PDBsum entry 1qzx

Signaling protein

PDB id: 1qzx

Contents

Protein chains

425 a.a. *

* Residue conservation analysis

PDB id:

1qzx

Name:

Signaling protein

Title:

Crystal structure of the complete core of archaeal srp and implications for inter-domain communication

Structure:

Signal recognition 54 kda protein. Chain: a, b. Synonym: srp54. Engineered: yes

Source:

Sulfolobus solfataricus. Organism_taxid: 2287. Gene: srp54. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

4.00Å R-factor: 0.313 R-free: 0.383

Authors:

K.R.Rosendal,K.Wild,G.Montoya,I.Sinning

Key ref:

K.R.Rosendal et al. (2003). Crystal structure of the complete core of archaeal signal recognition particle and implications for interdomain communication. Proc Natl Acad Sci U S A, 100, 14701-14706. PubMed id: 14657338 DOI: 10.1073/pnas.2436132100

Date:

18-Sep-03 Release date: 18-Nov-03

Protein chains

Q97ZE7  (SRP54_SULSO) -  Signal recognition particle 54 kDa protein from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 447 a.a.

Struc: 425 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: 10.1073/pnas.2436132100

Proc Natl Acad Sci U S A 100:14701-14706 (2003)

PubMed id: 14657338

Crystal structure of the complete core of archaeal signal recognition particle and implications for interdomain communication.

K.R.Rosendal, K.Wild, G.Montoya, I.Sinning.

ABSTRACT

Targeting of secretory and membrane proteins by the signal recognition particle (SRP) is evolutionarily conserved, and the multidomain protein SRP54 acts as the key player in SRP-mediated protein transport. Binding of a signal peptide to SRP54 at the ribosome is coordinated with GTP binding and subsequent complex formation with the SRP receptor. Because these functions are localized to distinct domains of SRP54, communication between them is essential. We report the crystal structures of SRP54 from the Archaeon Sulfolobus solfataricus with and without its cognate SRP RNA binding site (helix 8) at 4-A resolution. The two structures show the flexibility of the SRP core and the position of SRP54 relative to the RNA. A long linker helix connects the GTPase (G domain) with the signal peptide binding (M) domain, and a hydrophobic contact between the N and M domains relates the signal peptide binding site to the G domain. Hinge regions are identified in the linker between the G and M domains (292-LGMGD) and in the N-terminal part of the M domain, which allow for structural rearrangements within SRP54 upon signal peptide binding at the ribosome.

Selected figure(s)

Figure 2.
Fig. 2. Superposition of SRP54 with (red) and without (blue) RNA shown as a ribbon diagram. The RNA is omitted for clarity. A rotation axis (green) has been identified between the N and M domains by the program DYNDOM (50); the flexibility of SRP54 is indicated by a black arrow.

Figure 4.
Fig. 4. Structure of the proposed signal peptide binding site. (A) Closed conformation of the hydrophobic groove in the S. solfataricus SRP54/RNA complex. The finger loop is folded into the groove. Helix ML is not shown for clarity. Elements involved in signal peptide binding are named. (B) Superposition of the M domain of S. solfataricus (red) and T. aquaticus (blue) to visualize the different conformations of the signal peptide binding groove including the finger loop and helix M1b. Movements between structures are indicated by black arrows. The position of the conserved motifs GP (green) and PG (pink) differ significantly, the two "anchor" points (Leu-329 and Ile-374) are marked as spheres. (C) Structure of the M domain of T. aquaticus Ffh with the finger loop in an open conformation. A putative signal peptide (gray cylinder) is modeled into the binding site. (D) Model for the conformational changes in the SRP core. SRP54 is shown in a ribbon diagram; color code is as in Fig. 1 A. Rearrangements in SRP54 upon interaction with a signal peptide at the ribosome (see text) are indicated by arrows, the linker region LGMGD is indicated by a blue sphere, the anchor points Leu-329 and the N terminus of helix M2 (Ile-374) as well as the GP and PG motifs are shown as pink spheres. The M[N] domain is adjusted at the four pink spheres to adopt a conformation competent for signal peptide binding as shown in C. The GTP (space-filling model) and the signal peptide (gray cylinder) are placed in their respective binding sites.

Figures were selected by an automated process.