Crystallization and preliminary X-ray diffraction study of thermostable RNase HIII from Bacillus stearothermophilus

Identification of the substrate binding site in the N-terminal TBP-like domain of RNase H3

Ribonuclease H3 from Bacillus stearothermophilus (Bst-RNase H3) has the N-terminal TBP-like substrate-binding domain. To identify the substrate binding site in this domain, the mutant proteins of the intact protein and isolated N-domain, in which six of the seventeen residues corresponding to those involved in DNA binding of TBP are individually mutated to Ala, were constructed. All of them exhibited decreased enzymatic activities and/or substrate-binding affinities when compared to those of the parent proteins, suggesting that the N-terminal domain of RNase H3 uses the flat surface of the β-sheet for substrate binding as TBP to bind DNA. This domain may greatly change conformation upon substrate binding.

Purification and crystallization of RNase HIII from Staphylococcus aureus

As part of collaborative efforts to characterize virulence factors from Staphylococcus aureus, methods for the large-scale recombinant production of RNase HIII from S. aureus subspecies MRSA252 (Sa-RNase HIII) have been developed. RNase HIII-type ribonucleases are poorly characterized members of the RNase H group of endonucleases which hydrolyze RNA from RNA/DNA hybrids and are thought to be involved in DNA replication and repair. They are characterized by N-terminal extensions of unknown function that do not share sequence homology with the N-terminal extensions of bacterial RNases HI and RNases HII. Sa-RNase HIII was crystallized in the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a=48.9, b=74.2, c=127.5 Å, and diffracted to 2.6 Å resolution.

Crystal structure and structure-based mutational analyses of RNase HIII from Bacillus stearothermophilus: a new type 2 RNase H with TBP-like substrate-binding domain at the N terminus

Ribonuclease HIII (Bst-RNase HIII) from the moderate thermophile Bacillus stearothermophilus is a type 2 RNase H but shows poor amino acid sequence identity with another type 2 RNase H, RNase HII. It is composed of 310 amino acid residues and acts as a monomer. Bst-RNase HIII has a large N-terminal extension with unknown function and a unique active-site motif (DEDE), both of which are characteristics common to RNases HIII. To understand the role of these N-terminal extension and active-site residues, the crystal structure of Bst-RNase HIII was determined in both metal-free and metal-bound forms at 2.1-2.6 angstroms resolutions. According to these structures, Bst-RNase HIII consists of the N-terminal domain and C-terminal RNase H domain. The structures of the N and C-terminal domains were similar to those of TATA-box binding proteins and archaeal RNases HII, respectively. The steric configurations of the four conserved active-site residues were very similar to those of other type 1 and type 2 RNases H. Single Mn and Mg ions were coordinated with Asp97, Glu98, and Asp202, which correspond to Asp10, Glu48, and Asp70 of Escherichia coli RNase HI, respectively. The mutational studies indicated that the replacement of either one of these residues with Ala resulted in a great reduction of the enzymatic activity. Overproduction, purification, and characterization of the Bst-RNase HIII derivatives with N and/or C-terminal truncations indicated that the N-terminal domain and C-terminal helix are involved in substrate binding, but the former contributes to substrate binding more greatly than the latter.