title: Pseudomonas aeruginosa 4-amino-4-deoxychorismate lyase: spatial conservation of an active site tyrosine and classification of two types of enzyme.
abstract: 4-Amino-4-deoxychorismate lyase (PabC) catalyzes the formation of 4-aminobenzoate, and release of pyruvate, during folate biosynthesis. This is an essential activity for the growth of gram-negative bacteria, including important pathogens such as Pseudomonas aeruginosa. A high-resolution (1.75 Å) crystal structure of PabC from P. aeruginosa has been determined, and sequence-structure comparisons with orthologous structures are reported. Residues around the pyridoxal 5'-phosphate cofactor are highly conserved adding support to aspects of a mechanism generic for enzymes carrying that cofactor. However, we suggest that PabC can be classified into two groups depending upon whether an active site and structurally conserved tyrosine is provided from the polypeptide that mainly forms an active site or from the partner subunit in the dimeric assembly. We considered that the conserved tyrosine might indicate a direct role in catalysis: that of providing a proton to reduce the olefin moiety of substrate as pyruvate is released. A threonine had previously been suggested to fulfill such a role prior to our observation of the structurally conserved tyrosine. We have been unable to elucidate an experimentally determined structure of PabC in complex with ligands to inform on mechanism and substrate specificity. Therefore we constructed a computational model of the catalytic intermediate docked into the enzyme active site. The model suggests that the conserved tyrosine helps to create a hydrophobic wall on one side of the active site that provides important interactions to bind the catalytic intermediate. However, this residue does not appear to participate in interactions with the C atom that undergoes an sp(2) to sp(3) conversion as pyruvate is produced. The model and our comparisons rather support the hypothesis that an active site threonine hydroxyl contributes a proton used in the reduction of the substrate methylene to pyruvate methyl in the final stage of the mechanism.
authors.affiliation: Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, United Kingdom.
authors.forename: Patrick E F
authors.initials: PE
authors.lastname: O'Rourke
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Eadsforth
authors.forename: Paul K
authors.initials: PK
authors.lastname: Fyfe
authors.forename: Sharon M
authors.initials: SM
authors.lastname: Shepherd
authors.forename: William N
authors.initials: WN
authors.lastname: Hunter
mesh_terms: D010129:4-Aminobenzoic Acid / Q000737:chemistry; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000378:metabolism*; D001483:Base Sequence; D002384:Catalysis; D020134:Catalytic Domain; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray / Q000379:methods; D017931:DNA Primers / Q000737:chemistry; D019281:Dimerization; D004926:Escherichia coli / Q000378:metabolism; D008190:Lyases / Q000378:metabolism*; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D007652:Oxo-Acid-Lyases / Q000737:chemistry*; D011550:Pseudomonas aeruginosa / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D014461:Ultracentrifugation
chemical_list: D001426:Bacterial Proteins; D017931:DNA Primers; C079404:PabC protein, Bacteria; D008190:Lyases; D007652:Oxo-Acid-Lyases; C066600:aminodeoxychorismate lyase; D010129:4-Aminobenzoic Acid