PDBsum entry 3dhs

Hydrolase, RNA

PDB id: 3dhs

Contents

DNA/RNA

Metals

_OS ×15

PDB id:

3dhs

Name:

Hydrolase, RNA

Title:

Mapping metal-binding sites in the catalytic domain of bacterial rnase p RNA

Structure:

Rnase p RNA. Chain: a. Fragment: catalytic domain. Engineered: yes

Source:

Synthetic: yes. Other_details: RNA was prepared by in vitro transcription and is naturally found in bacillus stearothermophilus.

Resolution:

3.60Å R-factor: 0.290 R-free: 0.314

Authors:

N.R.Pace,A.V.Kazantsev,A.A.Krivenko

Key ref:

A.V.Kazantsev et al. (2009). Mapping metal-binding sites in the catalytic domain of bacterial RNase P RNA. Rna, 15, 266-276. PubMed id: 19095619

Date:

18-Jun-08 Release date: 27-Jan-09

DNA/RNA chain

G-U-U-A-A-U-C-A-U-G-C-U-C-G-G-G-U-A-A-U-C-G-C-U-G-C-G-G-C-C-G-G-U-U-U-C-G-G-C- 215 bases

Enzyme reactions

• Enzyme class: Chains : E.C.3.1.26.5 - ribonuclease P.
• Reaction: Endonucleolytic cleavage of RNA, removing 5'-extra-nucleotide from tRNA precursor.

Rna 15:266-276 (2009)

PubMed id: 19095619

Mapping metal-binding sites in the catalytic domain of bacterial RNase P RNA.

A.V.Kazantsev, A.A.Krivenko, N.R.Pace.

ABSTRACT

Ribonuclease P (RNase P) is a ribonucleoprotein enzyme that contains a universally conserved, catalytically active RNA component. RNase P RNA requires divalent metal ions for folding, substrate binding, and catalysis. Despite recent advances in understanding the structure of RNase P RNA, no comprehensive analysis of metal-binding sites has been reported, in part due to the poor crystallization properties of this large RNA. We have developed an abbreviated yet still catalytic construct, Bst P7Delta RNA, which contains the catalytic domain of the bacterial RNase P RNA and has improved crystallization properties. We use this mutant RNA as well as the native RNA to map metal-binding sites in the catalytic core of the bacterial RNase P RNA, by anomalous scattering in diffraction analysis. The results provide insight into the interplay between RNA structure and focalization of metal ions, and a structural basis for some previous biochemical observations with RNase P. We use electrostatic calculations to extract the potential functional significance of these metal-binding sites with respect to binding Mg(2+). The results suggest that with at least one important exception of specific binding, these sites mainly map areas of diffuse association of magnesium ions.