Dynamical Behavior of the CAT Domain from Cre Recombinase, in the Absence of and with the CIS Interaction of the N Helix

Abstract

Cre is a tyrosine recombinase that binds to DNA, promoting its scission, recombination, and ligation at specific sequences known as loxP sites. It is formed by two helical domains (CBD and CAT) separated by a flexible linker. It acts by forming a tetramer that is stabilised by the last C-terminal helix (N helix) and a pocket formed in the adjacent subunit (trans interaction). The lack of this helix leads to loss of Cre functions by impeding complex formation; furthermore, in the monomer context, the N helix could interact in cis with its own CAT domain near the DNA binding site, leading to an auto-inhibitory complex. A structural model explaining these results is still lacking.We generate structural models for the CAT domain in the absence of the N helix and for the interaction in cis, starting from crystallographic structures deposited in the PDB database (PDBID 1Q3U): CAT domain (residues 139 to 326) and segment 327 to 341 (N helix). For the cis interaction models, we used the ClusPro server. All-atom molecular dynamics simulations used the charmm36m forcefield, TIP3P water model, 303K and the GROMACS2018 software. Loss of the N helix results in an increase of flexibility in the CAT domain, with a clam-like motion of the trans binding site, while cis models showed that the N helix visits multiple conformations that may affect complex formation.