Mycobacterium tuberculosis Rv3651 is a triple sensor-domain protein

Abstract

The genome of the human pathogen Mycobacterium tuberculosis (Mtb) encodes ∼4,400 proteins, but one third of them have unknown functions. We solved the crystal structure of Rv3651, a hypothetical protein with no discernible similarity to proteins with known function. Rv3651 has a three-domain architecture that combines one cGMP-specific phosphodiesterases, adenylyl cyclases and FhlA (GAF) domain and two Per-ARNT-Sim (PAS) domains. GAF and PAS domains are sensor domains that are typically linked to signaling effector molecules. Unlike these sensor-effector proteins, Rv3651 is an unusual sensor domain-only protein with highly divergent sequence. The structure suggests that Rv3651 integrates multiple different signals and serves as a scaffold to facilitate signal transfer.

Keywords: GAF domain; Mycobacterium tuberculosis; PAS domain; proteins of unknown function.

Figure 1

Overall Rv3651 crystal structure. (A) Rv3651 is a rigid, extended, modular protein with three distinct domains. Each domain is centered around a 5‐ or 6‐stranded β‐sheet at the core. (B) Space filling model shows the tight packing of the three domains against each other. (C) A topology diagram (PDBsum9) of Rv3651 shows the β‐sheet register characteristic of GAF (domain 1) and PAS domains (domains 2 and 3). (D) 2F _o – F _c electron density map contoured at 1σ

Figure 2

The Rv3651 dimer and ligand binding site. (A) Overall view of the Rv3651 dimer showing the lung shape of the dimer, the three domains, and the helix crossover. Right: View of helix 1 crossover, rotated 90° and looking down the symmetry axis. (B) 2F _o – F _c electron density map contoured at 1σ showing the PEG molecule. (C) Domain 2 cartoon with PEG in space fill. (D) A Bacillus PAS domain with bound FMN in the same orientation