A model for Fis N‐terminus and Fis‐invertase recognition

Abstract

In this modeling, we show that the elusive Fis Nterminus involved in invertase-mediated site-specific DNA inversion is, by all indications, a hinged flapping loop. The prediction is based on a combined sequence and secondary structure alignment against known structures of protein segments, as well as a tetrapeptide fragment observed crystallographically. Its validity is strongly supported by the ability to interpret consistently the available mutagenesis data pertaining to this region including, especially, a series of deletion mutants which until this work had been a puzzle in the search for structural explanations. A model for Fis-invertase recognition is also proposed.

The transactivation region of the Fis protein that controls site-specific DNA inversion contains extended mobile beta -hairpin arms

“…Moreover, an arginine substitution at (Leu)27 inactivated all measured Fis activities and yielded an unstable protein in vivo (data not shown), consistent with the importance of this hydrophobic region to the Fis structure. A computer modeling study also predicted a hairpin structure at the Fis N-terminal region and previously pointed out these hydrophobic interactions surrounding Leu11 (Tzou et al, 1997). There are no observed interactions between the two β-hairpin arms in the dimer, with distances between the backbone atoms of the two closest strands (β-1 and βЈ-1) ranging from 11.6 to 14.6 Å.…”

Structural analysis of the transcriptional activation region on fis: crystal structures of six fis mutants with different activation properties 1 1Edited by R. Huber

“…The molecular surface of wild-type and mutant Fis proteins in the BC turn region. (a) Overall molecular surface for the crystal structure of wild-type Fis re®ned in this study, modeled with a bound DNA (Tzou & Hwang, 1997). Several residues in the BC turn region, Gln68, Arg71, Gly72 and Gln74, are located on a continuous protruding surface adjacent to the helix-turnhelix motif.…”

Modeling Helix-Turn-Helix Protein-Induced DNA Bending with Knowledge-Based Distance Restraints

“…X-ray-determined protein structures were extracted from their DNA-bound form for CAP and Rep (PDB entry code 1cgp for CAP, Schultz et al, 1991;2or1 for Rep, Aggarwal et al, 1988). For Fis (PDB 1fia, Kostrewa et al, 1991Kostrewa et al, , 1992, the predicted flap-hinge model (Tzou and Hwang, 1997) for its N-terminal domain was adopted to make a complete protein structure. In this model, the N-terminal domain, which was not resolved crystallographically for the wild type (Kostrewa et al, 1991(Kostrewa et al, , 1992Yuan et al, 1991), protrudes away from the C-terminal DNA-binding domain, and therefore should not have consequences for the present simulations (the predicted protruding of a hairpin Fis N-terminus was observed in a mutant structure (Safo et al, 1997) solved after the completion of the present work).…”