PDBsum entry: 2av5

Hydrolase

PDB-id: 2av5

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PROCHECK

Protein chains

106 a.a. *

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

2av5

Name:

Hydrolase

Title:

Crystal structure of pyrococcus furiosus pop5, an archaeal ribonuclease p protein

Structure:

Ribonuclease p protein component 2. Chain: a, b, c, d, e. Synonym: rnase p component 2. Engineered: yes. Mutation: yes

Source:

Pyrococcus furiosus. Organism_taxid: 2261. Gene: rnp2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

UniProt:

Chains A, B, C, D, E: Q8U151 (RNP2_PYRFU)

Seq:

120 a.a.

Struc:

106 a.a.*

Key:

PfamA domain

Secondary structure

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

Enzyme class:

E.C.3.1.26.5   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Endonucleolytic cleavage of RNA, removing 5'-extra-nucleotide from tRNA precursor.

Resolution:

3.15Å

R-factor:

0.232

R-free:

0.263

Authors:

R.C.Wilson,C.J.Bohlen,M.P.Foster,C.E.Bell

Key ref:

R.C.Wilson et al. (2006). Structure of Pfu Pop5, an archaeal RNase P protein.. Proc Natl Acad Sci U S A, 103, 873-878. [PubMed id: 16418270] [DOI: 10.1073/pnas.0508004103]

Date:

29-Aug-05

Release date:

24-Jan-06

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Key reference

DOI no: 10.1073/pnas.0508004103

Proc Natl Acad Sci U S A 103:873-878 (2006)

PubMed id: 16418270

Structure of Pfu Pop5, an archaeal RNase P protein.

R.C.Wilson, C.J.Bohlen, M.P.Foster, C.E.Bell.

ABSTRACT

We have used NMR spectroscopy and x-ray crystallography to determine the three-dimensional structure of PF1378 (Pfu Pop5), one of four protein subunits of archaeal RNase P that shares a homolog in the eukaryotic enzyme. RNase P is an essential and ubiquitous ribonucleoprotein enzyme required for maturation of tRNA. In bacteria, the enzyme's RNA subunit is responsible for cleaving the single-stranded 5' leader sequence of precursor tRNA molecules (pre-tRNA), whereas the protein subunit assists in substrate binding. Although in bacteria the RNase P holoenzyme consists of one large catalytic RNA and one small protein subunit, in archaea and eukarya the enzyme contains several (>/=4) protein subunits, each of which lacks sequence similarity to the bacterial protein. The functional role of the proteins is poorly understood, as is the increased complexity in comparison to the bacterial enzyme. Pfu Pop5 has been directly implicated in catalysis by the observation that it pairs with PF1914 (Pfu Rpp30) to functionally reconstitute the catalytic domain of the RNA subunit. The protein adopts an alpha-beta sandwich fold highly homologous to the single-stranded RNA binding RRM domain. Furthermore, the three-dimensional arrangement of Pfu Pop5's structural elements is remarkably similar to that of the bacterial protein subunit. NMR spectra have been used to map the interaction of Pop5 with Pfu Rpp30. The data presented permit tantalizing hypotheses regarding the role of this protein subunit shared by archaeal and eukaryotic RNase P.

Selected figure(s)

Figure 2.
Fig. 2. Crystal structure of Pfu Pop5. (a)2F[o] - F[c] electron density map of the -helical hairpin interface observed between neighboring molecules in the asymmetric unit, contoured at 1.0 . (b) Ribbon diagram of Pfu Pop5, colored according to secondary structure as assigned by DSSP (66). (c) Stereo view of Pfu Pop5 showing exposed aromatic and apolar side chains. Images were generated by using PYMOL (www.pymol.org).

Figure 3.
Fig. 3. Similarity of Pfu Pop5 to the bacterial RNase P protein and the RRM motif. (a) Similarity of three-dimensional structures of Pfu Pop5 (red) and the bacterial RNase P protein (gray; Bacillus subtilis; Protein Data Bank code 1A6F [PDB] ) (40); the structures were superimposed by aligning residues 31-44 in helix [1] of Pop5 with residues 60-73 in helix [2] of 1A6F. Note that the secondary structural elements are arranged in a different order: in Pfu Pop5 versus in the bacterial RNase P proteins. (b) Ribbon diagrams of Pfu Pop5 (red) and Homo sapiens U1A RRM1 (cyan; 1NU4) (44). (c) The Staphylococcus aureus RNase P protein, with sticks shown for residues identified as being involved in RNA interactions by chemical shift perturbation or crosslinking (6, 41). (d) Speculative model of Pfu Pop5 with the C-terminal helix (cyan) reoriented as for the bacterial RNase P protein, revealing the putative RNA-binding surface of Pfu Pop5. Apolar and positively charged side chains protrude from the surface of the -sheet. Such an orientation of helix [4] would allow access by single stranded RNA to the analogous aromatic and hydrophobic residues.

Figures were selected by the author.