PDBsum entry 1vcw

Hydrolase

PDB id: 1vcw

Contents

Protein chains

291 a.a. *

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure of the degs stress sensor: how a pdz domain recognizes misfolded protein and activates a protease.

Authors

C.Wilken, K.Kitzing, R.Kurzbauer, M.Ehrmann, T.Clausen.

Ref.

Cell, 2004, 117, 483-494. [DOI no: 10.1016/S0092-8674(04)00454-4]

PubMed id

15137941

Abstract

Gram-negative bacteria respond to misfolded proteins in the cell envelope with the sigmaE-driven expression of periplasmic proteases/chaperones. Activation of sigmaE is controlled by a proteolytic cascade that is initiated by the DegS protease. DegS senses misfolded protein in the periplasm, undergoes autoactivation, and cleaves the antisigma factor RseA. Here, we present the crystal structures of three distinct states of DegS from E. coli. DegS alone exists in a catalytically inactive form. Binding of stress-signaling peptides to its PDZ domain induces a series of conformational changes that activates protease function. Backsoaking of crystals containing the DegS-activator complex revealed the presence of an active/inactive hybrid structure and demonstrated the reversibility of activation. Taken together, the structural data illustrate in molecular detail how DegS acts as a periplasmic stress sensor. Our results suggest a novel regulatory role for PDZ domains and unveil a novel mechanism of reversible protease activation.

Figure 4.
Figure 4. Reversible Activation of DegS(A) The present structural data allow the description of three different states I, II, and III, which are defined by the conformation of the activation domain (Act: loops L1/L2/LD) and of loop L3. The molecular surfaces of the respective trimers are represented using a specific color code for the defining structural elements (red: peptide-free, green: peptide-bound conformation). The corresponding protomers are shown in a ribbon presentation. Structure III represents a hybrid structure with the activation domain in its active and loop L3 in its inactive conformation.(B) Stereo plot showing the active state of the activation domain with the newly formed interactions between loops L3/L2 of one subunit (green) and L1*/LD* of the molecular neighbor (light green). The model is shown together with the final 2Fo-Fc electron density map calculated at 2.4 Å resolution and contoured at 1.2 σ.(C) The ribbon plot shows the protease domain of DegS with mapped thermal motion factors (blue: rigid parts, red: flexible parts). The relevant active site loops are labeled. Note that only loops comprising the activation domain (L1, L2, LD) become more rigid, whereas loop L3 is still flexible. The average B values for the protease domain, LD, L1, L2, L3 are 41.2, 87.3, 70.9, n.d., 69.3 for the uncomplexed and 71.3, 61.0, 58.6, 110.5, 128.1 for the active form, respectively.

Figure 6.
Figure 6. Comparison of DegS and HtrA2 (Omi)The stereo picture shows an alignment of active DegS (green), inactive DegS (red), and HtrA2 (yellow). The chosen segment comprises DegS residues 195–204 (HtrA2 167–176), which include the active site serine and loop L1 that forms the oxyanion hole. Key residues are indicated as well as the 198 peptide that is important for DegS activation. Notably, the L1 backbone of HtrA2 has a similar turn structure as the inactive DegS.

The above figures are reprinted by permission from Cell Press: Cell (2004, 117, 483-494) copyright 2004.

Secondary reference #1

Title

Omp peptide signals initiate the envelope-Stress response by activating degs protease via relief of inhibition mediated by its pdz domain.

Authors

N.P.Walsh, B.M.Alba, B.Bose, C.A.Gross, R.T.Sauer.

Ref.

Cell, 2003, 113, 61-71. [DOI no: 10.1016/S0092-8674(03)00203-4]

PubMed id

12679035

Figure 2.
Figure 2. Binding of the YYF-COOH Peptide to the DegS PDZ Domain(A) HSQC NMR resonances of the ^15N-labeled DegS PDZ domain are shown in black. Resonances observed after addition of a roughly equivalent amount of the YYF-COOH peptide are shown in red. PDZ regions whose resonances shifted by more than 0.05 ppm are colored green in the model in the inset.(B) Binding of 6 μl aliquots of the YYF-COOH peptide (1.2 mM) to a solution of the DegS PDZ domain (77 μM) monitored by isothermal titration calorimetry. Both solutions contained 50 mM NaPO[4] [pH 7.5]. The black line is a fit of the experimental data to a binding isotherm with a K[d] of 0.52 μM and N = 1.02.

Figure 6.
Figure 6. Model for Peptide-Dependent Activation of DegSFor simplicity, DegS is shown as a monomer instead of a trimer.

The above figures are reproduced from the cited reference with permission from Cell Press