PDBsum entry 2oov

Oxidoreductase

PDB id: 2oov

Contents

Protein chains

(+ 0 more) 655 a.a. *

Ligands

GOL ×28

PO4 ×2

Metals

_CU ×6

Waters ×5055

* Residue conservation analysis

PDB id:

2oov

Name:

Oxidoreductase

Title:

Crystal structure of hansenula polymorpha amine oxidase to 1.7 angstroms

Structure:

Peroxisomal copper amine oxidase. Chain: a, b. Fragment: residues 13-672. Synonym: methylamine oxidase. Engineered: yes. Peroxisomal copper amine oxidase. Chain: c, d, e, f. Fragment: residues 13-672. Synonym: methylamine oxidase.

Source:

Pichia angusta. Organism_taxid: 4905. Gene: amo. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932.

Resolution:

1.70Å R-factor: 0.149 R-free: 0.178

Authors:

B.J.Johnson,C.M.Wilmot

Key ref:

B.J.Johnson et al. (2007). Exploring molecular oxygen pathways in Hansenula polymorpha copper-containing amine oxidase. J Biol Chem, 282, 17767-17776. PubMed id: 17409383 DOI: 10.1074/jbc.M701308200

Date:

26-Jan-07 Release date: 10-Apr-07

Protein chains

P12807  (AMO_PICAN) -  Peroxisomal primary amine oxidase from Pichia angusta

Seq: 692 a.a.

Struc: 655 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.4.3.21 - primary-amine oxidase.
• Reaction: a primary methyl amine + O2 + H2O = an aldehyde + H2O2 + NH4⁺

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

reference

DOI no: 10.1074/jbc.M701308200

J Biol Chem 282:17767-17776 (2007)

PubMed id: 17409383

Exploring molecular oxygen pathways in Hansenula polymorpha copper-containing amine oxidase.

B.J.Johnson, J.Cohen, R.W.Welford, A.R.Pearson, K.Schulten, J.P.Klinman, C.M.Wilmot.

ABSTRACT

The accessibility of large substrates to buried enzymatic active sites is dependent upon the utilization of proteinaceous channels. The necessity of these channels in the case of small substrates is questionable because diffusion through the protein matrix is often assumed. Copper amine oxidases contain a buried protein-derived quinone cofactor and a mononuclear copper center that catalyze the conversion of two substrates, primary amines and molecular oxygen, to aldehydes and hydrogen peroxide, respectively. The nature of molecular oxygen migration to the active site in the enzyme from Hansenula polymorpha is explored using a combination of kinetic, x-ray crystallographic, and computational approaches. A crystal structure of H. polymorpha amine oxidase in complex with xenon gas, which serves as an experimental probe for molecular oxygen binding sites, reveals buried regions of the enzyme suitable for transient molecular oxygen occupation. Calculated O(2) free energy maps using copper amine oxidase crystal structures in the absence of xenon correspond well with later experimentally observed xenon sites in these systems, and allow the visualization of O(2) migration routes of differing probabilities within the protein matrix. Site-directed mutagenesis designed to block individual routes has little effect on overall k(cat)/K(m) (O(2)), supporting multiple dynamic pathways for molecular oxygen to reach the active site.

Selected figure(s)

Figure 1.
FIGURE 1. Reactions catalyzed by copper amine oxidases are biogenesis (a) and catalysis (b). a, the protein derived cofactor, TPQ, is the product of biogenesis and generates the mature enzyme. P represents the rest of the polypeptide chain. b, catalysis is divided into two half-reactions, reductive and oxidative. R represents the moiety of the substrate amine, which varies from a hydrogen atom to a polypeptide.

Figure 5.
FIGURE 5. Comparison of CAO xenon binding sites. a, overlay of CAO xenon sites deposited in the PDB with a monomer of the HPAO/Xe complex. The backbone of HPAO is displayed and colored by domain: blue stick, D1; yellow stick, D2; green ribbon, D3. Xenon sites from individual complexes are coded by color (red, PSAO (PDB code 1w2z); yellow, PPLO (PDB code 1rky); blue, AGAO (PDB code 1rjo) magenta, HPAO (PDB code 2oqe)), except surface-bound xenon sites, which are displayed as gray spheres (31). The top inset shows the amine channel. The bottom inset shows a proposed molecular oxygen pathway identified in this study. The active site is shown in stick, and the copper is shown as a green sphere. b, the HPAO D3 -sandwich domain viewed from the dimer interface (90° rotation, cf. view in a). Only the xenon sites in the internal D3 -sandwich and close to the anteroom are shown. Colors are the same as in a, and arrows indicate the direction of molecular oxygen movement to the active site using the proposed pathway. The figure was generated using Pymol (20).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 17767-17776) copyright 2007.

Figures were selected by the author.