PDBsum entry 2pxt

Signaling protein/RNA

PDB id: 2pxt

Contents

Protein chain

69 a.a. *

DNA/RNA

Ligands

NCO ×8

* Residue conservation analysis

PDB id:

2pxt

Name:

Signaling protein/RNA

Title:

Variant 15 of ribonucleoprotein core of the e. Coli signal recognition particle

Structure:

4.5 s RNA. Chain: b. Fragment: domain iv. Engineered: yes. Mutation: yes. Signal recognition particle protein. Chain: a. Fragment: c terminal domain (residues 328-432). Synonym: fifty-four homolog, p48.

Source:

Synthetic: yes. Other_details: synthetic. Escherichia coli. Organism_taxid: 562. Gene: ffh. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.50Å R-factor: 0.223 R-free: 0.245

Authors:

A.Y.Keel,R.P.Rambo,R.T.Batey,J.S.Kieft

Key ref:

A.Y.Keel et al. (2007). A general strategy to solve the phase problem in RNA crystallography. Structure, 15, 761-772. PubMed id: 17637337 DOI: 10.1016/j.str.2007.06.003

Date:

14-May-07 Release date: 07-Aug-07

Protein chain

P0AGD7  (SRP54_ECOLI) -  Signal recognition particle protein from Escherichia coli (strain K12)

Seq: 453 a.a.

Struc: 69 a.a.*

* PDB and UniProt seqs differ at 10 residue positions (black crosses)

DNA/RNA chain

G-C-U-G-C-U-G-U-U-U-A-C-C-A-G-G-U-C-A-G-G-U-C-C-G-A-A-A-G-G-A-A-G-C-A-G-C-C-A- 49 bases

Enzyme reactions

• Enzyme class: E.C.3.6.5.4 - signal-recognition-particle GTPase.
• Reaction: GTP + H2O = GDP + phosphate + H⁺

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

reference

DOI no: 10.1016/j.str.2007.06.003

Structure 15:761-772 (2007)

PubMed id: 17637337

A general strategy to solve the phase problem in RNA crystallography.

A.Y.Keel, R.P.Rambo, R.T.Batey, J.S.Kieft.

ABSTRACT

X-ray crystallography of biologically important RNA molecules has been hampered by technical challenges, including finding heavy-atom derivatives to obtain high-quality experimental phase information. Existing techniques have drawbacks, limiting the rate at which important new structures are solved. To address this, we have developed a reliable means to localize heavy atoms specifically to virtually any RNA. By solving the crystal structures of thirteen variants of the G*U wobble pair cation binding motif, we have identified a version that when inserted into an RNA helix introduces a high-occupancy cation binding site suitable for phasing. This "directed soaking" strategy can be integrated fully into existing RNA crystallography methods, potentially increasing the rate at which important structures are solved and facilitating routine solving of structures using Cu-Kalpha radiation. This method already has been used to solve several crystal structures.

Selected figure(s)

Figure 2.
Figure 2. Engineered Cation Binding
(A) Electron density and structure of the wild-type SRP RNA-M domain complex, showing the portion of the helix that was varied. The view is into the major groove. Two cobalt (III) hexammine ions (magenta) are located near the phosphate backbone (upper right site) and two adjacent G-C pairs (lower left).
(B) Electron density and structure of the variant PM04, with the tandem wobble pairs shown in cyan and the resultant major groove-bound cobalt (III) hexammine in magenta.
(C) Anomalous difference Fourier map (contoured at 7 σ in red) of PM04 superimposed on the structure. The tandem wobble pairs are shown in cyan. The endogenous reference site is at the top, and the new engineered site at the bottom.
(D) Comparison of the very well-ordered reference site to the new site in PM04 in a 2F[o] − F[c] map, at 2 Å resolution, contoured at 2 σ.

Figure 4.
Figure 4. General Rules for Cation Binding in the Major Groove of G•U Motifs
(A) Schematic of the arrangement of major groove functional groups for PM01, PM05, and PM09. These three variants vary only in the orientation of flanking G-C pairs relative to the tandem G•U pairs. Blue circles are amine, red are carbonyls, and orange are purine N7 groups. In PM01, the two major groove amines (from cytosine) are placed away from the binding site due to the turn of the helix. In PM05 and PM09, the amines are placed in position to limit the mobility of the ion (shown in green). In addition, the location of carbonyls and N7 groups in the flanking sequences and close to the binding site make the ion more mobile as it attempts to satisfy multiple potential hydrogen binding partners.
(B) Schematic of the arrangement of major groove functional groups in the four single G•U pair containing variants. In single G•U pairs, the amines are best placed in the 3′ positions to withdraw them from the pocket.

The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2007, 15, 761-772) copyright 2007.

Figures were selected by an automated process.