X‐ray crystal structure of the N‐terminal region of Moloney murine leukemia virus integrase and its implications for viral DNA recognition

Abstract

The retroviral integrase (IN) carries out the integration of a dsDNA copy of the viral genome into the host DNA, an essential step for viral replication. All IN proteins have three general domains, the N-terminal domain (NTD), the catalytic core domain (CCD), and the C-terminal domain (CTD). The NTD includes an HHCC zinc finger-like motif, which is conserved in all retroviral IN proteins. Two crystal structures of Moloney murine leukemia virus (M-MuLV) IN N-terminal region (NTR) constructs that both include an N-terminal extension domain (NED, residues 1-44) and an HHCC zinc-finger NTD (residues 45-105), in two crystal forms are reported. The structures of IN NTR constructs encoding residues 1-105 (NTR1-105) and 8-105 (NTR8-105) were determined at 2.7 and 2.15 Å resolution, respectively and belong to different space groups. While both crystal forms have similar protomer structures, NTR1-105 packs as a dimer and NTR8-105 packs as a tetramer in the asymmetric unit. The structure of the NED consists of three anti-parallel β-strands and an α-helix, similar to the NED of prototype foamy virus (PFV) IN. These three β-strands form an extended β-sheet with another β-strand in the HHCC Zn2+ binding domain, which is a unique structural feature for the M-MuLV IN. The HHCC Zn2+ binding domain structure is similar to that in HIV and PFV INs, with variations within the loop regions. Differences between the PFV and MLV IN NEDs localize at regions identified to interact with the PFV LTR and are compared with established biochemical and virological data for M-MuLV.

Disrupting MLV integrase:BET protein interaction biases integration into quiescent chromatin and delays but does not eliminate tumor activation in a MYC/Runx2 mouse model

“…In the second model, modified histones may present a steric hindrance for IN binding. Both MLV and prototype foamy virus (PFV) encode an N-terminal extension domain (NED) [2,8] though PFV IN does not encode a homologous TP. Two loop regions within the PFV IN CCD-CCD dimer interface interact with the H2A-H2B heterodimer, specifically with the C-terminal helix of H2B and N-terminal of H2A [73][74][75].…”

“…The integration substrate generated through reverse transcription is linear viral DNA containing a copy of the long terminal repeat (LTR) at each end. Integration is driven by the viral integrase (IN), structurally defined by distinct functional domains and regions, including the N-terminal region (NTR) containing the N-terminal extension (NED) and HHCC zinc-binding domain (NTD) [2], the catalytic core domain (CCD) [3], and the C-terminal domain (CTD) containing an unstructured tail peptide (TP) [4,5]. Integration proceeds via two distinct IN catalytic activities; 3' processing and strand transfer.…”

Intact Viral Particle Counts Measured by Flow Virometry Provide Insight into the Infectivity and Genome Packaging Efficiency of Moloney Murine Leukemia Virus

“…The role of MLV as a prototypical retrovirus has been escalated by its genomic simplicity, originally thought to encode only the bare necessities for retroviral replication and infection: Gag, Pol, and Env (10). Dissection of the function of these three proteins and of the replication cycle of MLV has been invaluable for the field of retrovirology (11,12).…”

Alteration of gammaretroviral vector integration patterns by insertion of histone and leucine zipper into integrase

“…Since wild‐type MLV integrase structure has not been solved because of technical difficulties, experimentally obtaining the structure information for mutant integrases would be also challenging. Recently, the structure of only a fraction of MLV integrase, N‐terminal extension domain (NED), was experimentally determined (Guan et al, 2017). Instead, we attempted to predict the structures of wild‐type and mutant integrases using I‐TASSER (Zhang, 2008), one of the most advanced protein structure prediction tools, to speculatively assess how the insertion of histones or leucine zippers into internal positions of MLV integrase affects its structure.…”