PDBsum entry 1mn1

Peroxidase

PDB id: 1mn1

Contents

Protein chain

357 a.a. *

Ligands

NAG-NAG

HEM

Metals

_CA ×2

Waters ×251

* Residue conservation analysis

PDB id:

1mn1

Name:

Peroxidase

Title:

Manganese peroxidase substrate binding site mutant d179n

Structure:

Manganese peroxidase. Chain: a. Engineered: yes. Mutation: yes

Source:

Phanerochaete chrysosporium. Organism_taxid: 5306. Strain: ogc101. Variant: ogc107-1. Cellular_location: extracellular. Gene: mnp1. Expressed in: phanerochaete chrysosporium. Expression_system_taxid: 5306. Expression_system_variant: d179n-6.

Resolution:

2.00Å R-factor: 0.187

Authors:

M.Sundaramoorthy,T.L.Poulos

Key ref:

M.Sundaramoorthy et al. (1997). Crystal structures of substrate binding site mutants of manganese peroxidase. J Biol Chem, 272, 17574-17580. PubMed id: 9211904 DOI: 10.1074/jbc.272.28.17574

Date:

26-Apr-97 Release date: 04-Sep-97

Protein chain

Q02567  (PEM1_PHACH) -  Manganese peroxidase 1 from Phanerodontia chrysosporium

Seq: 378 a.a.

Struc: 357 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.11.1.13 - manganese peroxidase.
• Reaction: 2 Mn²⁺ + H2O2 + 2 H⁺ = 2 Mn³⁺ + 2 H2O
• Cofactor: Heme

Heme (Bound ligand (Het Group name = HEM) matches with 95.45% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1074/jbc.272.28.17574

J Biol Chem 272:17574-17580 (1997)

PubMed id: 9211904

Crystal structures of substrate binding site mutants of manganese peroxidase.

M.Sundaramoorthy, K.Kishi, M.H.Gold, T.L.Poulos.

ABSTRACT

Manganese peroxidase (MnP), an extracellular heme enzyme from the lignin-degrading basidiomycetous fungus, Phanerochaete chrysosporium, catalyzes the oxidation of MnII to MnIII. The latter, acting as a diffusible redox mediator, is capable of oxidizing a variety of lignin model compounds. The proposed MnII binding site of MnP consists of a heme propionate, three acidic ligands (Glu-35, Glu-39, and Asp-179), and two water molecules. Using crystallographic methods, this binding site was probed by altering the amount of MnII bound to the protein. Crystals grown in the absence of MnII, or in the presence of EDTA, exhibited diminished electron density at this site. Crystals grown in excess MnII exhibited increased electron density at the proposed binding site but nowhere else in the protein. This suggests that there is only one major MnII binding site in MnP. Crystal structures of a single mutant (D179N) and a double mutant (E35Q,D179N) at this site were determined. The mutant structures lack a cation at the MnII binding site. The structure of the MnII binding site is altered significantly in both mutants, resulting in increased access to the solvent and substrate.

Selected figure(s)

Figure 4.
Fig. 4. Stereo representations of refined structures and interactions around the MnII binding site in the D179N single mutant (A) and in the E35Q,D179N double mutant (B). In E35Q,D179N, Gln-35 is modeled in two conformations, and Wat-653 is present only in the open conformation of Gln-35. In D179N Wat-653 is fully occupied, and the extra space^ left by the movement of Glu-35 is occupied by Wat-441. Wat-653^ forms hydrogen bond interaction with the heme propionate, Glu-39, Asn-179, and a solvent (Wat-441 in the single mutant and Wat-650^ in the double mutant).

Figure 5.
Fig. 5. Edge-on view of van der Waals surface representations of native MnP (A), the D179N single mutant, down the MnII binding site (B), and the E35Q,D179N double mutant (C). The^ color coding is as follows: heme, red; side chain ligands, green; MnII, yellow; and mutated side chains, purple.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (1997, 272, 17574-17580) copyright 1997.

Figures were selected by an automated process.