Ribulose-bisphosphate carboxylase (type I)

 

Ribulose-1,5-bisphosphate carboxylase catalyses the only known mechanism whereby atmospheric carbon dioxide is fixed by living organisms. This enzyme is one of the most abundant on Earth, and of great economic importance. The enzyme has two types of subunit, the large are chloroplast encoded and the small subunit (of unknown function) is nuclear encoded. The active site contains a magnesium atom.

 

Reference Protein and Structure

Sequences
P00880 UniProt (4.1.1.39)
P04716 UniProt (4.1.1.39) IPR020888 (Sequence Homologues) (PDB Homologues)
Biological species
Synechococcus elongatus PCC 6301 (Bacteria) Uniprot
PDB
1rbl - STRUCTURE DETERMINATION AND REFINEMENT OF RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE FROM SYNECHOCOCCUS PCC6301 (2.2 Å) PDBe PDBsum 1rbl
Catalytic CATH Domains
3.20.20.110 CATHdb (see all for 1rbl)
Cofactors
Magnesium(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:4.1.1.39)

D-ribulose 1,5-bisphosphate(4-)
CHEBI:57870ChEBI
+
water
CHEBI:15377ChEBI
+
carbon dioxide
CHEBI:16526ChEBI
hydron
CHEBI:15378ChEBI
+
3-phosphonato-D-glycerate(3-)
CHEBI:58272ChEBI
Alternative enzyme names: D-ribulose 1,5-diphosphate carboxylase, D-ribulose-1,5-bisphosphate carboxylase, RuBP carboxylase, Carboxydismutase, Diphosphoribulose carboxylase, Ribulose 1,5-bisphosphate carboxylase, Ribulose 1,5-bisphosphate carboxylase/oxygenase, Ribulose 1,5-diphosphate carboxylase, Ribulose 1,5-diphosphate carboxylase/oxygenase, Ribulose bisphosphate carboxylase/oxygenase, Ribulose diphosphate carboxylase, Ribulose diphosphate carboxylase/oxygenase, Rubisco, RuBisCO, 3-phospho-D-glycerate carboxy-lyase (dimerizing),

Enzyme Mechanism

Introduction

This enzyme catalyses two opposing reaction, the first step in photosynthetic carbon dioxide fixation, the carboxylation of ribulose-1,5-bisphosphate (RuBP), and the first step in photorespiration, the oxygenation of RuBP. While the catalytic mechanism of the oxygenation is still not clear, the mechanism of the carboxylation of ribulose-1,5-bisphosphate (RuBP) is proposed as follows: Proton abstraction of the substrate, RuBP. Tautomerisation of the enediol to form a C2 carbanion. Carboxylation by electrophilic attack of CO2 on the enediolate. Hydration of the C3 ketone of the six-carbon intermediate. Carbon-carbon cleavage initiated by deprotonation of the hydroxyl oxygen atoms at the C3 centre of the six-carbon intermediate. Stereospecific protonation of the carbanion derived from C1 and C2 which produces the second molecule of D-3PGA.

Catalytic Residues Roles

UniProt PDB*
Lys331 Lys334(326)A Helps stabilise the negatively charged transition states and intermediates formed during the course of the reaction. electrostatic stabiliser
Lys172 Lys175(167)A Acts as a general acid/base. metal ligand, electrostatic stabiliser, proton donor
Glu201, Asp200 Glu204(196)A, Asp203(195)A Forms part of the magnesium binding site. metal ligand
Lys198 (ptm) Kxc201(193)A (ptm) This residue is post-translationally modified to a contain a carbamate group. It is the carbamate group that acts as a magnesium ligand. This residue also acts as a general acid/base through it's carbamate group. nucleophile, metal ligand, proton donor
His291 His294(286)A Acts as a general acid/base proton acceptor
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

bimolecular nucleophilic addition, tautomerisation (not keto-enol), proton transfer, assisted keto-enol tautomerisation, overall reactant used, bimolecular electrophilic addition, overall product formed, heterolysis, native state of enzyme is not regenerated

References

  1. Newman J et al. (1993), J Biol Chem, 268, 25876-25886. The X-ray structure of Synechococcus ribulose-bisphosphate carboxylase/oxygenase-activated quaternary complex at 2.2-A resolution. PMID:8245022.
  2. Tcherkez G (2013), Plant Cell Environ, 36, 1586-1596. Modelling the reaction mechanism of ribulose-1,5-bisphosphate carboxylase/oxygenase and consequences for kinetic parameters. DOI:10.1111/pce.12066. PMID:23305122.
  3. Bracher A et al. (2011), Nat Struct Mol Biol, 18, 875-880. Crystal structure of a chaperone-bound assembly intermediate of form I Rubisco. DOI:10.1038/nsmb.2090. PMID:21765418.
  4. Tabita FR et al. (2008), J Exp Bot, 59, 1515-1524. Distinct form I, II, III, and IV Rubisco proteins from the three kingdoms of life provide clues about Rubisco evolution and structure/function relationships. DOI:10.1093/jxb/erm361. PMID:18281717.
  5. Smith SA et al. (2004), J Biol Chem, 279, 25632-25637. Glycine 176 affects catalytic properties and stability of the Synechococcus sp. strain PCC6301 ribulose-1,5-bisphosphate carboxylase/oxygenase. DOI:10.1074/jbc.M401360200. PMID:15067012.
  6. Andersson I (1996), J Mol Biol, 259, 160-174. Large Structures at High Resolution: The 1.6 Å Crystal Structure of Spinach Ribulose-1,5- Bisphosphate Carboxylase/Oxygenase Complexed with 2-Carboxyarabinitol Bisphosphate. DOI:10.1006/jmbi.1996.0310. PMID:8648644.
  7. Newman J et al. (1994), Structure, 2, 495-502. Structure of an effector-induced inactivated state of ribulose 1,5-bisphosphate carboxylase/oxygenase: the binary complex between enzyme and xylulose 1,5-bisphosphate. DOI:10.1016/s0969-2126(00)00050-2. PMID:7922027.
  8. Newman J et al. (1993), Acta Crystallogr D Biol Crystallogr, 49, 548-560. Structure determination and refinement of ribulose 1,5-bisphosphate carboxylase/oxygenase from Synechococcus PCC6301. DOI:10.1107/S090744499300530X. PMID:15299492.

Catalytic Residues Roles

Residue Roles

Chemical Components

tautomerisation (not keto-enol)

Catalytic Residues Roles

Residue Roles
Kxc201(193)A (ptm) metal ligand
Asp203(195)A metal ligand
Glu204(196)A metal ligand
Lys175(167)A electrostatic stabiliser

Chemical Components

proton transfer, assisted keto-enol tautomerisation, overall reactant used

Catalytic Residues Roles

Residue Roles
Kxc201(193)A (ptm) metal ligand
Asp203(195)A metal ligand
Glu204(196)A metal ligand
Lys175(167)A electrostatic stabiliser
His294(286)A proton acceptor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic addition, ingold: bimolecular electrophilic addition

Catalytic Residues Roles

Residue Roles
Kxc201(193)A (ptm) metal ligand
Asp203(195)A metal ligand
Glu204(196)A metal ligand
Lys175(167)A electrostatic stabiliser
Lys334(326)A electrostatic stabiliser

Chemical Components

overall product formed, heterolysis

Catalytic Residues Roles

Residue Roles
Lys175(167)A metal ligand
Asp203(195)A metal ligand
Glu204(196)A metal ligand
Lys175(167)A electrostatic stabiliser
Lys334(326)A electrostatic stabiliser
Kxc201(193)A (ptm) proton donor
Lys175(167)A proton donor

Chemical Components

proton transfer, assisted keto-enol tautomerisation, overall product formed, native state of enzyme is not regenerated

Contributors

Christian Drew, Craig Porter, Gemma L. Holliday, James Willey