PDBsum entry 1jpj

Signaling protein

PDB id: 1jpj

Contents

Protein chain

294 a.a. *

Ligands

GNP

Waters ×59

* Residue conservation analysis

PDB id:

1jpj

Name:

Signaling protein

Title:

Gmppnp complex of srp gtpase ng domain

Structure:

Signal recognition particle protein. Chain: a. Fragment: ng domain. Synonym: fifty-four homolog. Engineered: yes

Source:

Thermus aquaticus. Organism_taxid: 271. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.30Å R-factor: 0.201 R-free: 0.306

Authors:

S.Padmanabhan,D.M.Freymann

Key ref:

S.Padmanabhan and D.M.Freymann (2001). The conformation of bound GMPPNP suggests a mechanism for gating the active site of the SRP GTPase. Structure, 9, 859-867. PubMed id: 11566135 DOI: 10.1016/S0969-2126(01)00641-4

Date:

02-Aug-01 Release date: 02-Feb-02

Protein chain

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

Seq: 430 a.a.

Struc: 294 a.a.

DOI no: 10.1016/S0969-2126(01)00641-4

Structure 9:859-867 (2001)

PubMed id: 11566135

The conformation of bound GMPPNP suggests a mechanism for gating the active site of the SRP GTPase.

S.Padmanabhan, D.M.Freymann.

ABSTRACT

BACKGROUND: The signal recognition particle (SRP) is a phylogenetically conserved ribonucleoprotein that mediates cotranslational targeting of secreted and membrane proteins to the membrane. Targeting is regulated by GTP binding and hydrolysis events that require direct interaction between structurally homologous "NG" GTPase domains of the SRP signal recognition subunit and its membrane-associated receptor, SR alpha. Structures of both the apo and GDP bound NG domains of the prokaryotic SRP54 homolog, Ffh, and the prokaryotic receptor homolog, FtsY, have been determined. The structural basis for the GTP-dependent interaction between the two proteins, however, remains unknown. RESULTS: We report here two structures of the NG GTPase of Ffh from Thermus aquaticus bound to the nonhydrolyzable GTP analog GMPPNP. Both structures reveal an unexpected binding mode in which the beta-phosphate is kinked away from the binding site and magnesium is not bound. Binding of the GTP analog in the canonical conformation found in other GTPase structures is precluded by constriction of the phosphate binding P loop. The structural difference between the Ffh complex and other GTPases suggests a specific conformational change that must accompany movement of the nucleotide from an "inactive" to an "active" binding mode. CONCLUSIONS: Conserved side chains of the GTPase sequence motifs unique to the SRP subfamily may function to gate formation of the active GTP bound conformation. Exposed hydrophobic residues provide an interaction surface that may allow regulation of the GTP binding conformation, and thus activation of the GTPase, during the association of SRP with its receptor.

Selected figure(s)

Figure 1.
Figure 1. GMPPNP Binding to the NG DomainOmit difference (F[o] - F[c]) electron density maps contoured at 3 s (light blue) and 6 s (dark blue) for (a) structure N1 and (b) structure N2a. The triplet of electron-dense peaks to the right in each image indicates the positions of the phosphate groups. Two residues, Gln107 and Thr112, define the top and bottom of the P loop jaws

The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 859-867) copyright 2001.

Figure was selected by the author.