Precorrin-2 dehydrogenase

 

Biosynthesis of the sirohaem cofactor is completed by Met8p, by a beta-NAD+-dependent dehydrogenation of precorrin-2 to produce sirohydrochlorin, followed by ferrochelation to generate sirohaem. Met8p has a similar role in cobalamin biosynthesis.

 

Reference Protein and Structure

Sequence
P15807 UniProt (1.3.1.76, 4.99.1.4) IPR028161 (Sequence Homologues) (PDB Homologues)
Biological species
Saccharomyces cerevisiae S288c (Baker's yeast) Uniprot
PDB
1kyq - Met8p: A bifunctional NAD-dependent dehydrogenase and ferrochelatase involved in siroheme synthesis. (2.2 Å) PDBe PDBsum 1kyq
Catalytic CATH Domains
3.40.50.720 CATHdb (see all for 1kyq)
Click To Show Structure

Enzyme Reaction (EC:1.3.1.76)

NAD(1-)
CHEBI:57540ChEBI
+
precorrin-2(7-)
CHEBI:58827ChEBI
→
hydron
CHEBI:15378ChEBI
+
NADH(2-)
CHEBI:57945ChEBI
+
sirohydrochlorin(8-)
CHEBI:58351ChEBI
Alternative enzyme names: CysG, Met8p, SirC, Precorrin-2 oxidase,

Enzyme Mechanism

Introduction

NAD-dependent dehydrogenation occurs by Asp 141 functioning as a catalytic general base to abstract a proton from the pyrrole nitrogen of ring C with concomitant hydride transfer from the prochiral bridge carbon to the nicotinamide ring of NAD. During ferrochelation Asp 141 again acts as a general base to remove additional protons from the pyrrole nitrogens during metal ion insertion.

Catalytic Residues Roles

UniProt PDB* (1kyq)
Asp141 Asp141A Asp 141 functions as a general base in both dehydrogenase and chelatase reactions by abstraction of protons from pyrrole nitrogens. proton acceptor, proton donor
*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

aromatic bimolecular nucleophilic addition, hydride transfer, proton transfer, overall reactant used, overall product formed, cofactor used, inferred reaction step, native state of enzyme regenerated

References

  1. Schubert HL et al. (2002), EMBO J, 21, 2068-2075. The structure of Saccharomyces cerevisiae Met8p, a bifunctional dehydrogenase and ferrochelatase. DOI:10.1093/emboj/21.9.2068. PMID:11980703.
  2. Leech HK et al. (2002), Biochem Soc Trans, 30, 610-613. Production of cobalamin and sirohaem in Bacillus megaterium: an investigation into the role of the branchpoint chelatases sirohydrochlorin ferrochelatase (SirB) and sirohydrochlorin cobalt chelatase (CbiX). PMID:12196147.

Step 1. Asp141 acts as a general base to deprotonate the pyrrole nitrogen of ring C of the substrate. This is accompanied by hydride transfer from the prochiral bridge carbon to NAD, forming the product and NADH.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp141A proton acceptor

Chemical Components

ingold: aromatic bimolecular nucleophilic addition, hydride transfer, proton transfer, overall reactant used, overall product formed, cofactor used

Step 2. In an inferred step Asp141 is deprotonated to regenerate the native state of the enzyme.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp141A proton donor

Chemical Components

proton transfer, inferred reaction step, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. Asp141 acts as a general base to deprotonate the pyrrole nitrogen of ring C of the substrate. This is accompanied by hydride transfer from the prochiral bridge carbon to NAD, forming the product and NADH.

Step 2. In an inferred step Asp141 is deprotonated to regenerate the native state of the enzyme.

Products.

Contributors

Gary McDowell, Gemma L. Holliday, Amelia Brasnett