PDBsum entry 1okk

Cell cycle

PDB id: 1okk

Contents

Protein chains

290 a.a. *

265 a.a. *

Ligands

GCP ×2

BZP ×2

SO4 ×11

EDO ×4

Metals

_MG ×2

Waters ×568

* Residue conservation analysis

PDB id:

1okk

Name:

Cell cycle

Title:

Homo-heterodimeric complex of the srp gtpases

Structure:

Signal recognition particle protein. Chain: a. Fragment: ng domain, residues 0-293. Synonym: fifty-four homolog, ffh. Engineered: yes. Cell division protein ftsy. Chain: d. Fragment: ng domain, residues 2-304. Engineered: yes

Source:

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

Biol. unit:

Dimer (from PDB file)

Resolution:

2.05Å R-factor: 0.156 R-free: 0.193

Authors:

P.J.Focia,D.M.Freymann

Key ref:

P.J.Focia et al. (2004). Heterodimeric GTPase core of the SRP targeting complex. Science, 303, 373-377. PubMed id: 14726591 DOI: 10.1126/science.1090827

Date:

26-Jul-03 Release date: 19-Jan-04

Protein chain

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

Seq: 430 a.a.

Struc: 290 a.a.

Protein chain

P83749  (FTSY_THEAQ) -  Signal recognition particle receptor FtsY from Thermus aquaticus

Seq: 304 a.a.

Struc: 265 a.a.

Enzyme reactions

• Enzyme class: Chains A, D: 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: 10.1126/science.1090827

Science 303:373-377 (2004)

PubMed id: 14726591

Heterodimeric GTPase core of the SRP targeting complex.

P.J.Focia, I.V.Shepotinovskaya, J.A.Seidler, D.M.Freymann.

ABSTRACT

Two structurally homologous guanosine triphosphatase (GTPase) domains interact directly during signal recognition particle (SRP)-mediated cotranslational targeting of proteins to the membrane. The 2.05 angstrom structure of a complex of the NG GTPase domains of Ffh and FtsY reveals a remarkably symmetric heterodimer sequestering a composite active site that contains two bound nucleotides. The structure explains the coordinate activation of the two GTPases. Conformational changes coupled to formation of their extensive interface may function allosterically to signal formation of the targeting complex to the signal-sequence binding site and the translocon. We propose that the complex represents a molecular "latch" and that its disengagement is regulated by completion of assembly of the GTPase active site.

Selected figure(s)

Figure 2.
Fig. 2. An extensive interaction surface. (A) The molecular surfaces of the Ffh monomer (left) and the FtsY monomer (right) are shown, shaded by the change in accessible surface area at each residue between the monomer and in the heterodimer. The blue areas define the protein-protein contact. The GTP binding motifs I to IV are indicated, and the Mg2+ nucleotide ligands are shown in ball and stick representation. A symmetric triangular contact region above the active site cavity is termed the latch. The IBD regions of the two proteins contact one another below the active site cleft. The packing orientation in the complex can be visualized by rotating the monomers to overlay the yellow asterisks. Arrows on the surface of the FtsY monomer highlight the orientation of the Asp/Lys framework (black) and the latch interface (pink) presented in the following panels. (B) The framework formed by Asp229(219) of the DGQ motif (see table S1) and Lys256(246) of motif IV from both monomers is shown superimposed to emphasize the symmetry between Ffh and FtsY in the complex. This symmetric interaction lies approximately along the diagonal ridge located above the active site clefts in (A). The lysine hydrogen bonds to both P-loops, thus bridging the interface. In all figures, residues from FtsY are labeled in gray italics font and from Ffh in black font. (C) The symmetric latch interface between the N and G domains, corresponding to the close loop contacts seen above the adjacent P-loops in Fig. 1A. The conserved hydrophobic residues of the ALLEADV motifs of the N domains (top) and the symmetric glycine pair of the DGQ motifs of the G domains (bottom) are shown along with the pair of bridging aspartate and glutamine residues.

Figure 3.
Fig. 3. Conformational changes generate the heterodimer interface. (A) The structure of the Ffh NG domain with GMPPNP bound (1JPJ [PDB] .pdb) (in lighter colors) is superimposed with its structure in the complex. The N domain moves as a rigid body toward helix 3 of the G domain; this shift, in turn, is coupled to conformational rearrangement in the DGQ motif at the N terminus of 3, enabling formation of the extensive heterodimeric contact there. Helix 4 moves with the N domain, accommodated by an 2.9 Å translation of the remainder of helix 3. Note the concurrent reorientation of the C-terminal helix. (B) G-domain conformational changes associated with complex formation are limited to the loops of conserved sequence motifs. The magnitude of the shifts are mapped so that the largest shifts ( 6.5 Å) are the darkest shaded regions. (C) Reorientation of motifs II and III upon complex formation. The left panel shows the Ffh NG GMPPNP structure, the right panel Ffh NG in the complex. The side chain of motif III residue Leu192 moves to insert into a pocket across the heterodimer interface, between the guanine base and Gly259(249) that follows motif IV. Movement of this leucine and the accompanying rearrangement of the motif III backbone allows the P-loop to open sufficiently to accommodate the nucleotide in an extended conformation (10). Motif II residues Asp135 and Arg138 move into the catalytic chamber. The same configuration is observed in FtsY.

The above figures are reprinted by permission from the AAAs: Science (2004, 303, 373-377) copyright 2004.

Figures were selected by an automated process.