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PDBsum entry 1te0

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protein Protein-protein interface(s) links
Hydrolase PDB id
1te0
Jmol
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 bacteria 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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AEE3  (DEGS_ECOLI) -  Serine endoprotease DegS
Seq:
Struc:
355 a.a.
318 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.107  - Peptidase Do.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     integral to external side of plasma membrane   5 terms 
  Biological process     cellular response to misfolded protein   2 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21247409 H.Schuhmann, U.Mogg, and I.Adamska (2011).
A new principle of oligomerization of plant DEG7 protease based on interactions of degenerated protease domains.
  Biochem J, 435, 167-174.  
19298369 B.O.Cezairliyan, and R.T.Sauer (2009).
Control of Pseudomonas aeruginosa AlgW protease cleavage of MucA by peptide signals and MucB.
  Mol Microbiol, 72, 368-379.  
19836340 J.Sohn, R.A.Grant, and R.T.Sauer (2009).
OMP peptides activate the DegS stress-sensor protease by a relief of inhibition mechanism.
  Structure, 17, 1411-1421.
PDB codes: 3gco 3gds 3gdu 3gdv
19150428 J.Sohn, and R.T.Sauer (2009).
OMP peptides modulate the activity of DegS protease by differential binding to active and inactive conformations.
  Mol Cell, 33, 64-74.  
18697939 J.Jiang, X.Zhang, Y.Chen, Y.Wu, Z.H.Zhou, Z.Chang, and S.F.Sui (2008).
Activation of DegP chaperone-protease via formation of large cage-like oligomers upon binding to substrate proteins.
  Proc Natl Acad Sci U S A, 105, 11939-11944.  
18174901 L.Vande Walle, M.Lamkanfi, and P.Vandenabeele (2008).
The mitochondrial serine protease HtrA2/Omi: an overview.
  Cell Death Differ, 15, 453-460.  
18983936 S.E.Ades (2008).
Regulation by destruction: design of the sigmaE envelope stress response.
  Curr Opin Microbiol, 11, 535-540.  
17981123 J.Sohn, R.A.Grant, and R.T.Sauer (2007).
Allosteric activation of DegS, a stress sensor PDZ protease.
  Cell, 131, 572-583.
PDB codes: 2qf0 2qf3 2qgr
17981109 N.Yan, and Y.Shi (2007).
Allosteric activation of a bacterial stress sensor.
  Cell, 131, 441-443.  
17962403 S.T.Runyon, Y.Zhang, B.A.Appleton, S.L.Sazinsky, P.Wu, B.Pan, C.Wiesmann, N.J.Skelton, and S.S.Sidhu (2007).
Structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3.
  Protein Sci, 16, 2454-2471.
PDB codes: 2joa 2p3w
  16946473 P.Wollmann, and K.Zeth (2006).
Expression, crystallization and preliminary X-ray analysis of the periplasmic stress sensory protein RseB from Escherichia coli.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 895-898.  
15978068 J.E.Mogensen, and D.E.Otzen (2005).
Interactions between folding factors and bacterial outer membrane proteins.
  Mol Microbiol, 57, 326-346.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.