title: Structural analysis of a ternary complex of allantoate amidohydrolase from Escherichia coli reveals its mechanics.
abstract: Purine metabolism plays a major role in regulating the availability of purine nucleotides destined for nucleic acid synthesis. Allantoate amidohydrolase catalyzes the conversion of allantoate to (S)-ureidoglycolate, one of the crucial alternate steps in purine metabolism. The crystal structure of a ternary complex of allantoate amidohydrolase with its substrate allantoate and an allosteric effector, a sulfate ion, from Escherichia coli was determined to understand better the catalytic mechanism and substrate specificity. The 2.25 A resolution X-ray structure reveals an alpha/beta scaffold akin to zinc exopeptidases of the peptidase M20 family and lacks the (beta/alpha)(8)-barrel fold characteristic of the amidohydrolases. Arrangement of the substrate and the two co-catalytic zinc ions at the active site governs catalytic specificity for hydrolysis of N-carbamyl versus the peptide bond in exopeptidases. In its crystalline form, allantoate amidohydrolase adopts a relatively open conformation. However, structural analysis reveals the possibility of a significant movement of domains via rotation about two hinge regions upon allosteric effector and substrate binding resulting in a closed catalytically competent conformation by bringing the substrate allantoate closer to co-catalytic zinc ions. Two cis-prolyl peptide bonds found on either side of the dimerization domain in close proximity to the substrate and ligand-binding sites may be involved in protein folding and in preserving the integrity of the catalytic site.
authors.affiliation: Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.
authors.forename: Rakhi
authors.initials: R
authors.lastname: Agarwal
authors.forename: Stephen K
authors.initials: SK
authors.lastname: Burley
authors.forename: Subramanyam
authors.initials: S
authors.lastname: Swaminathan
mesh_terms: D000481:Allantoin / Q000737:chemistry / Q000378:metabolism; D000495:Allosteric Site; D000595:Amino Acid Sequence; D001665:Binding Sites; D002384:Catalysis; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D019281:Dimerization; D004795:Enzyme Stability; D004926:Escherichia coli / Q000201:enzymology*; D019143:Evolution, Molecular; D020689:Exopeptidases / Q000378:metabolism; D008024:Ligands; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D040681:Structural Homology, Protein; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D014512:Ureohydrolases / Q000737:chemistry* / Q000378:metabolism*; D015032:Zinc / Q000378:metabolism
chemical_list: D008024:Ligands; D010455:Peptides; D000481:Allantoin; D020689:Exopeptidases; D014512:Ureohydrolases; C019657:allantoate amidohydrolase; D015032:Zinc