PDBsum entry: 1r6l

Transferase

PDB id: 1r6l

Contents

Protein chain

236 a.a. *

Ligands

SO4 ×6

NHE

Waters ×206

* Residue conservation analysis

PDB id:

1r6l

Name:

Transferase

Title:

Crystal structure of the tRNA processing enzyme rnase ph fro pseudomonas aeruginosa

Structure:

Ribonuclease ph. Chain: a. Synonym: rnase ph, tRNA nucleotidyltransferase. Engineered: yes

Source:

Pseudomonas aeruginosa. Organism_taxid: 287. Gene: rph. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Hexamer (from PDB file)

Resolution:

1.90Å R-factor: 0.221 R-free: 0.244

Authors:

J.M.Choi,E.Y.Park,J.H.Kim,S.K.Chang,Y.Cho

Key ref:

J.M.Choi et al. (2004). Probing the functional importance of the hexameric ring structure of RNase PH. J Biol Chem, 279, 755-764. PubMed id: 14573594 DOI: 10.1074/jbc.M309628200

Date:

15-Oct-03 Release date: 17-Feb-04

Protein chain

P50597  (RNPH_PSEAE) -  Ribonuclease PH

Seq: 239 a.a.

Struc: 236 a.a.

Enzyme reactions

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

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

 Gene Ontology (GO) functional annotation 

• Biological process: RNA processing (2 terms)
• Biochemical function: transferase activity (6 terms)

reference

DOI no: 10.1074/jbc.M309628200

J Biol Chem 279:755-764 (2004)

PubMed id: 14573594

Probing the functional importance of the hexameric ring structure of RNase PH.

J.M.Choi, E.Y.Park, J.H.Kim, S.K.Chang, Y.Cho.

ABSTRACT

RNase PH is a phosphate-dependent exoribonuclease that catalyzes the removal of nucleotides at the 3' end of the tRNA precursor, leading to the release of nucleoside diphosphate, and generates the CCA end during the maturation process. The 1.9-A crystal structures of the apo and the phosphate-bound forms of RNase PH from Pseudomonas aeruginosa reveal a monomeric RNase PH with an alpha/beta-fold tightly associated into a hexameric ring structure in the form of a trimer of dimers. A five ion pair network, Glu-63-Arg-74-Asp-116-Arg-77-Asp-118 and an ion-pair Glu-26-Arg-69 that are positioned symmetrically in the trimerization interface play critical roles in the formation of a hexameric ring. Single or double mutations of Arg-69, Arg-74, or Arg-77 in these ion pairs leads to the dissociation of the RNase PH hexamer into dimers without perturbing the overall monomeric structure. The dissociated RNase PH dimer completely lost its binding affinity and catalytic activity against a precursor tRNA. Our structural and mutational analyses of RNase PH demonstrate that the hexameric ring formation is a critical feature for the function of members of the RNase PH family.

Selected figure(s)

Figure 3.
FIG. 3. A phosphate-binding site in Pa RNase PH. The residues liganded to the phosphate ion are labeled. Arg-87, Gly-125, Thr-126, and Arg-127 interact with the phosphate ion. Certain conserved residues (Tyr-64, Thr-128, Tyr-178, and Asp-181) that interact in this region are also shown.

Figure 4.
FIG. 4. Two different views of an ion-pair network and an ion pair in the trimerization interface. a, the conserved and symmetrically positioned ion pairs Glu-63-Arg-74-Asp-116-Arg-77-Asp-118 and Arg-69-Glu-26 are shown in the trimerization interface. b, a close-up view of each ion-pair interaction. Ion-pairs are shown in dotted lines.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 755-764) copyright 2004.

Figures were selected by an automated process.