2IMO

Crystal structure of allantoate amidohydrolase from Escherichia coli at pH 4.6

Summary for 2IMO

• Entry DOI: 10.2210/pdb2imo/pdb
• Related: 1Z2L
• Descriptor: Allantoate amidohydrolase (2 entities in total)
• Functional Keywords: allantoate amidohydrolase, apoenzyme, allc, t1507, structural genomics, psi-2, protein structure initiative, new york sgx research center for structural genomics, nysgxrc, hydrolase
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 95513.47

Authors

Agarwal, R.,Burley, S.K.,Swaminathan, S.,New York SGX Research Center for Structural Genomics (NYSGXRC) (deposition date: 2006-10-04, release date: 2006-10-17, Last modification date: 2024-10-09)

Primary citation

Agarwal, R.,Burley, S.K.,Swaminathan, S.
Structural Analysis of a Ternary Complex of Allantoate Amidohydrolase from Escherichia coli Reveals its Mechanics.
J.Mol.Biol., 368:450-463, 2007

PubMed 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.

PubMed: 17362992
DOI: 10.1016/j.jmb.2007.02.028

Experimental method

X-RAY DIFFRACTION (2.8 Å)