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Protein Science (2006), 15:2579-2595. Published by Cold Spring Harbor Laboratory Press. Copyright © 2006 The Protein Society
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Characterization of two potentially universal turn motifs that shape the repeated five-residues fold—Crystal structure of a lumenal pentapeptide repeat protein from Cyanothece 51142

Garry W. Buchko1, Shuisong Ni1,4, Howard Robinson2, Eric A. Welsh3, Himadri B. Pakrasi3, and Michael A. Kennedy1,4

1 Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
2 Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA
3 Department of Biology, Washington University, St. Louis, Missouri 63130, USA

(RECEIVED June 19, 2006; FINAL REVISION August 21, 2006; ACCEPTED August 22, 2006)

The genome of the diurnal cyanobacterium Cyanothece sp. PCC 51142 has recently been sequenced and observed to contain 35 pentapeptide repeat proteins (PRPs). These proteins, while present throughout the prokaryotic and eukaryotic kingdoms, are most abundant in cyanobacteria. The sheer number of PRPs in cyanobacteria coupled with their predicted location in every cellular compartment argues for important, yet unknown, physiological and biochemical functions. To gain biochemical insights, the crystal structure for Rfr32, a 167-residue PRP with an N-terminal 29-residue signal peptide, was determined at 2.1 Å resolution. The structure is dominated by 21 tandem pentapeptide repeats that fold into a right-handed quadrilateral beta-helix, or Rfr-fold, as observed for the tandem pentapeptide repeats in the only other PRP structure, the mycobacterial fluoroquinoline resistance protein MfpA from Mycobacterium tuberculosis. Sitting on top of the Rfr-fold are two short, antiparallel {alpha}-helices, bridged with a disulfide bond, that perhaps prevent edge-to-edge aggregation at the C terminus. Analysis of the main-chain ({Phi},{Psi}) dihedral orientations for the pentapeptide repeats in Rfr32 and MfpA makes it possible to recognize the structural details for the two distinct types of four-residue turns adopted by the pentapeptide repeats in the Rfr-fold. These turns, labeled type II and type IV beta-turns, may be universal motifs that shape the Rfr-fold in all PRPs.

Keywords: cyanobacteria; beta-bridges; circular dichroism; thermal melt; right-handed parallel beta-helix; single-bridge beta-sheet; beta-bulges


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