Catalase (manganese dependent)

 

The catalases are important antioxidant defence enzymes found in a broad range of microorganisms in microaerophilic environments. Manganese catalase, isolated from Lactobacillus plantarum, is a nonheme catalase containing a binuclear manganese cluster, and is responsible for catalysing the disproportionation of hydrogen peroxide into water and dioxygen. The enzyme is a hexamer of identical subunits organised around a catalytic core of close-packed four-helix bundle domains.

Manganese catalase catalyses the disproportionation of toxic hydrogen peroxide into dioxygen and water. The overall reaction consists of two distinct half reactions involving alternate reduction and oxidation of the peroxide substrate. An m(1,3)-bridging glutamate anchors the two ions in the binuclear cluster, and each Mn is further coordinated by one histidine and one glutamate bound to opposite sides of the cluster. The Mn core is completed by two solvent derived oxygen bridges, which are structurally distinct.

 

Reference Protein and Structure

Sequence
P60355 UniProt (1.11.1.6) IPR007760 (Sequence Homologues) (PDB Homologues)
Biological species
Lactobacillus plantarum (Bacteria) Uniprot
PDB
1o9i - CRYSTAL STRUCTURE OF THE Y42F MUTANT OF MANGANESE CATALASE FROM LACTOBACILLUS PLANTARUM AT 1.33A RESOLUTION (1.33 Å) PDBe PDBsum 1o9i
Catalytic CATH Domains
1.20.1260.10 CATHdb (see all for 1o9i)
Cofactors
Manganese(3+) (2)
Click To Show Structure

Enzyme Reaction (EC:1.11.1.6)

hydrogen peroxide
CHEBI:16240ChEBI
dioxygen
CHEBI:15379ChEBI
+
water
CHEBI:15377ChEBI
Alternative enzyme names: CAT, Caperase, Catalase-peroxidase, Equilase, Optidase,

Enzyme Mechanism

Introduction

The hydrogen peroxide substrate becomes bound to the oxidised [3,3] state of the Mn cluster via a terminal oxygen, replacing the nonbridging solvent (W3) on the Mn1 subsite. The [3,3] cluster has a diamagnetic ground state, associated with the bis-m-bridged dimanganese core structure. The bridging ligands act as proton acceptor sites in this reaction and support electronic coupling between the two Mn ions. Two-electron reduction of the terminally bound peroxide by the dinuclear Mn (III) complex results in the release of the dioxygen product. This step is facilitated by the two oxygen bridges (W1 and W2) that electronically couple the Mn ions. Glu 178 is involved in transferring the peroxidic protons to active site bases during turnover. These bases are likely to be the solvent molecules themselves, tightly coupling proton transfer to metal-centred redox. The cluster, now in a [2,2] reduced state has labile bridging groups, which allow substantial substitutional insertion of peroxide into a bridging position of the reduced complex in forming an m(1,1) hydroperoxy intermediate. Therefore, the peroxide replaces the relatively weakly bound, doubly protonated (aquo) bridge. The resulting m(1,1) bridging mode favours heterolytic peroxide cleavage due to polarization of the O-O bond, and is activated towards reoxidation of the dimanganese core. The O-O bond may be further activated by vic to gem isomerisation of the peroxide protons with the Glu 178 shuttle catalysing the proton rearrangement, protonating the nonbridging oxygen of the bound substrate. Loss of water regenerates the [3,3] state of the cluster.

Catalytic Residues Roles

UniProt PDB* (1o9i)
His69, Glu35, His181, Glu148, Glu66 His69A, Glu35A, His181A, Glu148A, Glu66A Glu35 and His69 are coordinated to one Mn(III) in the cluster, while Glu148 and His181 are coordinated to the other Mn(III). Glu66 forms a bridge between the two metal ions. metal ligand
Glu178 Glu178A Glu 178 acts as a proton shuttle in both the reduction and oxidation half reactions. In the oxidation step, Glu 178 is positioned to shuttle protons from a terminally bound peroxide to the trans-Glu bridge. In the reductive half reaction, Glu 178 protonates a bridging peroxide, activating it towards O-O bond cleavage. proton shuttle (general acid/base), 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

coordination to a metal ion, proton transfer, electron transfer, redox reaction, overall product formed, native state of enzyme regenerated, bimolecular homolytic elimination, heterolysis

References

  1. Whittaker MM et al. (1999), Biochemistry, 38, 9126-9136. The Oxidized (3,3) State of Manganese Catalase. Comparison of Enzymes fromThermus thermophilusandLactobacillus plantarum†. DOI:10.1021/bi990499d. PMID:10413487.
  2. Whittaker MM et al. (2003), Eur J Biochem, 270, 1102-1116. Outer sphere mutagenesis of Lactobacillus plantarum manganese catalase disrupts the cluster core. Mechanistic implications. DOI:10.1046/j.1432-1033.2003.03459.x. PMID:12631270.
  3. Barynin VV et al. (2001), Structure, 9, 725-738. Crystal structure of manganese catalase from Lactobacillus plantarum. DOI:10.2210/pdb1jku/pdb. PMID:11587647.

Catalytic Residues Roles

Residue Roles
Glu178A proton shuttle (general acid/base)
Glu35A metal ligand
Glu66A metal ligand
His69A metal ligand
Glu148A metal ligand
His181A metal ligand

Chemical Components

coordination to a metal ion, proton transfer

Catalytic Residues Roles

Residue Roles
Glu35A metal ligand
Glu66A metal ligand
His69A metal ligand
Glu148A metal ligand
His181A metal ligand
Glu178A proton shuttle (general acid/base)

Chemical Components

electron transfer, proton transfer, redox reaction, overall product formed

Catalytic Residues Roles

Residue Roles
Glu35A metal ligand
Glu66A metal ligand
His69A metal ligand
Glu148A metal ligand
His181A metal ligand
Glu178A proton acceptor

Chemical Components

coordination to a metal ion, proton transfer

Catalytic Residues Roles

Residue Roles
Glu178A proton shuttle (general acid/base)
Glu35A metal ligand
Glu66A metal ligand
His69A metal ligand
Glu148A metal ligand
His181A metal ligand
Glu178A proton donor

Chemical Components

electron transfer, native state of enzyme regenerated, ingold: bimolecular homolytic elimination, heterolysis, overall product formed, redox reaction

Contributors

Emma Penn, Gemma L. Holliday, Amelia Brasnett