PDBsum entry 1ls1

Protein transport

PDB id: 1ls1

Contents

Protein chain

289 a.a. *

Ligands

OXY ×3

Metals

_MG

Waters ×316

* Residue conservation analysis

PDB id:

1ls1

Name:

Protein transport

Title:

T. Aquaticus ffh ng domain at 1.1a resolution

Structure:

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

Source:

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

Biol. unit:

Dimer (from PQS)

Resolution:

1.10Å R-factor: 0.137 R-free: 0.169

Authors:

U.D.Ramirez,G.Minasov,D.M.Freymann

Key ref:

U.D.Ramirez et al. (2002). Structural basis for mobility in the 1.1 A crystal structure of the NG domain of Thermus aquaticus Ffh. J Mol Biol, 320, 783-799. PubMed id: 12095255 DOI: 10.1016/S0022-2836(02)00476-X

Date:

16-May-02 Release date: 16-Nov-02

Protein chain

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

Seq: 430 a.a.

Struc: 289 a.a.

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/S0022-2836(02)00476-X

J Mol Biol 320:783-799 (2002)

PubMed id: 12095255

Structural basis for mobility in the 1.1 A crystal structure of the NG domain of Thermus aquaticus Ffh.

U.D.Ramirez, G.Minasov, P.J.Focia, R.M.Stroud, P.Walter, P.Kuhn, D.M.Freymann.

ABSTRACT

The NG domain of the prokaryotic signal recognition protein Ffh is a two-domain GTPase that comprises part of the prokaryotic signal recognition particle (SRP) that functions in co-translational targeting of proteins to the membrane. The interface between the N and G domains includes two highly conserved sequence motifs and is adjacent in sequence and structure to one of the conserved GTPase signature motifs. Previous structural studies have shown that the relative orientation of the two domains is dynamic. The N domain of Ffh has been proposed to function in regulating the nucleotide-binding interactions of the G domain. However, biochemical studies suggest a more complex role for the domain in integrating communication between signal sequence recognition and interaction with receptor. Here, we report the structure of the apo NG GTPase of Ffh from Thermus aquaticus refined at 1.10 A resolution. Although the G domain is very well ordered in this structure, the N domain is less well ordered, reflecting the dynamic relationship between the two domains previously inferred. We demonstrate that the anisotropic displacement parameters directly visualize the underlying mobility between the two domains, and present a detailed structural analysis of the packing of the residues, including the critical alpha4 helix, that comprise the interface. Our data allows us to propose a structural explanation for the functional significance of sequence elements conserved at the N/G interface.

Selected figure(s)

Figure 3.
Figure 3. Anisotropic temperature factors reflect coherent motion of the N-domain. The anisotropic ellipsoids of motion at the 90% probability level for the a-carbon atoms of helices aN1 and aN2 highlight the mobility of the main-chain atoms of the N-domain. The principal axes of vibration along both of the helices are largely coherent ( vert, similar up and down; compare with the ellipsoids near residue 1). The direction of this motion (presumably trapped substrates in the crystal) is similar to that seen between the apo and GDP complex crystal structures.

Figure 8.
Figure 8. Conserved residues at the NG interface contribute to a well-packed interface. Small probe contact dots[8] are shown at a dot density of 50 dots/Å2. The color of the dots indicates the types of interactions, with blue dots indicating wide contacts, greater than 0.25 Å, green indicating close contacts between 0 Å and 0.25 Å, yellow indicating small overlaps of less than 0.2 Å, and purple indicating hydrogen bonds. Hydrogen atoms are included in the analysis, but are not shown in the Figure. (a) The packing density around Gly253 and Gly254 (at the center) is especially tight for glycine residues and thus explains conservation of these two residues. (b) Leu257 appears to have relatively few interactions; however, those are with highly conserved residues, including Leu5, Val43, Leu38, and Leu82. Note the interaction between Leu5 and Leu257, which involves methyl hydrogen atoms of the two residues. (c) Interactions with Ser258, which is a completely conserved residue in the SRP GTPases. Both the Gly253/Gly254 and Ser258 interactions serve as the "glue" across the N/G interaction surface.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 320, 783-799) copyright 2002.

Figures were selected by the author.