3U3G

Structure of LC11-RNase H1 Isolated from Compost by Metagenomic Approach: Insight into the Structural Bases for Unusual Enzymatic Properties of Sto-RNase H1

Summary for 3U3G

• Entry DOI: 10.2210/pdb3u3g/pdb
• Descriptor: Ribonuclease H, CHLORIDE ION, UNKNOWN LIGAND, ... (4 entities in total)
• Functional Keywords: hydrolase, cleave the rna strand of rna/dna hybrid
• Biological source: uncultured organism
• Total number of polymer chains: 4
• Total formula weight: 62598.67

Authors

Nguyen, T.N.,Angkawidjaja, C.,Kanaya, E.,Koga, Y.,Takano, K.,Kanaya, S. (deposition date: 2011-10-05, release date: 2012-03-07, Last modification date: 2023-11-01)

Primary citation

Nguyen, T.N.,Angkawidjaja, C.,Kanaya, E.,Koga, Y.,Takano, K.,Kanaya, S.
Activity, stability, and structure of metagenome-derived LC11-RNase H1, a homolog of Sulfolobus tokodaii RNase H1
Protein Sci., 21:553-561, 2012

PubMed Abstract: Metagenome-derived LC11-RNase H1 is a homolog of Sulfolobus tokodaii RNase H1 (Sto-RNase H1). It lacks a C-terminal tail, which is responsible for hyperstabilization of Sto-RNase H1. Sto-RNase H1 is characterized by its ability to cleave not only an RNA/DNA hybrid but also a double-stranded RNA (dsRNA). To examine whether LC11-RNase H1 also exhibits both RNase H and dsRNase activities, LC11-RNase H1 was overproduced in Escherichia coli, purified, and characterized. LC11-RNase H1 exhibited RNase H activity with similar metal ion preference, optimum pH, and cleavage mode of substrate with those of Sto-RNase H1. However, LC11-RNase H1 did not exhibit dsRNase activity at any condition examined. LC11-RNase H1 was less stable than Sto-RNases H1 and its derivative lacking the C-terminal tail (Sto-RNase H1ΔC6) by 37 and 13 °C in T(m) , respectively. To understand the structural bases for these differences, the crystal structure of LC11-RNase H1 was determined at 1.4 Å resolution. The LC11-RNase H1 structure is highly similar to the Sto-RNase H1 structure. However, LC11-RNase H1 has two grooves on protein surface, one containing the active site and the other containing DNA-phosphate binding pocket, while Sto-RNase H1 has one groove containing the active site. In addition, LC11-RNase H1 contains more cavities and buried charged residues than Sto-RNase H1. We propose that LC11-RNase H1 does not exhibit dsRNase activity because dsRNA cannot fit to the two grooves on protein surface and that LC11-RNase H1 is less stable than Sto-RNase H1ΔC6 because of the increase in cavity volume and number of buried charged residues.

PubMed: 22389131
DOI: 10.1002/pro.2043

Experimental method

X-RAY DIFFRACTION (1.4 Å)