PMC

Conservation among PurR homologs. Side chains of residues invariant among the 21 homologs in Fig. are mapped onto the PurR dimer in this stereo diagram. Invariant residues cluster at opposite ends of the dimer on the surfaces of the winged-helix domain at the bottom and the PRT domain at the top. Sulfate ions and a buffer molecule are visible in these sites. Polypeptides are rendered as the C_α trace. View is identical to Fig. .

(A) Winged-helix domain of PurR. C_α atoms of the winged-helix domains of PurR (thick, gray C_α trace with the HTH motif in blue) and E. coli BirA () (thin black trace) are superimposed in this stereo diagram. Conserved regions thought to be important to function (HTH motif, N terminus, and wing) are colored blue. The termini of each domain are labeled. (B) PRT domain of PurR. C_α atoms of the PRT domains of PurR (gray trace with functionally important regions colored as in Fig. ) and L. donovanii APRTase () (thin black trace) The termini of each domain and gaps in the structure are labeled.

Electrostatic surface potential of PurR. The electrostatic potential of the molecular surface is color coded from red (−10kT) to blue (+10kT). The four panels represent the front of the dimer as in Fig. , the top of the dimer viewed into the PRPP site, the bottom of the dimer viewed onto the conserved surface of the winged helix domain, and the side of the dimer. The twofold axis of molecular symmetry is vertical in the front and side views and is indicated by an arrow. The dimer images appear asymmetric because of slight differences between subunits in the position of the flexible loop and in the identity of missing residues.

(A) The PRPP-binding site of PurR. The stereo view is color coded, with the PRT motif in violet, the PP_i loop in gold, and the flexible loop in red. Arg160 from the flexible loop of the other subunit of the dimer is green. This site corresponds to the substrate-binding site for PRTases. Sulfates bound to this site are shown. Residues in the PRPP-binding site that interact with the sulfate are labeled. Hydrogen bonds are shown as dotted lines. (B) Occlusion of a potential nucleophile-binding site. The adenine is modeled based on superposition of the PRPP-binding motifs from PurR and an APRTase-adenine complex (PDBcode 1QB7) (), while PRPP is modeled based on a similar superposition of a glutamine PRPP amidotransferase-PRPP analog complex (). Protein elements are from PurR. Phe205 from the PurR PRPP loop and Tyr102 from the PurR hood occlude the space that would bind a nucleophile in the PRTases.

(A) PurR dimer. The monomers are colored according to function (N termini, HTH motifs, and wings in blue; hoods in cyan; PP_i loops in gold; flexible loops in red; and PRPP motifs in purple). Other regions are green in one monomer and gray in the other and are semitransparent to aid in viewing the highlighted regions. In this view, the dimer dyad axis is vertical and in the plane of the page. Sulfate ions and a HEPES buffer molecule are rendered as bonds colored by atomic type (C, yellow; O, red; N, blue; and S, green). (B) PurR monomer. The stereo ribbon diagram is colored as the gray subunit in panel A. Secondary structures are labeled. Sulfate ions are shown as in panel A. Residues 163 to 167 and 275 to 285 are not displayed, as they are disordered.

Alignment of sequences with homology to both domains of B. subtilis PurR. Residues numbers above the alignment correspond to B. subtilis PurR. Biological sources and accession codes for the sequences are: Bsubt, B. subtilis (gi586880); Bhalo, B. halodurans (gi15612625); Linno, Listeria innocua (gi16799308); Lmono, Listeria monocytogenes (gi16802230); Banth, B. anthracis (gi21398009); Oihey, Oceanobacillus iheyensis (gi23097511); Sepid, Staphylococcus epidermidis (gi16024897); Saure, Staphylococcus aureus (gi15923486); Sagal, Streptococcus agalactiae (gi22537911); Spyog, Streptococcus pyogenes (gi15674448); Smuta, Streptococcus mutans (gi24378853); Spneu, Streptococcus pneumoniae (gi15901802); Llact, Lactococcus lactis (gi15674241); Lmese, Leuconostoc mesenteroides (gi23024251); Ooeni, Oenococcus oeni (gi23037595); Lgass, Lactobacillus gasseri (gi23003426); Dhafn, Desulfitobacterium hafniense (gi23111814); Cacet, Clostridium acetobutylicum (gi15896471); Cperf, C. perfringens (gi18311474); Cther, C. thermocellum (gi23020712); and Tteng, Thermoanaerobacter tengcongensis (gi20808923). Secondary structures are indicated above the sequence alignment (cylinders for helices, arrows for β strands, lines for coils, and dashed lines for disordered regions missing from the structure). Background colors reflect increasing similarity among the sequences, with similar residues highlighted in yellow, sites of conservative substitution in pink, and invariant residues in red. Regions of functional importance are labeled, and the secondary structures are colored as in Fig. .