The purine repressor of Bacillus subtilis: a novel combination of domains adapted for transcription regulation

J Bacteriol. 2003 Jul;185(14):4087-98. doi: 10.1128/JB.185.14.4087-4098.2003.


The purine repressor from Bacillus subtilis, PurR, represses transcription from a number of genes with functions in the synthesis, transport, and metabolism of purines. The 2.2-A crystal structure of PurR reveals a two-domain protein organized as a dimer. The larger C-terminal domain belongs to the PRT structural family, in accord with a sequence motif for binding the inducer phosphoribosylpyrophosphate (PRPP). The PRT domain is fused to a smaller N-terminal domain that belongs to the winged-helix family of DNA binding proteins. A positively charged surface on the winged-helix domain likely binds specific DNA sequences in the recognition site. A second positively charged surface surrounds the PRPP site at the opposite end of the PurR dimer. Conserved amino acids in the sequences of PurR homologs in 21 gram-positive bacteria cluster on the proposed recognition surface of the winged-helix domain and around the PRPP binding site at the opposite end of the molecule, supporting a common function of DNA and PRPP binding for all of the proteins. The structure supports a binding mechanism in which extended regions of DNA interact with extensive protein surface. Unlike most PRT proteins, which are phosphoribosyltransferases (PRTases), PurR lacks catalytic activity. This is explained by a tyrosine side chain that blocks the site for a nucleophile cosubstrate in PRTases. Thus, B. subtilis has adapted an enzyme fold to serve as an effector-binding domain and has used it in a novel combination with the DNA-binding winged-helix domain as a repressor of purine genes.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Adaptation, Physiological
  • Amino Acid Sequence
  • Bacillus subtilis / genetics
  • Bacillus subtilis / metabolism*
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Crystallization
  • Crystallography, X-Ray
  • DNA / chemistry
  • DNA / metabolism
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism
  • Dimerization
  • Gene Expression Regulation, Bacterial*
  • Models, Molecular
  • Molecular Sequence Data
  • Phosphoribosyl Pyrophosphate / metabolism
  • Protein Structure, Tertiary
  • Repressor Proteins / chemistry*
  • Repressor Proteins / metabolism
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Software
  • Structure-Activity Relationship
  • Transcription, Genetic*


  • Bacterial Proteins
  • DNA-Binding Proteins
  • PurR protein, Bacteria
  • Repressor Proteins
  • Phosphoribosyl Pyrophosphate
  • DNA

Associated data

  • PDB/1P41