PDBsum entry 2c04

Signaling protein

PDB id: 2c04

Contents

Protein chains

297 a.a. *

Ligands

GCP ×2

Metals

_CA ×2

Waters ×588

* Residue conservation analysis

PDB id:

2c04

Name:

Signaling protein

Title:

Gmppcp complex of srp gtpase ffh ng domain at ultra-high resolution

Structure:

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

Source:

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

Resolution:

1.15Å R-factor: 0.146 R-free: 0.180

Authors:

U.D.Ramirez,A.M.Preininger,D.M.Freymann

Key ref:

U.D.Ramirez et al. (2008). Nucleotide-binding flexibility in ultrahigh-resolution structures of the SRP GTPase Ffh. Acta Crystallogr D Biol Crystallogr, 64, 1043-1053. PubMed id: 18931411 DOI: 10.1107/S090744490802444X

Date:

25-Aug-05 Release date: 13-Feb-07

Protein chains

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

Seq: 430 a.a.

Struc: 297 a.a.

DOI no: 10.1107/S090744490802444X

Acta Crystallogr D Biol Crystallogr 64:1043-1053 (2008)

PubMed id: 18931411

Nucleotide-binding flexibility in ultrahigh-resolution structures of the SRP GTPase Ffh.

U.D.Ramirez, P.J.Focia, D.M.Freymann.

ABSTRACT

Two structures of the nucleotide-bound NG domain of Ffh, the GTPase subunit of the bacterial signal recognition particle (SRP), have been determined at ultrahigh resolution in similar crystal forms. One is GDP-bound and one is GMPPCP-bound. The asymmetric unit of each structure contains two protein monomers, each of which exhibits differences in nucleotide-binding conformation and occupancy. The GDP-bound Ffh NG exhibits two binding conformations in one monomer but not the other and the GMPPCP-bound protein exhibits full occupancy of the nucleotide in one monomer but only partial occupancy in the other. Thus, under the same solution conditions, each crystal reveals multiple binding states that suggest that even when nucleotide is bound its position in the Ffh NG active site is dynamic. Some differences in the positioning of the bound nucleotide may arise from differences in the crystal-packing environment and specific factors that have been identified include the relative positions of the N and G domains, small conformational changes in the P-loop, the positions of waters buried within the active site and shifts in the closing loop that packs against the guanine base. However, ;loose' binding may have biological significance in promoting facile nucleotide exchange and providing a mechanism for priming the SRP GTPase prior to its activation in its complex with the SRP receptor.

Selected figure(s)

Figure 4.
Figure 4 Conformational differences between the proteins are limited. Stereo diagrams of both monomers of structures DP and PCP superimposed on the C^ atoms of the G domains. The location of the binding site is indicated with a model of one conformation of the GDP in monomer A of structure DP. Monomer A of structure DP is shown in red and monomer B in blue; monomer A of structure PCP is shown in green and monomer B is shown in gold. Main-chain conformational differences among monomers of new structures occur at the NG-domain interface and five discrete regions in the G domain.

Figure 5.
Figure 5 The buried Lys117 contributes to nucleotide accommodation. A stereo diagram of the active site of monomer A of structure DP (bold colors) superimposed on the active site of structure 1ng1 (Mg-^2+-GDP Ffh NG; faded colors). Nucleotides and surrounding residues are shown with hydrogen-bonding interactions between two waters and Lys117 of monomer A of structure DP drawn as green dotted lines and those between one water and Lys117 of 1ng1 shown in faded magenta. A dioxane molecule (labeled `DOX') in the active site of structure DP may stabilize Lys117 in a single conformation.

The above figures are reprinted from an Open Access publication published by the IUCr: Acta Crystallogr D Biol Crystallogr (2008, 64, 1043-1053) copyright 2008.

Figures were selected by an automated process.