1O57

CRYSTAL STRUCTURE OF THE PURINE OPERON REPRESSOR OF BACILLUS SUBTILIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Purine Repressor of Bacillus Subtilis: A Novel Combination of Domains Adapted for Transcription Regulation

Sinha, S.C.Krahn, J.Shin, B.S.Tomchick, D.R.Zalkin, H.Smith, J.L.

(2003) J.Bacteriol. 185: 4087-4098


  • PubMed Abstract: 
  • 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 d ...

    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.


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PUR OPERON REPRESSOR
A, B, C, D
291Bacillus subtilis (strain 168)Gene Names: purR (yabI)
Find proteins for P37551 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P37551
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

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Download CCD File 
A, D
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
2PE
Query on 2PE

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Download CCD File 
A
NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
P6G
Query on P6G

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Download CCD File 
A, D
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

Download SDF File 
Download CCD File 
C, D
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.188 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 65.077α = 84.75
b = 72.156β = 84.03
c = 82.967γ = 67.47
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
MLPHAREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-26
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance