PDBsum entry 1soz

Hydrolase

PDB id: 1soz

Contents

Protein chains

281 a.a. *

257 a.a. *

Ligands

VAL-TYR-GLN-PHE ×2

Waters ×224

* Residue conservation analysis

PDB id:

1soz

Name:

Hydrolase

Title:

Crystal structure of degs protease in complex with an activating peptide

Structure:

Protease degs. Chain: a, b, c. Engineered: yes. Activating peptide. Chain: d, e. 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. Synthetic: yes

Biol. unit:

Pentamer (from PQS)

Resolution:

2.40Å R-factor: 0.213 R-free: 0.272

Authors:

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

Key ref:

C.Wilken et al. (2004). Crystal structure of the DegS stress sensor: How a PDZ domain recognizes misfolded protein and activates a protease. Cell, 117, 483-494. PubMed id: 15137941 DOI: 10.1016/S0092-8674(04)00454-4

Date:

16-Mar-04 Release date: 08-Jun-04

Protein chains

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

Seq: 355 a.a.

Struc: 281 a.a.*

Protein chain

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

Seq: 355 a.a.

Struc: 257 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C: E.C.3.4.21.107 - peptidase Do.

DOI no: 10.1016/S0092-8674(04)00454-4

Cell 117:483-494 (2004)

PubMed id: 15137941

Crystal structure of the DegS stress sensor: How a PDZ domain recognizes misfolded protein and activates a protease.

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

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.

Selected figure(s)

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.

Figures were selected by an automated process.