PDBsum entry: 1d6t

Hydrolase

PDB-id

1d6t

Contents

Description

Header details

Protein chain

* Residue conservation analysis

Tools

Image Generation

AstexViewer™@PDBe

Run PROCHECK

Clefts Calculation

PDB id:

1d6t

Name:

Hydrolase

Title:

Rnase p protein from staphylococcus aureus

Structure:

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

Source:

Staphylococcus aureus. Organism_taxid: 1280. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

UniProt:

P0A0H5 (RNPA_STAAU)

Seq:

117 a.a.

Struc:

117 a.a.

Key:		PfamA domain
		Secondary structure			CATH domain

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:

not givenÅ

NMR structure:

20 models

Authors:

C.Spitzfaden

Key ref:

C.Spitzfaden et al. (2000). The structure of ribonuclease P protein from Staphylococcus aureus reveals a unique binding site for single-stranded RNA.. J Mol Biol, 295, 105-115. [PubMed id: 10623511] [DOI: 10.1006/jmbi.1999.3341]

Date:

15-Oct-99

Release date:

18-Oct-00

Quick_links

RCSB

PDBe

SRS

MMDB

JenaLib

OCA

Proteopedia

CATH

SCOP

FSSP

HSSP

PDBSWS

ProSAT

Whatcheck

Procheck

Clefts

Surface

Key reference

DOI no: 10.1006/jmbi.1999.3341 J Mol Biol 295:105-115 (2000)

PubMed id: 10623511

The structure of ribonuclease P protein from Staphylococcus aureus reveals a unique binding site for single-stranded RNA.

C.Spitzfaden, N.Nicholson, J.J.Jones, S.Guth, R.Lehr, C.D.Prescott, L.A.Hegg, D.S.Eggleston.

ABSTRACT

Ribonuclease P (RNaseP) catalyses the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5' terminus. The prokaryotic RNaseP holoenzyme consists of a catalytic RNA component and a protein subunit (RNaseP protein), which plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme.We determined the three-dimensional high-resolution structure of the RNaseP protein from Staphylococcus aureus (117 amino acid residues) by nuclear magnetic resonance (NMR) spectroscopy in solution. The protein has an alphabeta-fold, similar to the ribonucleoprotein domain. We used small nucleic acid molecules as a model for the 5'-leader sequence to probe the propensity for generic single-stranded RNA binding on the protein surface. The NMR results reveal a contiguous interaction site, which is identical with the previously identified leader sequence binding site in RNaseP holoenzyme. The conserved arginine-rich motif does not bind single-stranded RNA. It is likely that this peptide segment binds selectively to double-stranded sections of P RNA, which are conformationally more rigid. Given the essentiality of RNaseP for the viability of the organism, knowledge of the S. aureus protein structure and insight into its interaction with RNA will help us to develop RNaseP and RNaseP protein as targets for novel antibiotics against this pathogen.

Selected figure(s)

Figure 3.
Figure 3. Solution structure of S. aureus RNaseP protein. (a) Superposition of the 20 conformers with the lowest DYANA target function of RNaseP protein from S. aureus (blue) and from B. subtilis (red; [Stams et al 1998]). The N, C^a and C' positions of residues 8-9, 13-35 and 42-113, which are well ordered in the NMR structure, were considered for superposition, but for clarity only C^a is shown. (b) Schematic drawing of the NMR-structure of RNaseP protein. Regular secondary structures are represented as arrows (b-sheet) or ribbon (a-helix). Individual side-chains are shown for residues with a high level of phylogenetic conservation according to the sequence alignment in Figure 4 (red, 100 %; yellow, > 70 %). Figure 6.
Figure 6. Substrate binding surface of RNaseP protein as defined by NMR spectroscopy. A C^a plot of the RNaseP protein structure is superimposed with the electrostatic potential surface of the residues in the interaction site as characterised by chemical shift perturbation. Purple cylinders indicate the position of the a-helices. The position of potential hydrogen-bonding donors and electrostatic charges within the binding site and at the edge of the b-sheet are indicated. The molecule is rotated by approximately 30° compared to Figure 3(b) to show the partial involvement of helix 3 in ligand interactions.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 295, 105-115) copyright 2000.

Figures were selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id Reference

19243011 L.A.Kirsebom, and S.Trobro (2009).
RNase P RNA-mediated cleavage.

IUBMB Life, 61, 189-200.

17868095 J.K.Smith, J.Hsieh, and C.A.Fierke (2007).
Importance of RNA-protein interactions in bacterial ribonuclease P structure and catalysis.

Biopolymers, 87, 329-338.

17919279 M.Gösringer, and R.K.Hartmann (2007).
Function of heterologous and truncated RNase P proteins in Bacillus subtilis.

Mol Microbiol, 66, 801-813.

17299131 S.Niranjanakumari, J.J.Day-Storms, M.Ahmed, J.Hsieh, N.H.Zahler, R.A.Venters, and C.A.Fierke (2007).
Probing the architecture of the B. subtilis RNase P holoenzyme active site by cross-linking and affinity cleavage.

RNA, 13, 521-535.

16980936 A.V.Kazantsev, and N.R.Pace (2006).
Bacterial RNase P: a new view of an ancient enzyme.

Nat Rev Microbiol, 4, 729-740.

16547047 C.Roberts, K.L.Anderson, E.Murphy, S.J.Projan, W.Mounts, B.Hurlburt, M.Smeltzer, R.Overbeek, T.Disz, and P.M.Dunman (2006).
Characterizing the effect of the Staphylococcus aureus virulence factor regulator, SarA, on log-phase mRNA half-lives.

J Bacteriol, 188, 2593-2603.

16418270 R.C.Wilson, C.J.Bohlen, M.P.Foster, and C.E.Bell (2006).
Structure of Pfu Pop5, an archaeal RNase P protein.

Proc Natl Acad Sci U S A, 103, 873-878.

PDB code: 2av5

16163391 A.H.Buck, A.B.Dalby, A.W.Poole, A.V.Kazantsev, and N.R.Pace (2005).
Protein activation of a ribozyme: the role of bacterial RNase P protein.

EMBO J, 24, 3360-3368.

16155184 E.Sharin, A.Schein, H.Mann, Y.Ben-Asouli, and N.Jarrous (2005).
RNase P: role of distinct protein cofactors in tRNA substrate recognition and RNA-based catalysis.

Nucleic Acids Res, 33, 5120-5132.

15973057 M.Kifusa, H.Fukuhara, T.Hayashi, and M.Kimura (2005).
Protein-protein interactions in the subunits of ribonuclease P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3.

Biosci Biotechnol Biochem, 69, 1209-1212.

14691942 J.Hsieh, A.J.Andrews, and C.A.Fierke (2004).
Roles of protein subunits in RNA-protein complexes: lessons from ribonuclease P.

Biopolymers, 73, 79-89.

15337847 J.J.Day-Storms, S.Niranjanakumari, and C.A.Fierke (2004).
Ionic interactions between PRNA and P protein in Bacillus subtilis RNase P characterized using a magnetocapture-based assay.

RNA, 10, 1595-1608.

14767080 L.S.Harlow, A.Kadziola, K.F.Jensen, and S.Larsen (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.

PDB codes: 1oyp 1oyr 1oys

15810434 T.A.Hall, and J.W.Brown (2004).
Interactions between RNase P protein subunits in archaea.

Archaea, 1, 247-254.

15317976 T.Numata, I.Ishimatsu, Y.Kakuta, I.Tanaka, and M.Kimura (2004).
Crystal structure of archaeal ribonuclease P protein Ph1771p from Pyrococcus horikoshii OT3: an archaeal homolog of eukaryotic ribonuclease P protein Rpp29.

RNA, 10, 1423-1432.

PDB code: 1v76

12799461 A.V.Kazantsev, A.A.Krivenko, D.J.Harrington, R.J.Carter, S.R.Holbrook, P.D.Adams, and N.R.Pace (2003).
High-resolution structure of RNase P protein from Thermotoga maritima.

Proc Natl Acad Sci U S A, 100, 7497-7502.

PDB code: 1nz0

14622001 D.J.Sidote, and D.W.Hoffman (2003).
NMR structure of an archaeal homologue of ribonuclease P protein Rpp29.

Biochemistry, 42, 13541-13550.

PDB code: 1pc0

12554950 H.W.Choe, D.G.Jeong, J.H.Park, R.Schlesinger, J.Labahn, K.P.Hofmann, and G.Büldt (2003).
Preliminary X-ray characterization of the ribonuclease P (C5 protein) from Escherichia coli: expression, crystallization and cryoconditions.

Acta Crystallogr D Biol Crystallogr, 59, 350-352.

14673079 W.P.Boomershine, C.A.McElroy, H.Y.Tsai, R.C.Wilson, V.Gopalan, and M.P.Foster (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.

PDB code: 1oqk

12077454 A.A.Krivenko, A.V.Kazantsev, C.Adamidi, D.J.Harrington, and N.R.Pace (2002).
Expression, purification, crystallization and preliminary diffraction analysis of RNase P protein from Thermotoga maritima.

Acta Crystallogr D Biol Crystallogr, 58, 1234-1236.

11880623 F.Houser-Scott, S.Xiao, C.E.Millikin, J.M.Zengel, L.Lindahl, and D.R.Engelke (2002).
Interactions among the protein and RNA subunits of Saccharomyces cerevisiae nuclear RNase P.

Proc Natl Acad Sci U S A, 99, 2684-2689.

12490703 J.H.Lee, H.Kim, J.Ko, and Y.Lee (2002).
Interaction of C5 protein with RNA aptamers selected by SELEX.

Nucleic Acids Res, 30, 5360-5368.

12466529 M.Jovanovic, R.Sanchez, S.Altman, and V.Gopalan (2002).
Elucidation of structure-function relationships in the protein subunit of bacterial RNase P using a genetic complementation approach.

Nucleic Acids Res, 30, 5065-5073.

12045094 S.Xiao, F.Scott, C.A.Fierke, and D.R.Engelke (2002).
Eukaryotic ribonuclease P: a plurality of ribonucleoprotein enzymes.

Annu Rev Biochem, 71, 165-189.

11258888 C.H.Henkels, J.C.Kurz, C.A.Fierke, and T.G.Oas (2001).
Linked folding and anion binding of the Bacillus subtilis ribonuclease P protein.

Biochemistry, 40, 2777-2789.

11557817 S.M.Sharkady, and J.M.Nolan (2001).
Bacterial ribonuclease P holoenzyme crosslinking analysis reveals protein interaction sites on the RNA subunit.

Nucleic Acids Res, 29, 3848-3856.

11142368 S.Altman, V.Gopalan, and A.Vioque (2000).
Varieties of RNase P: a nomenclature problem?

RNA, 6, 1689-1694.

10933810 W.A.Ziehler, J.J.Day, C.A.Fierke, and D.R.Engelke (2000).
Effects of 5' leader and 3' trailer structures on pre-tRNA processing by nuclear RNase P.

Biochemistry, 39, 9909-9916.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.