PDBsum entry: 1oqk

Hydrolase

PDB id: 1oqk

Contents

Protein chain

78 a.a. *

* Residue conservation analysis

PDB id:

1oqk

Name:

Hydrolase

Title:

Structure of mth11: a homologue of human rnase p protein rpp29

Structure:

Conserved protein mth11. Chain: a. Engineered: yes

Source:

Methanothermobacter thermautotrophicus. Organism_taxid: 145262. Gene: mth11. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

22 models

Authors:

W.P.Boomershine,C.A.Mcelroy,H.Tsai,V.Gopalan,M.P.Foster

Key ref:

W.P.Boomershine et al. (2003). Structure of Mth11/Mth Rpp29, an essential protein subunit of archaeal and eukaryotic RNase P. Proc Natl Acad Sci U S A, 100, 15398-15403. PubMed id: 14673079 DOI: 10.1073/pnas.2535887100

Date:

10-Mar-03 Release date: 13-Jan-04

Protein chain

O26119  (RNP1_METTH) -  Ribonuclease P protein component 1

Seq: 93 a.a.

Struc: 78 a.a.

Enzyme reactions

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

 Gene Ontology (GO) functional annotation 

• Cellular component: ribonuclease P complex (2 terms)
• Biological process: rRNA processing (3 terms)
• Biochemical function: hydrolase activity (4 terms)

DOI no: 10.1073/pnas.2535887100

Proc Natl Acad Sci U S A 100:15398-15403 (2003)

PubMed id: 14673079

Structure of Mth11/Mth Rpp29, an essential protein subunit of archaeal and eukaryotic RNase P.

W.P.Boomershine, C.A.McElroy, H.Y.Tsai, R.C.Wilson, V.Gopalan, M.P.Foster.

ABSTRACT

We have determined the solution structure of Mth11 (Mth Rpp29), an essential subunit of the RNase P enzyme from the archaebacterium Methanothermobacter thermoautotrophicus (Mth). RNase P is a ubiquitous ribonucleoprotein enzyme primarily responsible for cleaving the 5' leader sequence during maturation of tRNAs in all three domains of life. In eubacteria, this enzyme is made up of two subunits: a large RNA ( approximately 120 kDa) responsible for mediating catalysis, and a small protein cofactor ( approximately 15 kDa) that modulates substrate recognition and is required for efficient in vivo catalysis. In contrast, multiple proteins are associated with eukaryotic and archaeal RNase P, and these proteins exhibit no recognizable homology to the conserved bacterial protein subunit. In reconstitution experiments with recombinantly expressed and purified protein subunits, we found that Mth Rpp29, a homolog of the Rpp29 protein subunit from eukaryotic RNase P, is an essential protein component of the archaeal holoenzyme. Consistent with its role in mediating protein-RNA interactions, we report that Mth Rpp29 is a member of the oligonucleotide/oligosaccharide binding fold family. In addition to a structured beta-barrel core, it possesses unstructured N- and C-terminal extensions bearing several highly conserved amino acid residues. To identify possible RNA contacts in the protein-RNA complex, we examined the interaction of the 11-kDa protein with the full 100-kDa Mth RNA subunit by using NMR chemical shift perturbation. Our findings represent a critical step toward a structural model of the RNase P holoenzyme from archaebacteria and higher organisms.

Selected figure(s)

Figure 1.
Fig. 1. Sequence alignment of Mth Rpp29 with Rpp29 sequences from Archaea and Eukarya. Alignment was generated with CLUSTALW (57) and colored according to similarity by using a Risler scoring matrix (58); shaded residues indicate identity, and boxed residues indicate a global similarity score >0.7. Secondary structural features observed in the structure ensemble are indicated. Arrows indicate the core of the protein protected from trypsin digestion as identified by electrospray-MS (9,114 Da expected; 9,115 Da observed).

Figure 5.
Fig. 5. Identification of protein-RNA contacts by 1H-15N correlated NMR of the 113-kDa Mth Rpp29 -RNA complex. (a) Overlay of a portion of the HSQC spectra of free Mth Rpp29 (black) and the 1:1 complex between the 11-kDa (93 residues) protein and 102-kDa (314 nt) Mth P RNA (800 MHz, 50°C, 50 mM phosphate, 400 mM KCl). (b) Weighted average amide proton and nitrogen weighted-average shift perturbations (34) are mapped onto the ribbon diagram of the Rpp29 OB-fold by using a linear color ramp from gray (no change) to red [ [av](NH) = 0.15]. Residues in green are those for which the effect of RNA binding could not be assessed.

Figures were selected by the author.