PDBsum entry 2iyl

Cell cycle

PDB id

2iyl

Contents

			Protein chain

					271 a.a.

			Ligands

					GDP


					SO4 ×2

			Waters ×144

References listed in PDB file

Key reference

Title

X-Ray structure of the t. Aquaticus ftsy:gdp complex suggests functional roles for the c-Terminal helix of the srp gtpases.

Authors

J.Gawronski-Salerno, J.S.Coon, P.J.Focia, D.M.Freymann.

Ref.

Proteins, 2007, 66, 984-995. [DOI no: 10.1002/prot.21200]

PubMed id

17186523

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a perfect match.

Abstract

FtsY and Ffh are structurally similar prokaryotic Signal Recognition Particle GTPases that play an essential role in the Signal Recognition Particle (SRP)-mediated cotranslational targeting of proteins to the membrane. The two GTPases assemble in a GTP-dependent manner to form a heterodimeric SRP targeting complex. We report here the 2.1 A X-ray structure of FtsY from T. aquaticus bound to GDP. The structure of the monomeric protein reveals, unexpectedly, canonical binding interactions for GDP. A comparison of the structures of the monomeric and complexed FtsY NG GTPase domain suggests that it undergoes a conformational change similar to that of Ffh NG during the assembly of the symmetric heterodimeric complex. However, in contrast to Ffh, in which the C-terminal helix shifts independently of the other subdomains, the C-terminal helix and N domain of T. aquaticus FtsY together behave as a rigid body during assembly, suggesting distinct mechanisms by which the interactions of the NG domain "module" are regulated in the context of the two SRP GTPases.



	Figure 3. Figure 3. Common features of the structures of FtsY from different species. (A) Structures of FtsY from T. aquaticus, E. coli, M. mycoides, and T. maritima are aligned using a superimposition based on the motif I P-loop; the 1 helix that follows the motif is vertical at the center of each image. The 4 helix (labeled) defines the interface between the N and G subdomains. The C-terminal helix (highlighted in red) adopts a similar configuration in each of the structures, despite the slightly different orientation of each N domain. In the structures of the apo M. mycoides and T. maritima FtsY an N-terminal helix extension ( N1 , highlighted in blue) packs between the C-terminal helix and the N/G interface. In the E. coli structure the N-terminal polypeptide is poorly structured (blue coil) but appears to play a similar role. The GDP in the T. aquaticus FtsY complex is indicated with a CPK model. In each structure of the apo or GDP-bound state of FtsY shown here, the motif II and motif III loops (labeled) adopt distinct (or disordered) conformations. (B) The N/G linker peptide packs across a crystal contact, occupying space that would accommodate the N1 N-terminal helix seen in other structures of FtsY. The position of the N1 helix is indicated by a ghosted cylinder. The backbone atoms of the linker splayed across the crystal contact are shown as sticks; the hydrophobic sidechains of Leu^88, Phe^90, and Pro^92 (ball-and-stick) pack into a conserved hydrophobic pocket at the interface. The orientation of the C-terminal helix, C, is indicated by an axis line. The ribbon representation includes helices N2 and N4 of the N domain, and the 4 helix, the motif IV/DARGG loop that precedes it, and the closing loop (bottom) of the G domain, which together contribute to the hydrophobic pocket at the N/G interface.		Figure 5. Figure 5. The nucleotide position slips between the GDP and GMPPCP states. Following superposition of the FtsY:GDP monomeric and FtsY:GMPPCP complexed states of FtsY over the motif I P-loop (at right), the - and -phosphate groups of GDP and GMPPCP (labeled) remain fixed relative to each other, but the ribose and the guanine base shift by 1 Å between the two structures (1.04 Å at the 2-amino nitrogen, as indicated). This slip is tracked by movement of the motif IV loop and by the specificity determining carboxylate sidechain of Asp^258.

PROCHECK

	Headers