YIR029w: Yeast Allantoicase

(GIF)
A, topology diagram for the jelly roll motifs corresponding to the two allantoicase repeats, module A and B (diagram generated by Tops (35)). Secondary structure elements are labeled according to Fig. 4. Positions of conserved regions are boxed I, II, III, and IV. B, superposition of the allantoicase modules A and B, colored bronze and silver, respectively (same orientation as module A in C). Regions I, II, III, and IV are colored red and orange for modules A and B, respectively. All structure figures are generated by Pymol (pymol.sourceforge.net/). C, ribbon presentations of the allantoicase enzyme. The color of the secondary structure elements is identical to those of the above topology diagram. The two allantoicase modules are approximately related by a 90° rotation. Cter, C-terminal; Nter, N-terminal. D, projection of totally conserved (identified by ConSurf (36)) residues (in red) on the allantoicase surface (same orientations as C). The conserved residues cluster in two separated pockets coinciding with regions Ia, IIa, IIIa, and IVa and regions Ib, IIb, IIIb, and IVb, respectively.
Function Allantoicase
Fold Two jelly roll ?-sheet motifs
Resolution 2.6
Biological unit Homohexamer
PDB code 1SG3
Reference N. Leulliot, S. Quevillon-Cheruel, I. Sorel, M. Graille, P. Meyer, D. Liger, K. Blondeau, J. Janin and H. Van Tilbeurgh, J. Biol. Chem. 279 (2004), pp. 23447-23452. Full text

Allantoicase (EC 3.5.3.4 [EC] ) catalyzes the conversion of allantoate into ureidoglycolate and urea, one of the final steps in the degradation of purines to urea. The mechanism of most enzymes involved in this pathway, which has been known for a long time, is unknown. In this paper we describe the three-dimensional crystal structure of the yeast allantoicase determined at a resolution of 2.6 Å by single anomalous diffraction. This constitutes the first structure for an enzyme of this pathway. The structure reveals a repeated jelly roll beta-sheet motif, also present in proteins of unrelated biochemical function. Allantoicase has a hexameric arrangement in the crystal (dimer of trimers). Analysis of the protein sequence against the structural data reveals the presence of two totally conserved surface patches, one on each jelly roll motif. The hexameric packing concentrates these patches into conserved pockets that probably constitute the active site.