Crystallographic analysis of an RNA polymerase σ-subunit fragment complexed with −10 promoter element ssDNA: quadruplex formation as a possible tool for engineering crystal contacts in protein–ssDNA complexes

Abstract

Structural studies of -10 promoter element recognition by domain 2 of the RNA polymerase σ subunit [Feklistov & Darst (2011), Cell, 147, 1257-1269] reveal an unusual crystal-packing arrangement dominated by G-quartets. The 3'-terminal GGG motif of the oligonucleotide used in crystallization participates in G-quadruplex formation with GGG motifs from symmetry-related complexes. Stacking between neighboring G-quadruplexes results in the formation of pseudo-continuous four-stranded columns running throughout the length of the crystal (G-columns). Here, a new crystal form is presented with a different arrangement of G-columns and it is proposed that the fortuitous finding of G-quartet packing could be useful in engineering crystal contacts in protein-ssDNA complexes.

Engineering Crystal Packing in RNA Structures I: Past and Future Strategies for Engineering RNA Packing in Crystals

“…The quartet adopts a square and planar structure where four guanine bases form hydrogen-bonding interactions through their WC and Hoogsteen edges (the structures of RNA G-quadruplexes have been reviewed recently [87]). In the crystal structure of the σ-subunit of RNA polymerase in complex with a 10-nt ssDNA, the 3 terminal GGG flips out into the solvent to form a pseudo-continuous G-quadruplex column, which forms the main crystal lattice [88]. At the crystal packing interface, a string of 3 G's flipped out from each complex to form three sets of trans Hoogsteen/WC base pairs with one symmetry-related complex and trans WC/Hoogsteen base pairs with another symmetry-related complex.…”