PDBsum entry 2a11

Transcription,translation,hydrolase

PDB id: 2a11

Contents

Protein chain

154 a.a. *

Metals

_CA ×2

Waters ×161

* Residue conservation analysis

PDB id:

2a11

Name:

Transcription,translation,hydrolase

Title:

Crystal structure of nuclease domain of ribonuclase iii from mycobacterium tuberculosis

Structure:

Ribonuclease iii. Chain: a. Fragment: nuclease domain. Synonym: rnase iii. Engineered: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Gene: rnc. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.10Å R-factor: 0.259 R-free: 0.286

Authors:

D.L.Akey,J.M.Berger,Mycobacterium Tuberculosis Structural Proteomics Project (Xmtb)

Key ref:

D.L.Akey and J.M.Berger (2005). Structure of the nuclease domain of ribonuclease III from M. tuberculosis at 2.1 A. Protein Sci, 14, 2744-2750. PubMed id: 16155207 DOI: 10.1110/ps.051665905

Date:

17-Jun-05 Release date: 05-Jul-05

Protein chain

P9WH03  (RNC_MYCTU) -  Ribonuclease 3 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 240 a.a.

Struc: 154 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.26.3 - ribonuclease Iii.
• Reaction: Endonucleolytic cleavage to 5'-phosphomonoester.

DOI no: 10.1110/ps.051665905

Protein Sci 14:2744-2750 (2005)

PubMed id: 16155207

Structure of the nuclease domain of ribonuclease III from M. tuberculosis at 2.1 A.

D.L.Akey, J.M.Berger.

ABSTRACT

RNase III enzymes are a highly conserved family of proteins that specifically cleave double-stranded (ds)RNA. These proteins are involved in a diverse group of functions, including ribosomal RNA processing, mRNA maturation and decay, snRNA and snoRNA processing, and RNA interference. Here we report the crystal structure of the nuclease domain of RNase III from the pathogen Mycobacterium tuberculosis. Although globally similar to other RNase III folds, this structure has some features not observed in previously reported models. These include the presence of an additional metal ion near the catalytic site, as well as conserved secondary structural elements that are proposed to have functional roles in the recognition of dsRNAs.

Selected figure(s)

Figure 2.
Figure 2. (A) Stereo diagram of dimer interface showing the surface of one monomer and the interacting region from the adjacent monomer. The surface regions corresponding to the polar side-chain atoms which bridge the interface are colored: Glu68 OE1 and OE2, red; Tyr130 OH, red; and Arg42 NH1 and NH2, blue. The box outlines the region shown in B. (B) 2F[o]-F[c] refined electron density map contoured at 1.5 detailing the interaction between Arg42 and backbone carbonyls of residues Phe60' through Ser67' of the dimermate. (C) A-form dsRNA modeled on the TB nuclease domain so that the scissile phosphates (green spheres) lie adjacent to the A-site metal ions (yellow spheres). The 2°-site ions are shown in magenta. The bases forming the two-nucleotide overhang product are indicated with orange bars. This arrangement places the minor groove corresponding to the distal box "anti-determinant" bases (cyan) (Zhang and Nicholson 1997) in close proximity to helices 2' and 5' (red). Surface electrostatics calculation using APBS (D) (Baker et al. 2001) and surface conservation (E) (Glaser et al. 2003) show negatively charged and conserved surface residues which align with the proposed dsRNA binding region.

The above figure is reprinted by permission from the Protein Society: Protein Sci (2005, 14, 2744-2750) copyright 2005.

Figure was selected by an automated process.