An unusual helix turn helix motif in the catalytic core of HIV-1 integrase binds viral DNA and LEDGF.
BACKGROUND
Integrase (IN) of the type 1 human immunodeficiency virus (HIV-1) catalyzes the integration of viral DNA into host cellular DNA. We identified a bi-helix motif (residues 149-186) in the crystal structure of the catalytic core (CC) of the IN-Phe185Lys variant that consists of the alpha(4) and alpha(5) helices connected by a 3 to 5-residue turn. The motif is embedded in a large array of interactions that stabilize the monomer and the dimer.


RESULTS
We describe the conformational and binding properties of the corresponding synthetic peptide. This displays features of the protein motif structure thanks to the mutual intramolecular interactions of the alpha(4) and alpha(5) helices that maintain the fold. The main properties are the binding to: 1- the processing-attachment site at the LTR (long terminal repeat) ends of virus DNA with a K(d) (dissociation constant) in the sub-micromolar range; 2- the whole IN enzyme; and 3- the IN binding domain (IBD) but not the IBD-Asp366Asn variant of LEDGF (lens epidermal derived growth factor) lacking the essential Asp366 residue. In our motif, in contrast to the conventional HTH (helix-turn-helix), it is the N terminal helix (alpha(4)) which has the role of DNA recognition helix, while the C terminal helix (alpha(5)) would rather contribute to the motif stabilization by interactions with the alpha(4) helix.


CONCLUSIONS
The motif, termed HTHi (i, for inverted) emerges as a central piece of the IN structure and function. It could therefore represent an attractive target in the search for inhibitors working at the DNA-IN, IN-IN and IN-LEDGF interfaces.
Merad
Hayate
H
LBPA, CNRS (UMR 8113)-Ecole Normale Supérieure de Cachan, Cachan, France.
Porumb
Horea
H
Zargarian
Loussiné
L
René
Brigitte
B
Hobaika
Zeina
Z
Maroun
Richard G
RG
Mauffret
Olivier
O
Fermandjian
Serge
S
D000595:Amino Acid Sequence; D004279:DNA, Viral / Q000378:metabolism*; D019427:HIV Integrase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D015497:HIV-1 / Q000201:enzymology*; D019077:Helix-Turn-Helix Motifs; D006801:Humans; D036341:Intercellular Signaling Peptides and Proteins / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009841:Oligonucleotides / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D010455:Peptides / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
D004279:DNA, Viral; D036341:Intercellular Signaling Peptides and Proteins; D009841:Oligonucleotides; D010455:Peptides; C119380:lens epithelium-derived growth factor; D019427:HIV Integrase