PDBsum entry 1o87

Protein transport

PDB id: 1o87

Contents

Protein chains

295 a.a. *

Ligands

FMT ×5

GDP ×2

Metals

_MG ×4

_CL

Waters ×274

* Residue conservation analysis

PDB id:

1o87

Name:

Protein transport

Title:

A new mggdp complex of the ffh ng domain

Structure:

Signal recognition particle protein. Chain: a, b. Fragment: ng gtpase domain, residues 1-296. Synonym: fifty-four homolog, ffh. Engineered: yes

Source:

Thermus aquaticus. Organism_taxid: 271. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.10Å R-factor: 0.197 R-free: 0.237

Authors:

D.M.Freymann

Key ref:

P.J.Focia et al. (2004). Novel protein and Mg2+ configurations in the Mg2+GDP complex of the SRP GTPase ffh. Proteins, 54, 222-230. PubMed id: 14696184 DOI: 10.1002/prot.10598

Date:

25-Nov-02 Release date: 02-Jan-04

Protein chains

O07347  (SRP54_THEAQ) -  Signal recognition particle protein from Thermus aquaticus

Seq: 430 a.a.

Struc: 295 a.a.

DOI no: 10.1002/prot.10598

Proteins 54:222-230 (2004)

PubMed id: 14696184

Novel protein and Mg2+ configurations in the Mg2+GDP complex of the SRP GTPase ffh.

P.J.Focia, H.Alam, T.Lu, U.D.Ramirez, D.M.Freymann.

ABSTRACT

Ffh is the signal sequence recognition and targeting subunit of the prokaryotic signal recognition particle (SRP). Previous structural studies of the NG GTPase domain of Ffh demonstrated magnesium-dependent and magnesium-independent binding conformations for GDP and GMPPNP that are believed to reflect novel mechanisms for exchange and activation in this member of the GTPase superfamily. The current study of the NG GTPase bound to Mg(2+)GDP reveals two new binding conformations-in the first the magnesium interactions are similar to those seen previously, however, the protein undergoes a conformational change that brings a conserved aspartate into its second coordination sphere. In the second, the protein conformation is similar to that seen previously, but the magnesium coordination sphere is disrupted so that only five oxygen ligands are present. The loss of the coordinating water molecule, at the position that would be occupied by the oxygen of the gamma-phosphate of GTP, is consistent with that position being privileged for exchange during phosphate release. The available structures of the GDP-bound protein provide a series of structural snapshots that illuminate steps along the pathway of GDP release following GTP hydrolysis.

Selected figure(s)

Figure 1.
Figure 1. Ribbon diagram of the nucleotide bound protein. The ribbon diagram of monomer A of the Mg^2+GDP complex of the Ffh NG domain is oriented to view into the active site. The -helical N domain is in light blue, and the G domain is in light green. The motif I P-loop at the center of the G domain interacts with the phosphate groups of GDP (ball-and-stick). Motif II to the left, and motif III to the center right (indicated), interact with the bound magnesium ion through intervening water molecules. The hydrated magnesium ion is shown as a CPK representation. The carboxylate group of Asp248 hydrogen-bonds the guanine base; the carboxylate of Asp135 contributes to the second coordination sphere of the magnesium in monomer A, but is usually found in a different conformation (see text).

Figure 3.
Figure 3. Difference in magnesium ion hydration in monomers A and B. The 2Fo-Fc electron density maps of the hydrated magnesium ions in the active sites of monomers A and B are shown, contoured at 1.0 . In monomer A, each of the coordinating water molecules is clearly defined. In contrast, although three coordinating waters are well defined in monomer B, and the temperature factors of the magnesium ions and coordinating waters are similar, no coordinating water at position 1 (asterisk) is visible in the electron density map. As this position is the site of interaction with the -phosphate oxygen of bound GTP, facile exchange may be functionally significant. The magnesium omit difference map allowed for an identical interpretation. Thr112 and the phosphate groups of the bound GDP are shown in each figure. The map cover radius was 1.1 Å, including the missing water position.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 54, 222-230) copyright 2004.

Figures were selected by the author.