Structural Analysis of a Ternary Complex of Allantoate Amidohydrolase from Escherichia coli Reveals its Mechanics

Rakhi Agarwal, Stephen K. Burley, Subramanyam Swaminathan

Research output: Contribution to journalArticlepeer-review

26 Scopus citations


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 Å resolution X-ray structure reveals an α/β scaffold akin to zinc exopeptidases of the peptidase M20 family and lacks the (β/α)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.

Original languageEnglish (US)
Pages (from-to)450-463
Number of pages14
JournalJournal of molecular biology
Issue number2
StatePublished - Apr 27 2007
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology


  • allantoate amidohydrolase
  • allosteric effector
  • crystal structure
  • di-zinc-dependent exopeptidases
  • hinge region

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