PDBsum entry 1te0

Hydrolase

PDB id: 1te0

Contents

Protein chains

318 a.a. *

Waters ×163

* Residue conservation analysis

PDB id:

1te0

Name:

Hydrolase

Title:

Structural analysis of degs, a stress sensor of the bacterial periplasm

Structure:

Protease degs. Chain: a, b. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: degs, hhob, htrh, b3235, z4594, ecs4108. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Trimer (from PDB file)

Resolution:

2.20Å R-factor: 0.247 R-free: 0.295

Authors:

R.B.G.Ravelli,K.Zeth

Key ref:

K.Zeth (2004). Structural analysis of DegS, a stress sensor of the bacterial periplasm. FEBS Lett, 569, 351-358. PubMed id: 15225661 DOI: 10.1016/j.febslet.2004.06.012

Date:

24-May-04 Release date: 30-Nov-04

Protein chains

P0AEE3  (DEGS_ECOLI) -  Serine endoprotease DegS from Escherichia coli (strain K12)

Seq: 355 a.a.

Struc: 318 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.4.21.107 - peptidase Do.

DOI no: 10.1016/j.febslet.2004.06.012

FEBS Lett 569:351-358 (2004)

PubMed id: 15225661

Structural analysis of DegS, a stress sensor of the bacterial periplasm.

K.Zeth.

ABSTRACT

Regulated proteolysis is a key event in transmembrane signalling between intracellular compartments. In Escherichia coli the membrane-bound protease DegS has been identified as the periplasmic stress sensor for unfolded outer membrane proteins (OMPs). DegS inititates a proteolytic cascade resulting in the release of sigmaE the transcription factor of periplasmic genes. The crystal structure of DegS protease reported at 2.2 A resolution reveals a trimeric complex with the monomeric protease domain in an inhibited state followed by the inhibitory PDZ domain. Noteably, domain architecture and communication of DegS are remarkably to homologous proteins known to date. Here the domain interface is mechanically locked by three intradomain salt bridges. Co-crystallisation trials in the presence of a 10-residue activating peptide did not result in significant structural intradomain shifts nor distortions in the crystal packing. These observations imply a mode of activation indicative of peptide-induced structural shifts imposed to the protease domain rather than disturbing the PDZ-protease interface.

Selected figure(s)

Figure 1.
Fig. 1. Crystal structure of the substrate sensor DegS from E. coli. (a) Schematic representation of DegS structure showing the protease domain in brown and the PDZ domain in blue. N- and C-termini (NT, CT), the β-strands (β1–β18), α-helices (α1–α9) and loop structures (L1–L6) important for the function are indicated. Residues of the catalytic triade and the domain interface are highlighted and marked by dotted circles. (b) Close-up of the 2|F[obs]−F[calc]| electron density map calculated around the protease active center and contoured at 1.2σ. The residues forming the catalytic triade (His96, Asp126 and Ser201) are marked. (c) A close-up view of the intramolecular hydrophilic contacts between protease (brown) and PDZ (blue) domain. Important residues of the interface are marked with numbers according to the DegS sequence.

Figure 3.
Fig. 3. Structural comparison of Htra proteins. (a) Structural alignment of the protease backbone atoms. N- and C-termini (NT, CT), loop5 (L5) and resdiues of the catalytic triade are assigned in ball and stick for clarity. The following colour code was used: DegS is magenta, DegP is cyan and HtrA2/Omi is coloured in blue. (b) Structural alignment of the PDZ domain with the same colour code used in (a). Selected secondary structure elements are marked. (c) Overlay of the active site residues from DegS, DegP, HtrA2/Omi and trypsin (in green). Residue numbers are assigned with respect to the DegS sequence. (d) Crystal structure of DegP with the protease domain superimposed onto DegS and the domain colour code according to the DegS structure in Fig. 1(a). (e) Crystal structure of HtrA2/Omi with the protease domain structurally aligned to DegS and the same colour code as for figure (d).

The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2004, 569, 351-358) copyright 2004.

Figures were selected by an automated process.