Structural and functional analysis of PucM, a hydrolase in the ureide pathway and a member of the transthyretin-related protein family

doi:10.1073/pnas.0600523103

Structural and functional analysis of PucM, a hydrolase in the ureide pathway and a member of the transthyretin-related protein family

*School of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Seoul 151-921, Korea;
^†Proteome Research Laboratory, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-333, Korea; and
^‡Pohang Accelerator Laboratory, Pohang 790-784, Korea

Edited by Janet M. Thornton, European Bioinformatics Institute, Cambridge, United Kingdom, and approved May 11, 2006 (received for review January 20, 2006)

Abstract

The ureide pathway, which produces ureides from uric acid, is an essential purine catabolic process for storing and transporting the nitrogen fixed in leguminous plants and some bacteria. PucM from Bacillus subtilis was recently characterized and found to catalyze the second reaction of the pathway, hydrolyzing 5-hydroxyisourate (HIU), a product of uricase in the first step. PucM has 121 amino acid residues and shows high sequence similarity to the functionally unrelated protein transthyretin (TTR), a thyroid hormone-binding protein. Therefore, PucM belongs to the TTR-related proteins (TRP) family. The crystal structures of PucM at 2.0 Å and its complexes with the substrate analogs 8-azaxanthine and 5,6-diaminouracil reveal that even with their overall structure similarity, homotetrameric PucM and TTR are completely different, both in their electrostatic potential and in the size of the active sites located at the dimeric interface. Nevertheless, the absolutely conserved residues across the TRP family, including His-14, Arg-49, His-105, and the C-terminal Tyr-118–Arg-119–Gly-120–Ser-121, indeed form the active site of PucM. Based on the results of site-directed mutagenesis of these residues, we propose a possible mechanism for HIU hydrolysis. The PucM structure determined for the TRP family leads to the conclusion that diverse members of the TRP family would function similarly to PucM as HIU hydrolase.

Footnotes

^§To whom correspondence should be addressed: E-mail: srheesnu{at}snu.ac.kr
Author contributions: S.R. designed research; D.-K.J. and Y.L. performed research; S.G.P., B.C.P., G.-H.K., and S.R. analyzed data; and S.G.P. and S.R. wrote the paper.
Conflict of interest statement: No conflicts declared.
This paper was submitted directly (Track II) to the PNAS office.
Data deposition: The atomic coordinates have been deposited in the Protein Data Bank, www.pdb.org (PDB ID codes 2H0E for PucM, 2H0F for PucM–AZX, and 2H0J for PucM–DAU complex).
Abbreviations:

Abbreviations:

TTR,

transthyretin;

TRP,

TTR-related protein;

HIU,

5-hydroxyisourate;

OHCU,

2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline;

HIUHase,

HIU hydrolase;

AZX,

8-azaxanthine;

DAU,

5,6-diaminouracil;

T4,

thyroxine;

rmsd,

rms deviation.