shown shown here in CPK ball & stick. Asp 203 and Glu 204 bind to and position the magnesium ion. The carbamylated lysine residue KCX 201 coordinates Mg<sup>2+</sup> and initiates catalysis by extracting a proton from C3 of RUBP. Note the proximity of the carbamyl group to carbon 3 in this structure. His 294 acts as a catalytic base in the carboxylation step of the mechanism and accepts a proton from the hydroxyl of carbon 3. Mg<sup>2+</sup> is coordinated by six ligands. In addition to oxygen atoms in the three residues already mentioned, the ion binds to two oxygen atoms of RUBP. The 6th ligand is either water or in the carboxylation step it binds the incoming CO<sub>2</sub>. In the structure shown, Mg<sup>2+</sup> is bound to the carboxyl group in CAP that corresponds to the fixed CO<sub>2</sub> in the hydrated intermediate.</StructureSection> | <scene name='46/463261/8ruc_active-site/10'>Residues that are involved in catalysis</scene> are shown shown here in CPK ball & stick. Asp 203 and Glu 204 bind to and position the magnesium ion. The carbamylated lysine residue KCX 201 coordinates Mg<sup>2+</sup> and initiates catalysis by extracting a proton from C3 of RUBP. Note the proximity of the carbamyl group to carbon 3 in this structure. His 294 acts as a catalytic base in the carboxylation step of the mechanism and accepts a proton from the hydroxyl of carbon 3. Mg<sup>2+</sup> is coordinated by six ligands. In addition to oxygen atoms in the three residues already mentioned, the ion binds to two oxygen atoms of RUBP. The 6th ligand is either water or in the carboxylation step it binds the incoming CO<sub>2</sub>. In the structure shown, Mg<sup>2+</sup> is bound to the carboxyl group in CAP that corresponds to the fixed CO<sub>2</sub> in the hydrated intermediate. | ||
==3D structures of RuBisCO== | |||
[[RuBisCO 3D structures]] | |||
</StructureSection> | |||
==3D structures of RuBisCO== | ==3D structures of RuBisCO== | ||
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* RuBisCO | * RuBisCO | ||
** [[1aus]] - spRBCO – spinach<br /> | |||
** [[4hhh]] – RBCO - pea<br /> | |||
** [[1mlv]] - pRBCO large subunit<br /> | |||
** [[1rld]], [[3rub]], [[3t15]], [[3zw6]], [[4rub]] – tRBCO – tobacco<br /> | |||
** [[3thg]] – RBCO – creosote bush<br /> | |||
** [[5wsk]] – RBCO - wheat<br /> | |||
** [[3rg6]], [[1rbl]] – SeRBCO – ''Synechococcus elongatus''<br /> | ** [[3rg6]], [[1rbl]] – SeRBCO – ''Synechococcus elongatus''<br /> | ||
** [[2ybv]] - RBCO – ''Thermosynechococcus elongatus''<br /> | ** [[2ybv]] - RBCO – ''Thermosynechococcus elongatus''<br /> | ||
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** [[1uzh]], [[1gk8]] – CrRBCO – ''Chlamydomonas reinhardtii''<br /> | ** [[1uzh]], [[1gk8]] – CrRBCO – ''Chlamydomonas reinhardtii''<br /> | ||
** [[1uw9]], [[1uwa]] – CrRBCO (mutant) <br /> | ** [[1uw9]], [[1uwa]] – CrRBCO (mutant) <br /> | ||
** [[1svd]] – RBCD – ''Halothiobacillus neapolitanus''<br /> | ** [[1uzd]] – CrRBCO/spRBCO <br /> | ||
** [[1svd]], [[6uew]] – RBCD – ''Halothiobacillus neapolitanus''<br /> | |||
** [[1bxn]] – RBCO – ''Cupriavidus necator''<br /> | ** [[1bxn]] – RBCO – ''Cupriavidus necator''<br /> | ||
** [[5rub]] - RrRBCO – ''Rhododpirillum rubrum''<br /> | ** [[5rub]] - RrRBCO – ''Rhododpirillum rubrum''<br /> | ||
** [[1rba]] - RrRBCO (mutant)<br /> | ** [[1rba]] - RrRBCO (mutant)<br /> | ||
** [[2wvw]] – RBCO – ''Anabena'' – Cryo EM<br /> | ** [[2wvw]] – RBCO – ''Anabena'' – Cryo EM<br /> | ||
** [[2vdh]], [[2vdi]], [[2v67]], [[2v68]], [[2v63]], [[2v69]], [[2v6a]] - CrRBCO (mutant) <br /> | ** [[2vdh]], [[2vdi]], [[2v67]], [[2v68]], [[2v63]], [[2v69]], [[2v6a]] - CrRBCO (mutant) <br /> | ||
** [[2cxe]], [[2cwx]] – PhRBCO - ''Pyrococcus horikoshii''<br /> | ** [[2cxe]], [[2cwx]] – PhRBCO - ''Pyrococcus horikoshii''<br /> | ||
** [[1geh]] – TkRBCO – ''Thermococcus kodakaraensis''<br /> | ** [[1geh]] – TkRBCO – ''Thermococcus kodakaraensis''<br /> | ||
**[[3wqp]] – TkRBCD (mutant)<br /> | |||
** [[1iwa]] - GpRBCO – ''Galdieria partita''<br /> | ** [[1iwa]] - GpRBCO – ''Galdieria partita''<br /> | ||
** [[1tel]] – RBCO large subunit – ''Chlorobium tepidum''<br /> | ** [[1tel]] – RBCO large subunit – ''Chlorobium tepidum''<br /> | ||
** [[5c2c]] - GaRBCO – ''Gallionella''<br /> | ** [[5c2c]] - GaRBCO – ''Gallionella''<br /> | ||
** [[ | **[[6hun]] – RBCD – ''Hyperthermus butylicus''<br /> | ||
**[[5oya]] – RBCD – ''Chaetocerus socialis'' – Cryo EM<br /> | |||
**[[5mz2]] – RBCD – ''Thalassiosira antarctica''<br /> | |||
* RuBisCO complex with inhibitor 2-CABP | * RuBisCO complex with inhibitor 2-CABP | ||
** [[1upm]], [[1upp]], [[1rbo]], [[3ruc]], [[8ruc]] - spRBCO + 2-CABP + cation<br /> | |||
** [[1ir1]] - spRBCO + 2-CABP + CO2 + Mg<br /> | |||
** [[8ruc]] - spRBCO + 2-CABP<br /> | |||
** [[1wdd]] – rRBCO + 2-CABP – rice<br /> | |||
** [[1rlc]] - tRBCO + 2-CABP <br /> | |||
** [[3kdn]], [[3a12]] – TkRBCO III + 2-CABP <br /> | ** [[3kdn]], [[3a12]] – TkRBCO III + 2-CABP <br /> | ||
** [[3kdo]], [[3a13]] - TkRBCO III (mutant) + 2-CABP<br /> | ** [[3kdo]], [[3a13]] - TkRBCO III (mutant) + 2-CABP<br /> | ||
** [[1ir2]] - CrRBCO + 2-CABP <br /> | ** [[1ir2]] - CrRBCO + 2-CABP <br /> | ||
** [[1bwv]] - GpRBCO + 2-CABP <br /> | ** [[1bwv]] - GpRBCO + 2-CABP <br /> | ||
**[[4lf1]] - RpRBCO + 2-CABP<br /> | **[[4lf1]] - RpRBCO + 2-CABP<br /> | ||
**[[5han]], [[5hao]], [[5hjx]], [[5hjy]], [[5hk4]], [[5koz]], [[5hat]], [[5hql]], [[5hqm]] - RpRBCO (mutant) + 2-CABP<br /> | **[[5han]], [[5hao]], [[5hjx]], [[5hjy]], [[5hk4]], [[5koz]], [[5hat]], [[5hql]], [[5hqm]] - RpRBCO (mutant) + 2-CABP<br /> | ||
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**[[5nv3]] - RBCO + 2-CABP - ''Rhodobacter sphaeroides''<br /> | **[[5nv3]] - RBCO + 2-CABP - ''Rhodobacter sphaeroides''<br /> | ||
** [[3zxw]] - SeRBCO + 2-CABP<br /> | ** [[3zxw]] - SeRBCO + 2-CABP<br /> | ||
** [[5iu0]] - RBCO + 2-CABP - ''Arabidopsis thaliana''<br /> | ** [[5iu0]] - RBCO + 2-CABP - ''Arabidopsis thaliana''<br /> | ||
** [[5mac]] - RBCO + 2-CABP - ''Methanococcoides burtonii''<br /> | ** [[5mac]] - RBCO + 2-CABP - ''Methanococcoides burtonii''<br /> | ||
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* RuBisCO other complexes | * RuBisCO other complexes | ||
** [[2h21]] – pRBCO | ** [[2h21]] – pRBCO large subunit + AdoMet <br /> | ||
** [[2h23]] - pRBCO | ** [[2h23]] - pRBCO large subunit + AdoHcy<br /> | ||
** [[2h2e]], [[1ozv]], [[1p0y]] - pRBCO | ** [[2h2e]], [[1ozv]], [[1p0y]] - pRBCO large subunit + AdoMet + lysine<br /> | ||
** [[2h2j]] - pRBCO | ** [[2h2j]] - pRBCO large subunit + sinefungin<br /> | ||
** [[1ej7]] – tRBCO + phosphate <br /> | |||
** [[3axk]] – rRBCO + NADP<br /> | |||
** [[3axm]] – rRBCO + 6-phosphogluconic acid<br /> | |||
** [[2d69]] – PhRBCO + sulfate<br /> | ** [[2d69]] – PhRBCO + sulfate<br /> | ||
** [[2rus]] - RrRBCO + CO2 + Mg<br /> | ** [[2rus]] - RrRBCO + CO2 + Mg<br /> | ||
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** [[4f0k]] - GsRBCO + CO2 + Mg<br /> | ** [[4f0k]] - GsRBCO + CO2 + Mg<br /> | ||
** [[4f0m]] - GsRBCO + Mg<br /> | ** [[4f0m]] - GsRBCO + Mg<br /> | ||
** [[ | **[[6hbc]] – SeRBCO + CCMM – Cryo EM<br /> | ||
}} | }} | ||