RuBisCO: Difference between revisions

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Michal Harel, Alice Harmon, Joel L. Sussman, Alexander Berchansky

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-{{STRUCTURE_1rcx|  PDB=1rcx  | SIZE=400| SCENE= |right|CAPTION=Spinach RuBisCO 8 large and 8 small chains complex with substrate ribulose-1,5- bisphosphate, [[1rcx]] }}
+<StructureSection load='1rcx' size='350' side='right' caption='Spinach RuBisCO 8 large and 8 small chains complex with substrate ribulose-1,5- bisphosphate, [[1rcx]]'>
+== Function ==
-'''Ribulose-1,5-bisphosphate carboxylase oxygenase – RuBisCO''' (RBCO) catalyzes the first step in carbon fixation.  RBCO carboxylates or oxygenates ribulose-1,5-bisphosphate (RUBP) with CO<sub>2</sub> or O<sub>2</sub>, respectively.  RBCO from flowering plants usually consists of eight large subunits and eight  small subunits.  2-carboxylarabinitol-1,5-bisphosphate (2-CABP) is an inhibitor of RCBO.  Some additional details in [[Ribulose-1,5-bisphosphate carboxylase/oxygenase]].
+'''Ribulose-1,5-bisphosphate carboxylase oxygenase – RuBisCO''' (RBCO) catalyzes the first step in photosynthetic carbon fixation, and it is the most abundant protein on earth.  RBCO can either carboxylate or oxygenate ribulose-1,5-bisphosphate (RUBP) with CO<sub>2</sub> or O<sub>2</sub>, respectively.  RBCO from flowering plants consists of eight large subunits and eight  small subunits.
+See [[Calvin cycle]], [[Rubisco and Crop Output]], and [[RuBisCO (Hebrew)]].
+== Structural Features ==
-{{TOC limit|limit=2}}
 == Quaternery Structure ==
-The Rubisco <scene name='46/463261/Rubisco_spacefill_holoenzyme/1'>holoenzyme</scene> is shown in spacefill with its 8 large subunits in shades of blue and and its 8 small subunits in shades of yellow.  The large subunits are arranged in head-to-toe pairs like staves in a barrel and the small subunits are arranged at the ends of the barrel. The large subunits contain the active sites and the function of the small subunits is not understood.
+The structure of the Rubisco <scene name='46/463261/Rubisco_spacefill_holoenzyme/1'>holoenzyme</scene> from spinach is shown in spacefill with its 8 large subunits in shades of blue and and its 8 small subunits in shades of yellow.  The large subunits are arranged in head-to-toe pairs like staves in a barrel and the small subunits are arranged at the ends of the barrel. The large subunits contain the active sites and the function of the small subunits is not understood.
 == Large Subunit Structure ==
-(under construction)
-Here is an isolated <scene name='46/463261/Rubisco_lsu_pair/7'>pair of large subunits</scene>. Each subunit has a large C-terminal lobe and a small N-terminal lobe, and the subunits are arranged head-to-toe (antiparallel) in the pair. <scene name='46/463261/Rubisco_lsu_pair/5'>Two active sites</scene> are located in the interface of the large subunit pair. The subunits are shown in cartoon with one shown in the secondary structure color scheme. Each active sites is occupied by RUBP, which is shown in CPK spacefill. Both lobes of the large subunit contain alpha helices (pink) and beta strands (yellow).
+This isolated <scene name='46/463261/Rubisco_lsu_pair/7'>pair of large subunits</scene> shows that each subunit has a large C-terminal lobe and a small N-terminal lobe, and the subunits are arranged head-to-toe (antiparallel). <scene name='46/463261/Rubisco_lsu_pair/5'>Two active sites</scene> are located in the interface of the large subunit pair. The subunits are shown in cartoon with one shown in the secondary structure color scheme. Each active site is occupied by RUBP, which is shown in CPK spacefill. Here is a <scene name='46/463261/Rubisco_lsu_monomer/1'>single large subunit</scene> showing that both lobes contain alpha helices (pink) and beta strands (yellow). The large lobe is dominated by an <scene name='46/463261/Rubisco_lsu_monomer/2'>α-β barrel</scene> (amino acids 166-409), which contributes most of the residues that form the active site. One residue from the N-terminal lobe of the adjacent large subunit <scene name='46/463261/Asn123/1'>Asn 123</scene> completes the active site. This scene shows RUBP in spacefill and CPK in one of the active sites in the dimer. Both subunits are shown in transparent cartoon with the α-β barrel is pink and yellow. Asn 123 from the adjacent subunit is in blue spacefill, and residues 121-129 are shown in blue cartoon. This residue does not contribute to catalysis, and it will not be considered further.
 == Active Site Structure ==
-(under construction)
-The active site is formed by an α-β barrel, which comprises the C-terminal lobe of the large subunit,  and some residues contributed by the N-terminal lobe of the adjacent subunit.  Here is an <scene name='46/463261/Rubisco_lsu_pair/5'>isolated pair of subunits</scene>, , and here is the α-β barrel of that subunit.
-== 3D Structures of RuBisCO ==
-''Updated February 2013''
-===RuBisCO===
-[[3rg6]], [[1rbl]] – SeRBCO – ''Synechococcus elongatus''<br />
-[[2ybv]] - RBCO – ''Thermosynechococcus elongatus''<br />
-[[3qfw]] - RBCO large subunit – ''Rhodopseudomonas palustris''<br />
-[[1uzh]], [[1gk8]] – CrRBCO – ''Chlamydomonas reinhardtii''<br />
-[[1uw9]], [[1uwa]] – CrRBCO (mutant) <br />
-[[1svd]] – RBCD – ''Halothiobacillus neapolitanus''<br />
-[[1bxn]] – RBCO – ''Cupriavidus necator''<br />
-[[1aus]] - spRBCO – spinach<br />
-[[1rba]] - RrRBCO (mutant) – ''Rhododpirillum rubrum''<br />
-[[5rub]] - RrRBCO<br />
-[[2wvw]] – RBCO – ''Anabena'' – Cryo EM<br />
-[[2vdh]], [[2vdi]], [[2v67]], [[2v68]], [[2v63]], [[2v69]], [[2v6a]] - CrRBCO  (mutant) <br />
-[[1mlv]] - pRBCO LSMT – pea<br />
-[[2cxe]], [[2cwx]] – PhRBCO - ''Pyrococcus horikoshii''<br />
-[[1uzd]] – CrRBCO/spRBCO <br />
-[[1geh]] – TkRBCO – ''Thermococcus kodakaraensis''<br />
-[[1iwa]] - GpRBCO – ''Galdieria partita''<br />
-[[1tel]] – RBCO large subunit – ''Chlorobium tepidum''<br />
-[[1rld]], [[3rub]], [[3t15]], [[3zw6]], [[4rub]] – tRBCO – tobacco<br />
-[[3thg]] – RBCO – creosote bush<br />
-[[4hhh]] – RBCO - pea
-===RuBisCO complex with inhibitor 2-CABP===
-[[3kdn]], [[3a12]] – TkRBCO III + 2-CABP <br />
-[[3kdo]], [[3a13]] - TkRBCO III (mutant) + 2-CABP<br />
-[[1ir2]] - CrRBCO + 2-CABP <br />
-[[1upm]], [[1upp]], [[1rbo]], [[3ruc]], [[8ruc]] - spRBCO + 2-CABP + cation<br />
-[[1ir1]] - spRBCO + 2-CABP + CO2 + Mg<br />
-[[1wdd]] – rRBCO + 2-CABP – rice<br />
-[[1bwv]] - GpRBCO + 2-CABP <br />
-[[1rlc]] - tRBCO + 2-CABP
-===RuBisCO complex with product===
-[[1aa1]] – spRBCO + phosphoglycerate<br />
-[[1rus]] - RrRBCO + phosphoglycerate<br />
-===RuBisCO complex with substrate===
-[[1rcx]], [[1rxo]] – spRBCO + ribulose-1,5-bisphosphate<br />
-[[9rub]] - RrRBCO + ribulose-1,5-bisphosphate<br />
-[[1rsc]] - SeRBCO + xylulose-1,5-bisphosphate<br />
-[[1rco]] - spRBCO + xylulose-diol-1,5-bisphosphate<br />
-[[3zxw]] - SeRBCO + carboxyarabinitol-1,5-bisphosphate
-===RuBisCO complexes===
-[[2h21]] – pRBCO LSMT + AdoMet <br />
-[[2h23]] - pRBCO LSMT + AdoHcy<br />
-[[2h2e]], [[1ozv]], [[1p0y]] - pRBCO LSMT + AdoMet + lysine<br />
-[[2h2j]] - pRBCO LSMT + sinefungin<br />
-[[2d69]] – PhRBCO + sulfate<br />
-[[2rus]] - RrRBCO + CO2 + Mg<br />
-[[4f0h]] – GsRBCO + O2 – ''Galdieria sulphuraria''<br />
-[[4f0k]] - GsRBCO + CO2 + Mg<br />
-[[4f0m]] - GsRBCO + Mg<br />
-[[1ej7]] – tRBCO + phosphate <br />
-[[3axk]] – rRBCO + NADP<br />
-[[3axm]] – rRBCO + 6PG
+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.
+==3D structures of RuBisCO==
+[[RuBisCO 3D structures]]
+</StructureSection>
+=See Also=
+*[[Ribulose-1,5-bisphosphate carboxylase/oxygenase]]<br />
+* For Hebrew [[RuBisCO (Hebrew)]].
+=References=
+<references/>
 [[Category:Topic Page]]