ATP hydrolysis in Rho: Identifying active site residues and their roles

Abstract

Escherichia coli transcription termination factor Rho is a hexameric RNA/DNA helicase that terminates transcription using energy derived from the hydrolysis of ATP. The ATP binding sites of Rho are located at the interfaces of adjoining subunit Cterminal domains and have the Walker A and B motifs, characteristic of many ATPases (Skordalakes & Berger, 2003; Richardson 2002). Available Rho crystal structures capture the protein with its active site in an open configuration that must close to permit ATP hydrolysis. Because of this, the identities of active site residues predicted to mediate ATP hydrolysis are uncertain. To determine which amino acids activate water, stabilize transition state, sense the γ- phosphoryl group, and coordinate the magnesium ion of MgATP, we have carried out site-specific mutagenesis on candidate residues which are conserved across bacterial species, and characterized the relevant properties of the mutant proteins. The residues chosen were E211 as the water activator, R212 as the γ sensor, R366 as the arginine finger, and D265 as the residue that coordinates Mg2+. Each mutant protein was investigated for its ability to oligomerize as hexamers, assayed for ATPase activity, ATP and RNA binding, and pre-steady-state kinetics. The results show that the mutant proteins form hexamers similarly as to wild type Rho. The RhoE211 mutants display at least a 200-fold lower activity as ATPases, bind both ATP and RNA with similar affinities as the wild type protein, and display no burst in pre-steady-state kinetics. RhoR212A protein has 20-fold lower activity as an ATPase compared to wild type Rho, binds ATP with at least a 50-fold weaker affinity, and RNA with a 2-fold higher KD compared to wild type Rho. RhoR366A functions as an ATPase with 50-fold lower activity, binds RNA with similar affinity as wild type Rho and binds ATP with a 5- fold weaker affinity. RhoD265N displays 150-fold lower ATPase activity compared to the wild type enzyme, binds ATP with a 10-fold weaker affinity, and binds RNA with similar affinity as wild type Rho. Pre-steady-state kinetics studies indicate that the mutant proteins investigated show no burst kinetics, indicating a failure or a significantly slower rate of the hydrolysis (chemistry) step. It is possible that the rate-limiting step is the chemistry step in these mutant proteins, contrary to the wild type protein where the chemistry step is much faster (300/s). Together, the results obtained are consistent with the proposed roles for these residues: E211 is involved in activating a water molecule, R212 functions as the γ sensor, R366 functions as the arginine finger and D265 is involved in coordination of the Mg2+ ion. This study has elucidated the mechanism of ATP hydrolysis, by determining some of the key residues involved in the hydrolysis reaction. This study is only a part of the characterization of the active site residues. There might be other residues involved in one or all of the functions proposed. Utilizing the findings from this study, other experiments and models can be implemented to understand how Rho hydrolyzes ATP and utilizes the energy to move along the RNA molecule and functions as a helicase.