From Proteopedia

Revision as of 14:41, 17 January 2014

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 CO₂ or O₂, respectively. RBCO from flowering plants consists of eight large subunits and eight small subunits.

Structural Features

spinqualitylabelsall models Spinach RuBisCO 8 large and 8 small chains complex with substrate ribulose-1,5- bisphosphate, 1rcx Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image Quaternery Structure The structure of the Rubisco 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 This isolated 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). 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 showing that both lobes contain alpha helices (pink) and beta strands (yellow). The large lobe is dominated by an (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 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 The structure of spinach Rubisco bound to the naturally occurring inhibitor 2-carboxylarabinitol-1,5-bisphosphate (CAP) and Mg2+ (8ruc[1]), implicates residues that are involved in the catalytic mechanism Image:RubiscoMechanism.pdf. The structure of CAP (left figure) is similar to the hydrated reaction intermediate that is formed following the addition of CO2 to RUBP. Here is an (cartoon and colored for secondary structure) with CAP and and Mg2+ in CPK spacefill. This 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 Mg2+ (the RUBP-bidning residue contributed by the N-terminal lobe of the adjacent subunit is not shown). The involved are acidic residues that interact with Mg2+, basic residues and histidines that interact with phosphate and hydroxyl groups, polar residues that interact with hydroxyl groups, one hydrophobic residue, and backbone atoms (white ball & stick) of several residues. 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 Mg2+ 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. Mg2+ 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 CO2. In the structure shown, Mg2+ is bound to the carboxyl group in CAP that corresponds to the fixed CO2 in the hydrated intermediate.

3D Structures of RuBisCO

Updated February 2013

RuBisCO

3rg6, 1rbl – SeRBCO – Synechococcus elongatus
2ybv - RBCO – Thermosynechococcus elongatus
3qfw - RBCO large subunit – Rhodopseudomonas palustris
1uzh, 1gk8 – CrRBCO – Chlamydomonas reinhardtii
1uw9, 1uwa – CrRBCO (mutant)
1svd – RBCD – Halothiobacillus neapolitanus
1bxn – RBCO – Cupriavidus necator
1aus - spRBCO – spinach
1rba - RrRBCO (mutant) – Rhododpirillum rubrum
5rub - RrRBCO
2wvw – RBCO – Anabena – Cryo EM
2vdh, 2vdi, 2v67, 2v68, 2v63, 2v69, 2v6a - CrRBCO (mutant)
1mlv - pRBCO LSMT – pea
2cxe, 2cwx – PhRBCO - Pyrococcus horikoshii
1uzd – CrRBCO/spRBCO
1geh – TkRBCO – Thermococcus kodakaraensis
1iwa - GpRBCO – Galdieria partita
1tel – RBCO large subunit – Chlorobium tepidum
1rld, 3rub, 3t15, 3zw6, 4rub – tRBCO – tobacco
3thg – RBCO – creosote bush
4hhh – RBCO - pea

RuBisCO complex with inhibitor 2-CABP

3kdn, 3a12 – TkRBCO III + 2-CABP
3kdo, 3a13 - TkRBCO III (mutant) + 2-CABP
1ir2 - CrRBCO + 2-CABP
1upm, 1upp, 1rbo, 3ruc, 8ruc - spRBCO + 2-CABP + cation
1ir1 - spRBCO + 2-CABP + CO2 + Mg
1wdd – rRBCO + 2-CABP – rice
1bwv - GpRBCO + 2-CABP
1rlc - tRBCO + 2-CABP

RuBisCO complex with product

1aa1 – spRBCO + phosphoglycerate
1rus - RrRBCO + phosphoglycerate

RuBisCO complex with substrate

1rcx, 1rxo – spRBCO + ribulose-1,5-bisphosphate
9rub - RrRBCO + ribulose-1,5-bisphosphate
1rsc - SeRBCO + xylulose-1,5-bisphosphate
1rco - spRBCO + xylulose-diol-1,5-bisphosphate
3zxw - SeRBCO + carboxyarabinitol-1,5-bisphosphate

RuBisCO complexes

2h21 – pRBCO LSMT + AdoMet
2h23 - pRBCO LSMT + AdoHcy
2h2e, 1ozv, 1p0y - pRBCO LSMT + AdoMet + lysine
2h2j - pRBCO LSMT + sinefungin
2d69 – PhRBCO + sulfate
2rus - RrRBCO + CO2 + Mg
4f0h – GsRBCO + O2 – Galdieria sulphuraria
4f0k - GsRBCO + CO2 + Mg
4f0m - GsRBCO + Mg
1ej7 – tRBCO + phosphate
3axk – rRBCO + NADP
3axm – rRBCO + 6PG

See Also

Some additional details can be found in Ribulose-1,5-bisphosphate carboxylase/oxygenase.

References

1. ↑ Andersson I. Large structures at high resolution: the 1.6 A crystal structure of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase complexed with 2-carboxyarabinitol bisphosphate. J Mol Biol. 1996 May 31;259(1):160-74. PMID:8648644 doi:10.1006/jmbi.1996.0310