PDBsum entry 1oyr

Transferase

PDB id: 1oyr

Contents

Protein chains

(+ 0 more) 242 a.a. *

Ligands

SO4 ×12

Metals

_CD ×3

* Residue conservation analysis

PDB id:

1oyr

Name:

Transferase

Title:

Crystal structure of the phosphorolytic exoribonuclease rnase ph from bacillus subtilis

Structure:

Ribonuclease ph. Chain: a, b, c, d, e, f. Synonym: rnase ph, tRNA nucleotidyltransferase. Ec: 2.7.7.56

Source:

Bacillus subtilis. Organism_taxid: 1423

Biol. unit:

Hexamer (from PQS)

Resolution:

3.10Å R-factor: 0.278 R-free: 0.289

Authors:

L.S.Harlow,A.Kadziola,K.F.Jensen,S.Larsen

Key ref:

L.S.Harlow et al. (2004). Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis and implications for its quaternary structure and tRNA binding. Protein Sci, 13, 668-677. PubMed id: 14767080 DOI: 10.1110/ps.03477004

Date:

07-Apr-03 Release date: 09-Mar-04

Protein chains

P28619  (RNPH_BACSU) -  Ribonuclease PH from Bacillus subtilis (strain 168)

Seq: 245 a.a.

Struc: 242 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.7.56 - tRNA nucleotidyltransferase.
• Reaction: tRNA(n+1) + phosphate = tRNA(n) + a ribonucleoside 5'-diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1110/ps.03477004

Protein Sci 13:668-677 (2004)

PubMed id: 14767080

Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis and implications for its quaternary structure and tRNA binding.

L.S.Harlow, A.Kadziola, K.F.Jensen, S.Larsen.

ABSTRACT

RNase PH is a member of the family of phosphorolytic 3' --> 5' exoribonucleases that also includes polynucleotide phosphorylase (PNPase). RNase PH is involved in the maturation of tRNA precursors and especially important for removal of nucleotide residues near the CCA acceptor end of the mature tRNAs. Wild-type and triple mutant R68Q-R73Q-R76Q RNase PH from Bacillus subtilis have been crystallized and the structures determined by X-ray diffraction to medium resolution. Wild-type and triple mutant RNase PH crystallize as a hexamer and dimer, respectively. The structures contain a rare left-handed beta alpha beta-motif in the N-terminal portion of the protein. This motif has also been identified in other enzymes involved in RNA metabolism. The RNase PH structure and active site can, despite low sequence similarity, be overlayed with the N-terminal core of the structure and active site of Streptomyces antibioticus PNPase. The surface of the RNase PH dimer fit the shape of a tRNA molecule.

Selected figure(s)

Figure 1.
Figure 1. Stereo views of the B. subtilis RNase PH monomer. (A) Ribbon representation showing the secondary structure elements with labels and ball-and-stick representation of sulfate ions. C[ ]positions for mutated residues Arg68, Arg73, and Arg76 are marked with white balls. (B) C[ ]trace of the monomer with dots every 10 residues and labels every 20 residues. This figure and Figure 2 Go-were made using the program MOLSCRIPT (Kraulis 1991).

Figure 5.
Figure 5. Close-up stereo view at the active site residues with sixfold averaged electron density. Nitrogen, oxygen, sulfur, and carbon atoms are dark gray, medium gray, light gray, and white, respectively. The 2mF[obs] - DF[calc] total density is shown with weak line contours at a 1 level and the mF[obs] - DF[calc] difference density is shown with strong lines and contoured at 4 . The carboxylate groups of Asp 181 and Asp 187 are unexpectedly close but residual density present in between may indicate the presence of a positive countercharge, for example, a partially occupied Cd^2+ ion (not included in the model). This figure was made with BOBSCRIPT (Esnouf 1999).

The above figures are reprinted by permission from the Protein Society: Protein Sci (2004, 13, 668-677) copyright 2004.

Figures were selected by an automated process.