PDBsum entry 1a6f

Endonuclease

PDB id: 1a6f

Contents

Protein chain

113 a.a. *

Ligands

SO4

Metals

_ZN ×2

Waters ×10

* Residue conservation analysis

PDB id:

1a6f

Name:

Endonuclease

Title:

Rnase p protein from bacillus subtilis

Structure:

Ribonuclease p protein. Chain: a. Synonym: rnase p protein. Engineered: yes. Mutation: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Cell_line: bl21. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.60Å R-factor: 0.205 R-free: 0.317

Authors:

T.Stams,D.W.Christianson

Key ref:

T.Stams et al. (1998). Ribonuclease P protein structure: evolutionary origins in the translational apparatus. Science, 280, 752-755. PubMed id: 9563955 DOI: 10.1126/science.280.5364.752

Date:

24-Feb-98 Release date: 23-Mar-99

Protein chain

P25814  (RNPA_BACSU) -  Ribonuclease P protein component from Bacillus subtilis (strain 168)

Seq: 116 a.a.

Struc: 113 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

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

DOI no: 10.1126/science.280.5364.752

Science 280:752-755 (1998)

PubMed id: 9563955

Ribonuclease P protein structure: evolutionary origins in the translational apparatus.

T.Stams, S.Niranjanakumari, C.A.Fierke, D.W.Christianson.

ABSTRACT

The crystal structure of Bacillus subtilis ribonuclease P protein is reported at 2.6 angstroms resolution. This protein binds to ribonuclease P RNA to form a ribonucleoprotein holoenzyme with optimal catalytic activity. Mutagenesis and biochemical data indicate that an unusual left-handed betaalphabeta crossover connection and a large central cleft in the protein form conserved RNA binding sites; a metal binding loop may comprise a third RNA binding site. The unusual topology is partly shared with ribosomal protein S5 and the ribosomal translocase elongation factor G, which suggests evolution from a common RNA binding ancestor in the primordial translational apparatus.

Selected figure(s)

Figure 2.
Fig. 2. Space-filling model of B. subtilis RNase P protein. Site-directed mutagenesis studies with the E. coli C5 protein (18) identify residues important for holoenzyme function (yellow); B. subtilis numbering is used. Solvent-exposed residues in the^ central cleft (Phe^16, Phe^20), on helix B (the RNR motif: Arg60, Asn61, Lys64, Arg65), or on strand 3 (Arg45) most likely contact RNA. Interestingly, the Arg45 His substitution in C5 protein (B. subtilis numbering) results in a temperature-sensitive phenotype defective in holoenzyme assembly (18); correspondingly, this substitution must alter a critical contact between the protein and RNA subunits. Substitution of^ a buried residue (Phe^107, which appears as tryptophan in C5 protein) probably slightly perturbs the overall tertiary structure, thereby compromising the overall complementarity of protein and RNA subunits in the^ holoenzyme. Photocross-linking studies with the B. subtilis holoenzyme^ (19) identify residues on the protein subunit that contact the^ RNA subunit (green), including residues at the NH[2]-terminus (Arg7) and helix C (Arg108, Ser111) that flank helix B. These studies also implicate Ser49 (red) and the central cleft for binding the 5 leader sequence^ of pre-tRNA^Asp in the holoenzyme-substrate complex.

Figure 3.
Fig. 3. Ribbon plots (25) of the COOH-terminal domain of ribosomal protein S5 (20) (PDB accession code 1PKP), RNase P protein, and domain IV of the ribosomal translocase, EF-G (21) (PDB accession code 1DAR). Left-handed crossovers are highlighted in yellow. Topological similarities suggest evolutionary divergence from a primordial ribosomal ancestor.

The above figures are reprinted by permission from the AAAs: Science (1998, 280, 752-755) copyright 1998.

Figures were selected by an automated process.