PDBsum entry 2ffh

Protein transport

PDB id: 2ffh

Contents

Protein chains

407 a.a. *

Ligands

SO4 ×3

Metals

_CD ×16

* Residue conservation analysis

PDB id:

2ffh

Name:

Protein transport

Title:

The signal sequence binding protein ffh from thermus aquaticus

Structure:

Protein (ffh). Chain: a, b, c. Fragment: residues 1-425. Synonym: fifty-four homolog, p48. Engineered: yes. Mutation: yes. Other_details: the expression insert was generated by pcr

Source:

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

Biol. unit:

Hexamer (from PQS)

Resolution:

3.20Å R-factor: 0.257 R-free: 0.296

Authors:

R.J.Keenan,D.M.Freymann,P.Walter,R.M.Stroud

Key ref:

R.J.Keenan et al. (1998). Crystal structure of the signal sequence binding subunit of the signal recognition particle. Cell, 94, 181-191. PubMed id: 9695947 DOI: 10.1016/S0092-8674(00)81418-X

Date:

29-Jun-99 Release date: 16-Jul-99

Protein chains

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

Seq: 430 a.a.

Struc: 407 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1016/S0092-8674(00)81418-X

Cell 94:181-191 (1998)

PubMed id: 9695947

Crystal structure of the signal sequence binding subunit of the signal recognition particle.

R.J.Keenan, D.M.Freymann, P.Walter, R.M.Stroud.

ABSTRACT

The crystal structure of the signal sequence binding subunit of the signal recognition particle (SRP) from Thermus aquaticus reveals a deep groove bounded by a flexible loop and lined with side chains of conserved hydrophobic residues. The groove defines a flexible, hydrophobic environment that is likely to contribute to the structural plasticity necessary for SRP to bind signal sequences of different lengths and amino acid sequence. The structure also reveals a helix-turn-helix motif containing an arginine-rich alpha helix that is required for binding to SRP RNA and is implicated in forming the core of an extended RNA binding surface.

Selected figure(s)

Figure 6.
Figure 6. The Hydrophobic Groove of the M Domain Is Not Empty in the CrystalThe flexible finger loop of one M domain (magenta; residues 337–355 shown) inserts into the proposed signal sequence binding groove of another M domain (white, molecular surface representation), forming a hydrophobic cavity in the center of the groove that may contain detergent from the crystallization solution. This protein–protein interaction may represent an example of the extent to which the M domain has evolved to accommodate a wide variety of hydrophobic sequences.

Figure 7.
Figure 7. The Arginine-Rich, Helix-Turn-Helix Motif of the M Domain(A) Stereo view of the HTH motif (αM3 to αM4) and a third helix (αM2) of the M domain (green) superimposed onto the corresponding region from the lac repressor (blue) ([9]). The least-squares overlap of α carbons was performed using LSQMAN ( [24]). Conserved residues contributing to the compact hydrophobic core of the lac repressor are indicated, along with their counterparts in the M domain. Helix αM4 extends beyond helix α2 of the lac repressor by vert, similar 3 additional turns and contains basic residues at an extended C terminus; these characteristics are similar to the recognition helix of homeodomain DNA-binding proteins ([14]).(B) Stereo view of the conserved SRP RNA-binding motif of Ffh. This view is rotated vert, similar 90° about the vertical axis with respect to the orientation in Figure 7A. Positively charged side chains located in helix αM3 are likely to mediate the specific interaction of the M domain with SRP RNA. Arg-387 and Arg-361 form well-ordered salt bridges with the conserved residues Glu-373 and Glu-398, respectively.

The above figures are reprinted by permission from Cell Press: Cell (1998, 94, 181-191) copyright 1998.

Figures were selected by an automated process.