Structural Basis for Functional Tetramerization of Lentiviral Integrase

Alfred Labeja,Francesca Di Nunzio,Peter Cherepanov,Stephen Hare,Alan Engelman,Jeremy Luban,Jimin Wang

doi:10.1371/journal.ppat.1000515

Alfred Labeja, Francesca Di Nunzio + Show 5 more

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https://doi.org/10.1371/journal.ppat.1000515

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Abstract

Experimental evidence suggests that a tetramer of integrase (IN) is the protagonist of the concerted strand transfer reaction, whereby both ends of retroviral DNA are inserted into a host cell chromosome. Herein we present two crystal structures containing the N-terminal and the catalytic core domains of maedi-visna virus IN in complex with the IN binding domain of the common lentiviral integration co-factor LEDGF. The structures reveal that the dimer-of-dimers architecture of the IN tetramer is stabilized by swapping N-terminal domains between the inner pair of monomers poised to execute catalytic function. Comparison of four independent IN tetramers in our crystal structures elucidate the basis for the closure of the highly flexible dimer-dimer interface, allowing us to model how a pair of active sites become situated for concerted integration. Using a range of complementary approaches, we demonstrate that the dimer-dimer interface is essential for HIV-1 IN tetramerization, concerted integration in vitro, and virus infectivity. Our structures moreover highlight adaptable changes at the interfaces of individual IN dimers that allow divergent lentiviruses to utilize a highly-conserved, common integration co-factor.

Highlights

To establish productive infection, a retrovirus must insert the reverse-transcribed form of its genome into a host cell chromosome
We report two crystal structures containing the N-terminal and catalytic core domains from a lentiviral integrase in complex with its co-factor lens epithelium derived growth factor (LEDGF)
Comparison of the structural arrangements observed in our crystals elucidates the details of the integrase tetramerization interface, reveals its dramatic flexibility and the mechanism by which a pair of active sites can be brought into close proximity

Summary

Introduction

A retrovirus must insert the reverse-transcribed form of its genome into a host cell chromosome. This process critically depends on two reactions, 39processing and strand transfer, catalyzed by the viral enzyme integrase (IN) (reviewed in [1]). During 39-procesing, IN endonucleolytically removes two or three nucleotides from the 39-termini of viral DNA to expose 39-OH groups of invariant CA dinucleotides. These are subsequently utilized in a pair of coordinated transesterification reactions, resulting in the insertion of both viral DNA termini across the major groove of chromosomal DNA. CCDs of divergent retroviral INs invariably crystallize as dimers, with isomorphous dimer interfaces [9–

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