Journal:JSB:1

Structural and functional insights into a dodecameric molecular machine – The RuvBL1/RuvBL2 complex

Sabine Gorynia, Tiago M. Bandeiras, Filipa G. Pinho, Colin E. McVey, Clemens Vonrhein, Adam Round, Dmitri I. Svergun, Peter Donner, Pedro M. Matias and Maria Arménia Carrondo ^[1]

Molecular Tour

RuvBL1 (RuvB-like 1; 2c9o ^[2]; colored magenta) and its homolog RuvBL2 are evolutionarily highly conserved AAA+ ATPases essential for many cellular activities. They play an important role in chromatin remodeling, transcriptional regulation and DNA damage repair. RuvBL1 and RuvBL2 are overexpressed in different types of cancer and interact with major oncogenic factors, such as β-catenin and c-myc regulating their function. Since the full-length complex did not crystallize, mutants of RuvBL1 and RuvBL2 with a two-thirds truncation of the flexible domain II were generated: RuvBL1deltaDII (R1∆DII) and RuvBL2deltaDII (R2∆DII). Crystals of the selenomethionine derivative of the R1∆DII/R2∆DII complex diffracted to 3 Å resolution and led to the determination of the three-dimensional structure of the complex. The structure reveals a dodecamer consisting of two heterohexameric rings with alternating RuvBL1 and RuvBL2 monomers (the RuvBL1 and the RuvBL2 monomers in the dodecamer are colored darkmagenta and cyan, respectively) bound to ADP/ATP (click on RuvBL1 or, alternatively on RuvBL2 to see protein/nucleotide interactions). The two heterohexamers interact with each other via the retained part of domain II, which is however poorly visible in the electron density maps, probably because the complex was not crystallized in a single conformational state. This is also hinted by evidence that in the RuvBL1 monomers, ATP was partly hydrolyzed to ADP. The dodecameric quaternary structure of the R1ΔDII/R2ΔDII complex observed in the crystal structure was confirmed by small-angle X-ray scattering analysis. RuvBL1 and RuvBL2 share 43 % sequence identity and 65 % sequence similarity and therefore the 3D structures of R1deltaDII and R2deltaDII are very similar. Due to the low data resolution, and even though the crystal structure could be solved by molecular replacement using a truncated RuvBL1 model, the use of a selenomethionine derivative was essential to elucidate the complex composition, since only one methionine residue is conserved out of 11 in R1ΔDII and 12 in R2ΔDII.

Interestingly, truncation of domain II led to a substantial increase in ATP consumption of RuvBL1, RuvBL2 and their complex. In addition, we present evidence that DNA unwinding of the human RuvBL proteins can be auto-inhibited by domain II, which is not present in the homologous bacterial helicase RuvB. The alternation of charges in the central channel of the dodecamer shown below, combined with the diameter of the channel (ranging between 17 and 21 Å) suggests interactions with single-stranded nucleic acids.

Electrostatic potential mapped at the molecular surface for the R1deltaDII/R2deltaDII dodecamer. (a) top view and (b) cross-section view showing the central channel. (c) cross-section view of the SV40 Ltag hexamer complexed with ATP (PDB 1svm), included for comparison. In (a) and (b) the R1deltaDII and R2deltaDII monomers are colored gold and cyan, respectively. In (c) the SV40 monomers are alternately colored gold and cyan.

Our data give new insights into the molecular arrangement of RuvBL1 and RuvBL2 and strongly suggest that in vivo activities of these highly interesting therapeutic drug targets are regulated by cofactors inducing conformational changes via domain II in order to modulate the enzyme complex into its active state.

PDB reference: The dodecameric human RuvBL1:RuvBL2 complex with truncated domains II, 2xsz.