4E2S

Crystal structure of (S)-Ureidoglycine Aminohydrolase from Arabidopsis thaliana in complex with its substrate, (S)-Ureidoglycine

Summary for 4E2S

• Entry DOI: 10.2210/pdb4e2s/pdb
• Related: 4E2Q
• Descriptor: Ureidoglycine aminohydrolase, MANGANESE (II) ION, (2S)-amino(carbamoylamino)ethanoic acid, ... (4 entities in total)
• Functional Keywords: bi-cupin, (s)-ureidoglycine aminohydrolase, manganese binding, endoplasmic reticulumn, hydrolase
• Biological source: Arabidopsis thaliana (mouse-ear cress,thale-cress)
• Cellular location: Endoplasmic reticulum : Q8GXV5
• Total number of polymer chains: 16
• Total formula weight: 486678.64

Authors

Shin, I.,Rhee, S. (deposition date: 2012-03-09, release date: 2012-04-18, Last modification date: 2024-03-20)

Primary citation

Shin, I.,Percudani, R.,Rhee, S.
Structural and functional insights into (S)-ureidoglycine aminohydrolase, key enzyme of purine catabolism in Arabidopsis thaliana
J.Biol.Chem., 287:18796-18805, 2012

PubMed Abstract: The ureide pathway has recently been identified as the metabolic route of purine catabolism in plants and some bacteria. In this pathway, uric acid, which is a major product of the early stage of purine catabolism, is degraded into glyoxylate and ammonia via stepwise reactions of seven different enzymes. Therefore, the pathway has a possible physiological role in mobilization of purine ring nitrogen for further assimilation. (S)-Ureidoglycine aminohydrolase enzyme converts (S)-ureidoglycine into (S)-ureidoglycolate and ammonia, providing the final substrate to the pathway. Here, we report a structural and functional analysis of this enzyme from Arabidopsis thaliana (AtUGlyAH). The crystal structure of AtUGlyAH in the ligand-free form shows a monomer structure in the bicupin fold of the β-barrel and an octameric functional unit as well as a Mn(2+) ion binding site. The structure of AtUGlyAH in complex with (S)-ureidoglycine revealed that the Mn(2+) ion acts as a molecular anchor to bind (S)-ureidoglycine, and its binding mode dictates the enantioselectivity of the reaction. Further kinetic analysis characterized the functional roles of the active site residues, including the Mn(2+) ion binding site and residues in the vicinity of (S)-ureidoglycine. These analyses provide molecular insights into the structure of the enzyme and its possible catalytic mechanism.

PubMed: 22493446
DOI: 10.1074/jbc.M111.331819

Experimental method

X-RAY DIFFRACTION (2.59 Å)