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Journal of Bacteriology, July 2003, p. 4087-4098, Vol. 185, No. 14
0021-9193/03/$08.00+0     DOI: 10.1128/JB.185.14.4087-4098.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

The Purine Repressor of Bacillus subtilis: a Novel Combination of Domains Adapted for Transcription Regulation

Sangita C. Sinha,1,{dagger} Joseph Krahn,1,{ddagger} Byung Sik Shin,2 Diana R. Tomchick,1,§ Howard Zalkin,2 and Janet L. Smith1*

Departments of Biological Sciences,1 Biochemistry, Purdue University, West Lafayette, Indiana 479072

Received 31 January 2003/ Accepted 29 April 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-Å 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.

* Corresponding author. Mailing address: Department of Biological Sciences, Purdue University, 915 W. State St., West Lafayette, IN 47907. Phone: (765) 494-9246. Fax: (765) 496-1189. E-mail: smithj{at}purdue.edu.

{dagger} Present address: Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390.

{ddagger} Present address: National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709.

§ Present address: Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390.

Journal of Bacteriology, July 2003, p. 4087-4098, Vol. 185, No. 14
0021-9193/03/$08.00+0     DOI: 10.1128/JB.185.14.4087-4098.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.



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