title: Structural evidence for the partially oxidized dipyrromethene and dipyrromethanone forms of the cofactor of porphobilinogen deaminase: structures of the Bacillus megaterium enzyme at near-atomic resolution.
abstract: The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses an early step of the tetrapyrrole-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor, which is covalently linked by a thioether bridge to an invariant cysteine residue (Cys241 in the Bacillus megaterium enzyme). The cofactor is extended during the reaction by the sequential addition of the four substrate molecules, which are released as a linear tetrapyrrole product. Expression in Escherichia coli of a His-tagged form of B. megaterium PBGD has permitted the X-ray analysis of the enzyme from this species at high resolution, showing that the cofactor becomes progressively oxidized to the dipyrromethene and dipyrromethanone forms. In previously solved PBGD structures, the oxidized cofactor is in the dipyromethenone form, in which both pyrrole rings are approximately coplanar. In contrast, the oxidized cofactor in the B. megaterium enzyme appears to be in the dipyrromethanone form, in which the C atom at the bridging α-position of the outer pyrrole ring is very clearly in a tetrahedral configuration. It is suggested that the pink colour of the freshly purified protein is owing to the presence of the dipyrromethene form of the cofactor which, in the structure reported here, adopts the same conformation as the fully reduced dipyrromethane form.
authors.affiliation: School of Biological Sciences, University of Punjab, New Campus, Lahore-54590, Pakistan.
authors.forename: N
authors.initials: N
authors.lastname: Azim
authors.affiliation: School of Biosciences, University of Kent, Stacey Building, Canterbury CT2 7NJ, England.
authors.forename: E
authors.initials: E
authors.lastname: Deery
authors.affiliation: School of Biosciences, University of Kent, Stacey Building, Canterbury CT2 7NJ, England.
authors.forename: M J
authors.initials: MJ
authors.lastname: Warren
authors.affiliation: Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England.
authors.forename: B A A
authors.initials: BA
authors.lastname: Wolfenden
authors.affiliation: Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England.
authors.forename: P
authors.initials: P
authors.lastname: Erskine
authors.affiliation: Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England.
authors.forename: J B
authors.initials: JB
authors.lastname: Cooper
authors.affiliation: Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England.
authors.forename: A
authors.initials: A
authors.lastname: Coker
authors.affiliation: Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England.
authors.forename: S P
authors.initials: SP
authors.lastname: Wood
authors.affiliation: School of Biological Sciences, University of Punjab, New Campus, Lahore-54590, Pakistan.
authors.forename: M
authors.initials: M
authors.lastname: Akhtar
mesh_terms: D000595:Amino Acid Sequence; D001410:Bacillus megaterium / Q000201:enzymology* / Q000378:metabolism; D003460:Crystallization; D018360:Crystallography, X-Ray; D011163:Hydroxymethylbilane Synthase / Q000737:chemistry* / Q000378:metabolism; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D011162:Porphobilinogen / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism
chemical_list: C507544:dipyrromethene; C056776:dipyrromethane cofactor; D011162:Porphobilinogen; D011163:Hydroxymethylbilane Synthase
keywords: dipyrromethane cofactor; porphobilinogen deaminase; tetrapyrrole biosynthesis