Biliverdin reductase
Biliverdin reductase is an evolutionarily conserved soluble protein found primarily in mammalian species. The enzyme reduces the gamma-methylene bridge of biliverdin to form bilirubin in the presence of the NAD(P)H cofactor. The reductase is also a serine/threonine kinase which is activated by oxygen radicals and traslocates into the nucleus in response to cGMP and oxidative stress. The substrate and product are immune function modulators and, based on their anti-oxidant properties, it has been suggested, although not universally accepted that biliverdin and bilirubin play a protective role in the cell.
Reference Protein and Structure
- Sequence
-
P46844
(1.3.1.24)
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Rattus norvegicus (Norway rat)
- PDB
-
1gcu
- CRYSTAL STRUCTURE OF RAT BILIVERDIN REDUCTASE AT 1.4 A
(1.4 Å)
- Catalytic CATH Domains
-
3.30.360.10
3.40.50.720
(see all for 1gcu)
Enzyme Mechanism
Introduction
Biliverdin reductase catalyses the reduction of the biliverdin gamma-methylene bridge with a hydride donated by the NAD(P)H cofactor, initiated by proton transfer from a residue to the pyrrole ring nitrogen. It is unknown whether the protonation and hydride transfer are concerted or sequential. Mutagenesis has shown catalytic activity to remain at 50% when the putative general acid Tyr 97 is mutated to Ala, indicating that this residue is not essential for catalysis, although no other acid has been identified. Instead of a general acid role, the residue may influence the substrate conformation, and so increasing hydride transfer reactivity. Surrounding Glu residues are thought to stabilise the positively charged NAD(P)+.
Catalytic Residues Roles
| UniProt | PDB* (1gcu) | ||
| Tyr97 | Tyr97A | The residue is thought to act as a general acid towards the pyrrole ring nitrogen before hydride transfer, although its removal does not knock out reactivity. The residue is then reprotonated by the solvent, with the residue's pKa being influence by interactions with Ser170 and Arg171. While it is the only available general acid, it is thought that the hydride transfer may instead by driven by conformational changes. | proton acceptor, electrostatic stabiliser, proton donor |
| Glu123 | Glu123A | The residue's negatively charged side chain is thought to stabilise the positively charged NAD(P)+ cofactor after hydride transfer to the biliverdin substrate. This electrostatic interaction could play a major role in driving the reaction, since the removal of the putative general acid by mutagenesis does not wipe out reactivity. | electrostatic stabiliser |
| Glu96, Glu126 | Glu96A, Glu126A | The residue's negatively charged side chain is thought to stabilise the positively charged NAD(P)+ cofactor after hydride transfer to the biliverdin substrate. This electrostatic interaction could play a major role in driving the reaction, since the removal of the putative general acid by mutagenesis does not wipe out reactivity. | electrostatic stabiliser |
| Ser170 | Ser170A | The residue is thought to influence the pKa of Tyr97, facilitating reprotonation from the solvent. | electrostatic stabiliser |
| Arg171 | Arg171A | The residue is thought to influence the pKa of Tyr97, facilitating reprotonation from the solvent. | electrostatic stabiliser |
Chemical Components
proton transfer, bimolecular nucleophilic addition, aromatic unimolecular elimination by the conjugate base, hydride transfer, overall product formed, overall reactant used, cofactor used, inferred reaction step, native state of enzyme regeneratedReferences
- Whitby FG et al. (2002), J Mol Biol, 319, 1199-1210. Crystal Structure of a Biliverdin IXα Reductase Enzyme–Cofactor Complex. DOI:10.1016/s0022-2836(02)00383-2. PMID:12079357.
- McDonagh AF (2010), Free Radic Biol Med, 49, 814-820. The biliverdin–bilirubin antioxidant cycle of cellular protection: Missing a wheel? DOI:10.1016/j.freeradbiomed.2010.06.001. PMID:20547221.
- Smith LJ et al. (2008), Biochem J, 411, 475-484. Computational and experimental studies on the catalytic mechanism of biliverdin-IXbeta reductase. DOI:10.1042/BJ20071495. PMID:18241201.
- Lerner-Marmarosh N et al. (2005), Proc Natl Acad Sci U S A, 102, 7109-7114. Human biliverdin reductase: A member of the insulin receptor substrate family with serine/threonine/tyrosine kinase activity. DOI:10.1073/pnas.0502173102. PMID:15870194.
Step 1. The methene bridge accepts a hydride from the nicotinamide C4 carbon and the nitrogen of the C ring pyrrole accepts a proton from Tyr97. The proton and hydride transfers may be concerted (as shown) or sequential.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Tyr97A | electrostatic stabiliser |
| Ser170A | electrostatic stabiliser |
| Arg171A | electrostatic stabiliser |
| Glu96A | electrostatic stabiliser |
| Glu123A | electrostatic stabiliser |
| Glu126A | electrostatic stabiliser |
| Tyr97A | proton donor |
Chemical Components
proton transfer, ingold: bimolecular nucleophilic addition, ingold: aromatic unimolecular elimination by the conjugate base, hydride transfer, overall product formed, overall reactant used, cofactor used
Step 2. In an inferred step Tyr97 is reprotonated to regenerate the native state of the enzyme.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Tyr97A | proton acceptor |
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