Crystal structure of PucM in the presence of 5,6-diaminouracil

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 

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

Jung, D.-K.Lee, Y.Park, S.G.Park, B.C.Kim, G.-H.Rhee, S.

(2006) Proc Natl Acad Sci U S A 103: 9790-9795

  • DOI: https://doi.org/10.1073/pnas.0600523103
  • Primary Citation of Related Structures:  
    2H0E, 2H0F, 2H0J

  • PubMed 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 A 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.

  • Organizational Affiliation

    School of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Seoul 151-921, Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transthyretin-like protein pucM
A, B
121Bacillus subtilisMutation(s): 6 
Find proteins for O32142 (Bacillus subtilis (strain 168))
Explore O32142 
Go to UniProtKB:  O32142
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO32142
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on URN

Download Ideal Coordinates CCD File 
C4 H6 N4 O2
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 
  • Space Group: P 42 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.956α = 90
b = 72.956β = 90
c = 145.127γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2006-06-27 
  • Deposition Author(s): Rhee, S.

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description