PDBsum entry 2ivd

Oxidoreductase

PDB id: 2ivd

Contents

Protein chains

449 a.a. *

Ligands

ACJ ×2

FAD ×2

GOL ×5

TWN

Waters ×288

* Residue conservation analysis

PDB id:

2ivd

Name:

Oxidoreductase

Title:

Structure of protoporphyrinogen oxidase from myxococcus xanthus with acifluorfen

Structure:

Protoporphyrinogen oxidase. Chain: a, b. Synonym: ppo, ppox. Engineered: yes

Source:

Myxococcus xanthus. Organism_taxid: 34. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.30Å R-factor: 0.235 R-free: 0.283

Authors:

H.R.Corradi,A.V.Corrigall,E.Boix,C.G.Mohan,E.D.Sturrock,P.N.Meissner, K.R.Acharya

Key ref:

H.R.Corradi et al. (2006). Crystal structure of protoporphyrinogen oxidase from Myxococcus xanthus and its complex with the inhibitor acifluorfen. J Biol Chem, 281, 38625-38633. PubMed id: 17046834 DOI: 10.1074/jbc.M606640200

Date:

12-Jun-06 Release date: 17-Oct-06

Protein chains

P56601  (PGOX_MYXXA) -  Protoporphyrinogen oxidase from Myxococcus xanthus

Seq: 471 a.a.

Struc: 449 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

reference

DOI no: 10.1074/jbc.M606640200

J Biol Chem 281:38625-38633 (2006)

PubMed id: 17046834

Crystal structure of protoporphyrinogen oxidase from Myxococcus xanthus and its complex with the inhibitor acifluorfen.

H.R.Corradi, A.V.Corrigall, E.Boix, C.G.Mohan, E.D.Sturrock, P.N.Meissner, K.R.Acharya.

ABSTRACT

Protoporphyrinogen IX oxidase, a monotopic membrane protein, which catalyzes the oxidation of protoporphyrinogen IX to protoporphyrin IX in the heme/chlorophyll biosynthetic pathway, is distributed widely throughout nature. Here we present the structure of protoporphyrinogen IX oxidase from Myxococcus xanthus, an enzyme with similar catalytic properties to human protoporphyrinogen IX oxidase that also binds the common plant herbicide, acifluorfen. In the native structure, the planar porphyrinogen substrate is mimicked by a Tween 20 molecule, tracing three sides of the macrocycle. In contrast, acifluorfen does not mimic the planarity of the substrate but is accommodated by the shape of the binding pocket and held in place by electrostatic and aromatic interactions. A hydrophobic patch surrounded by positively charged residues suggests the position of the membrane anchor, differing from the one proposed for the tobacco mitochondrial protoporphyrinogen oxidase. Interestingly, there is a discrepancy between the dimerization state of the protein in solution and in the crystal. Conserved structural features are discussed in relation to a number of South African variegate porphyria-causing mutations in the human enzyme.

Selected figure(s)

Figure 1.
FIGURE 1. A, the structure of mxPPOX showing FAD (yellow) and AF (green) bound and the three pseudodomains. The pseudo-domains and some helices (H) and strands (S) are labeled. B, overlay of mxPPOX (blue) and mtPPOX (gray). C, mxPPOX with the residues equivalent to those involved in VP in human PPOX displayed in pink. D, close-up of the VP equivalent residues. E, schematic of the PPOX substrate protoporphyrinogen IX drawn with MDL® ISIS/Draw 2.5. F, surface representation rotated 90° around the x axis from A. The membrane-binding domain colored according to charge, showing the bottom potential membrane-interacting surface. Blue indicates positive charge and white/gray the hydrophobic surfaces. The FAD and substrate-binding domains are in brown and forest green, respectively. AF (light blue) and FAD (yellow) can be partially seen through the hydrophobic channel.

Figure 3.
FIGURE 3. Illustration of the crystal packing in P42[1]2; the FAD-binding pseudo-domain is in brown, the substrate-binding pseudo-domain in forest green, and the membrane-binding pseudo-domain in marine blue. A, two-fold symmetry of the asymmetric unit. B, asymmetric unit with the membrane-binding pseudo-domain represented as a charged surface (positive charge in blue, negative charge in red, and hydrophobic areas in gray), showing the small area of interaction at the two-fold axis. C, two-fold rotation of the asymmetric unit in the crystal. D, four-fold rotation axis.

The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2006, 281, 38625-38633) copyright 2006.

Figures were selected by an automated process.