PDBsum entry 1fx3

Transport protein

PDB id: 1fx3

Contents

Protein chains

143 a.a. *

135 a.a. *

Waters ×63

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure of the bacterial protein export chaperone secb.

Authors

Z.Xu, J.D.Knafels, K.Yoshino.

Ref.

Nat Struct Biol, 2000, 7, 1172-1177. [DOI no: 10.1038/82040]

PubMed id

11101901

Abstract

SecB is a bacterial molecular chaperone involved in mediating translocation of newly synthesized polypeptides across the cytoplasmic membrane of bacteria. The crystal structure of SecB from Haemophilus influenzae shows that the molecule is a tetramer organized as a dimer of dimers. Two long channels run along the side of the molecule. These are bounded by flexible loops and lined with conserved hydrophobic amino acids, which define a suitable environment for binding non-native polypeptides. The structure also reveals an acidic region on the top surface of the molecule, several residues of which have been implicated in binding to SecA, its downstream target.

Figure 3.
Figure 3. The proposed peptide binding channel. a, The solvent accessible surface of SecB. On the left, the exposed surface is colored based on the underlying atoms: all backbone atoms, white; all noncharged polar and charged chain atoms (Asn, Gln, Ser, Thr, Cys, Asp, Glu, Arg, Lys and His), blue; all hydrophobic side chain atoms (Ala, Val, Leu, Ile, Pro, Phe, Tyr, Trp and Met), yellow. On the right, the exposed surface encompassing the two proposed peptide binding subsites is highlighted. b, Ribbon drawing of the SecB tetramer viewed from the side of the molecule. The orientation is the same as in (a). The two subsites are shown in two zoom-in views. Residues lining subsite 1 are colored purple and those lining subsite 2 are colored cyan. For the purpose of clarity, only one subunit was drawn in each of the zoom-in views. The residues lining the two sites are all hydrophobic with the exception of Thr 53. c, Schematic drawing of a PTB domain and a SecB monomer. The shared structural motif is highlighted in gray. The peptide binding sites are represented by hatched rectangles. Grasp36 was used to produce (a); Molscript34 and POV-ray35 were used to produce (b).

Figure 4.
Figure 4. The proposed SecA binding site. The orientation is orthogonal to that in Fig. 3. The drawing on the left is the solvent accessible surface of the SecB tetramer. The surface encompassing Asp 27, Glu 31, and Glu 86 is colored green; the surface encompassing Ile 84 is colored yellow. These four residues have been shown to be important for SecB's interaction with SecA^7, 16. The drawing on the right is the same surface except that it is colored based on the electrostatic potential of the molecule (ranging from -10 to +10kT). Figure produced using Grasp36.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 1172-1177) copyright 2000.