1Z2L

Crystal structure of Allantoate-amidohydrolase from E.coli K12 in complex with substrate Allantoate

Summary for 1Z2L

• Entry DOI: 10.2210/pdb1z2l/pdb
• Descriptor: Allantoate amidohydrolase, ZINC ION, SULFATE ION, ... (5 entities in total)
• Functional Keywords: allantoate-amidohydrolase, allantoate, allc, purine catabolism, allantoin utilization, t1507, structural genomics, psi, 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: 94829.30

Authors

Agarwal, R.,Swaminathan, S.,Burley, S.K.,New York SGX Research Center for Structural Genomics (NYSGXRC) (deposition date: 2005-03-08, release date: 2005-03-22, Last modification date: 2024-02-14)

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 (2.25 Å)