PDBsum entry: 1sez

Oxidoreductase

PDB id: 1sez

Contents

Protein chains

465 a.a. *

Ligands

FAD ×2

OMN ×2

TON ×2

Waters ×143

* Residue conservation analysis

PDB id:

1sez

Name:

Oxidoreductase

Title:

Crystal structure of protoporphyrinogen ix oxidase

Structure:

Protoporphyrinogen oxidase, mitochondrial. Chain: a, b. Synonym: ppo ii, protoporphyrinogen ix oxidase isozyme ii, ppx ii, px-2. Engineered: yes

Source:

Nicotiana tabacum. Common tobacco. Organism_taxid: 4097. Gene: ppxii, ppox2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.90Å R-factor: 0.227 R-free: 0.293

Authors:

M.Koch,C.Breithaupt,R.Kiefersauer,J.Freigang,R.Huber, A.Messerschmidt

Key ref:

M.Koch et al. (2004). Crystal structure of protoporphyrinogen IX oxidase: a key enzyme in haem and chlorophyll biosynthesis. EMBO J, 23, 1720-1728. PubMed id: 15057273 DOI: 10.1038/sj.emboj.7600189

Date:

19-Feb-04 Release date: 13-Apr-04

Protein chains

O24164  (PPOM_TOBAC) -  Protoporphyrinogen oxidase, mitochondrial

Seq: 504 a.a.

Struc: 465 a.a.

Enzyme reactions

• Enzyme class: E.C.1.3.3.4 - Protoporphyrinogen oxidase.
• Pathway: Porphyrin Biosynthesis (later stages)
• Reaction: Protoporphyrinogen-IX + 3 O₂ = protoporphyrin-IX + 3 H₂O₂
• Cofactor: FAD

FAD (Bound ligand (Het Group name = FAD) corresponds exactly)

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

 Gene Ontology (GO) functional annotation 

• Cellular component: mitochondrion (1 term)
• Biological process: oxidation reduction (3 terms)
• Biochemical function: oxidoreductase activity (2 terms)

reference

DOI no: 10.1038/sj.emboj.7600189

EMBO J 23:1720-1728 (2004)

PubMed id: 15057273

Crystal structure of protoporphyrinogen IX oxidase: a key enzyme in haem and chlorophyll biosynthesis.

M.Koch, C.Breithaupt, R.Kiefersauer, J.Freigang, R.Huber, A.Messerschmidt.

ABSTRACT

Protoporphyrinogen IX oxidase (PPO), the last common enzyme of haem and chlorophyll biosynthesis, catalyses the oxidation of protoporphyrinogen IX to protoporphyrin IX. The membrane-embedded flavoprotein is the target of a large class of herbicides. In humans, a defect in PPO is responsible for the dominantly inherited disease variegate porphyria. Here we present the crystal structure of mitochondrial PPO from tobacco complexed with a phenyl-pyrazol inhibitor. PPO forms a loosely associated dimer and folds into an FAD-binding domain of the p-hydroxybenzoate-hydrolase fold and a substrate-binding domain that enclose a narrow active site cavity beneath the FAD and an alpha-helical membrane-binding domain. The active site architecture suggests a specific substrate-binding mode compatible with the unusual six-electron oxidation. The membrane-binding domains can be docked onto the dimeric structure of human ferrochelatase, the next enzyme in haem biosynthesis, embedded in the opposite side of the membrane. This modelled transmembrane complex provides a structural explanation for the uncoupling of haem biosynthesis observed in variegate porphyria patients and in plants after inhibiting PPO.

Selected figure(s)

Figure 5.
Figure 5 Active site of PPO. (A) The active site cavity with all ligands. The inhibitor INH (green) is shown with its electron density (steel blue) and is positioned by the residues Arg98, Leu356, Leu372 and Phe392. The coordination of the cofactor FAD (red -orange) surrounded by the electron density (grass-green) resembles that of MAO (Binda et al, 2002) and PAO (Binda et al, 1999). The detergent molecule Triton X-100 (blue) has bound into the entrance of the product channel; the aliphatic trimethylethyl group of the octyl group is not defined in the electron density (gold -yellow). The omit electron density map is displayed at 1.0 contour level. (B) Binding tunnel for FAD, substrate and Triton X-100. The adenosyl moiety of FAD (red -orange) is exposed to solvent, the active site cavity is opened towards the membrane. The FAD cofactor (red -orange), the inhibitor INH (green) and a Triton X-100 detergent molecule (blue), which bind into the tunnel, are shown. (C) Surface representation of the active site cavity. The active site cavity is very narrow and the substrate is held tightly by ionic interaction of one propionyl oxygen from ring C with N[H2] of Arg98, by stacking of ring B between Leu356 and Leu372 and by aromatic stacking interaction of ring A with Phe392, thus rotation of the substrate during the reaction is unlikely. (D) Active site cavity with bound FAD (red -orange), inhibitor INH (light green) and the modelled substrate protoporphyrinogen IX (PRP, green) and the product protoporphyrin IX (POP, cyan). The FAD-N[5] atom, responsible for the hydride abstraction from the methylene bridge between ring A and D (C[20] atom), is close to the C[20] atom.

Figure 6.
Figure 6 Proposed reaction mechanism of PPO. The oxidation of protoporphyrinogen IX to protoporphyrin IX occurs in three steps, whereby each time the FAD cofactor is reduced by the tetrapyrrol ring and reoxidised by an oxygen molecule that is reduced to hydrogen peroxide. The reaction always starts at the C[20] atom of the tetrapyrrol ring by hydride transfer, followed by hydrogen rearrangements that take place in the whole ring system by enamine -imine tautomerisations (Jordan, 1991).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 1720-1728) copyright 2004.

Figures were selected by an automated process.