Crystal Structure of Quinohemoprotein Amine Dehydrogenase from Pseudomonas putida: IDENTIFICATION OF A NOVEL QUINONE COFACTOR ENCAGED BY MULTIPLE THIOETHER CROSS-BRIDGES

Atsuko Satoh,Jong-Keun Kim,Ikuko Miyahara,Bart Devreese,Isabel Vandenberghe,Ayse Hacisalihoglu,Toshihide Okajima,Shun'Ichi Kuroda,Osao Adachi,Johannis A Duine,Jozef Van Beeumen,Katsuyuki Tanizawa,Ken Hirotsu

doi:10.1074/jbc.m109090200

Abstract

The crystal structure of a quinohemoprotein amine dehydrogenase from Pseudomonas putida has been determined at 1.9-A resolution. The enzyme comprises three non-identical subunits: a four-domain alpha-subunit that harbors a di-heme cytochrome c, a seven-bladed beta-propeller beta-subunit that provides part of the active site, and a small gamma-subunit that contains a novel cross-linked, proteinous quinone cofactor, cysteine tryptophylquinone. More surprisingly, the catalytic gamma-subunit contains three additional chemical cross-links that encage the cysteine tryptophylquinone cofactor, involving a cysteine side chain bridged to either an Asp or Glu residue all in a hitherto unknown thioether bonding with a methylene carbon atom of acidic amino acid side chains. Thus, the structure of the 79-residue gamma-subunit is quite unusual, containing four internal cross-links in such a short polypeptide chain that would otherwise be difficult to fold into a globular structure.

Highlights

The crystal structure of a quinohemoprotein amine dehydrogenase from Pseudomonas putida has been determined at 1.9-Å resolution
A number of modified amino acids have been identified in proteins that are generated by post-translational oxidation or non-oxidation processes [1, 2]
Quinohemoprotein amine dehydrogenases (QH-AmDH) from Gram-negative bacteria represent a new type in the quinoprotein class of amine-oxidizing enzymes because they contain a quinone and one or two hemes as a redox active group [7, 8] providing an opportunity for intramolecular electron transfer

Summary

Hg IV

10.6 1 0.64 0.27 a Heavy atoms derivative: Hg I and Hg II, Baker’s Dimercurial; Hg III, K2(HgI4); Hg IV, ethylmercuricthiosalicylic acid; Pt, PtCl2(NH2CH2CH2NH2). b The enzyme complexed with pNPH. 10.6 1 0.64 0.27 a Heavy atoms derivative: Hg I and Hg II, Baker’s Dimercurial; Hg III, K2(HgI4); Hg IV, ethylmercuricthiosalicylic acid; Pt, PtCl2(NH2CH2CH2NH2). C Values in parentheses are for the highest resolution cells

Rsym ϭ

RESULTS AND DISCUSSION

TABLE II Refinement and model statistics