PDBsum entry 4e2s

Hydrolase

PDB id: 4e2s

Contents

Protein chains

(+ 10 more) 258 a.a.

Ligands

UGY ×16

Metals

_MN ×16

Waters ×598

PDB id:

4e2s

Name:

Hydrolase

Title:

Crystal structure of (s)-ureidoglycine aminohydrolase from arabidopsis thaliana in complex with its substrate, (s)-ureidoglycine

Structure:

Ureidoglycine aminohydrolase. Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p. Fragment: unp residues 36-298. Synonym: (s)-ureidoglycine aminohydrolase. Engineered: yes

Source:

Arabidopsis thaliana. Mouse-ear cress,thale-cress. Organism_taxid: 3702. Gene: ylba, uglyah, at4g17050, at4g17050. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.59Å R-factor: 0.209 R-free: 0.271

Authors:

I.Shin,S.Rhee

Key ref:

I.Shin et al. (2012). Structural and functional insights into (S)-ureidoglycine aminohydrolase, key enzyme of purine catabolism in Arabidopsis thaliana. J Biol Chem, 287, 18796-18805. PubMed id: 22493446

Date:

09-Mar-12 Release date: 18-Apr-12

Protein chains

Q8GXV5  (UGHY_ARATH) -  (S)-ureidoglycine aminohydrolase from Arabidopsis thaliana

Seq: 298 a.a.

Struc: 258 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.3.26 - (S)-ureidoglycine aminohydrolase.
• Reaction: (S)-2-ureidoglycine + H2O = (S)-ureidoglycolate + NH4⁺

(S)-2-ureidoglycine + H2O = (S)-ureidoglycolate (Bound ligand (Het Group name = UGY) matches with 80.00% similarity) + NH4(+)

• Cofactor: Mn(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

J Biol Chem 287:18796-18805 (2012)

PubMed id: 22493446

Structural and functional insights into (S)-ureidoglycine aminohydrolase, key enzyme of purine catabolism in Arabidopsis thaliana.

I.Shin, R.Percudani, S.Rhee.

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.