PDBsum entry 3gdv

Hydrolase/hydrolase activator

PDB id: 3gdv

Contents

Protein chains

296 a.a. *

Ligands

TYR-GLN-PHE ×3

Waters ×78

* Residue conservation analysis

PDB id:

3gdv

Name:

Hydrolase/hydrolase activator

Title:

Crystal structure of degs h198p/d320a mutant modified by dfp and in complex with yqf peptide

Structure:

Degs protease. Chain: a, b, c. Fragment: full-length without membrane anchor. Engineered: yes. Mutation: yes. Yqf peptide. Chain: d, e, f. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k-12. Gene: b3235, degs, hhob, htrh, jw3204. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes

Resolution:

2.49Å R-factor: 0.193 R-free: 0.224

Authors:

J.Sohn,R.A.Grant,R.T.Sauer

Key ref:

J.Sohn et al. (2009). OMP peptides activate the DegS stress-sensor protease by a relief of inhibition mechanism. Structure, 17, 1411-1421. PubMed id: 19836340 DOI: 10.1016/j.str.2009.07.017

Date:

24-Feb-09 Release date: 31-Mar-09

Protein chains

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

Seq: 355 a.a.

Struc: 296 a.a.*

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

Enzyme reactions

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

DOI no: 10.1016/j.str.2009.07.017

Structure 17:1411-1421 (2009)

PubMed id: 19836340

OMP peptides activate the DegS stress-sensor protease by a relief of inhibition mechanism.

J.Sohn, R.A.Grant, R.T.Sauer.

ABSTRACT

In the E. coli periplasm, C-terminal peptides of misfolded outer-membrane porins (OMPs) bind to the PDZ domains of the trimeric DegS protease, triggering cleavage of a transmembrane regulator and transcriptional activation of stress genes. We show that an active-site DegS mutation partially bypasses the requirement for peptide activation and acts synergistically with mutations that disrupt contacts between the protease and PDZ domains. Biochemical results support an allosteric model, in which these mutations, active-site modification, and peptide/substrate binding act in concert to stabilize proteolytically active DegS. Cocrystal structures of DegS in complex with different OMP peptides reveal activation of the protease domain with varied conformations of the PDZ domain and without specific contacts from the bound OMP peptide. Taken together, these results indicate that the binding of OMP peptides activates proteolysis principally by relieving inhibitory contacts between the PDZ domain and the protease domain of DegS.

Selected figure(s)

Figure 3.
Figure 3. Structures
(A) Cartoon representation of the OMP-peptide bound H198P/D320A DegS trimer (3GDV). The protease domains of different subunits are colored green, cyan, and magenta, except the L3 loop, which is colored black; the PDZ domains are colored slate blue. The YQF OMP peptide and the modified active-site serine (Mis^201) are shown in CPK representation.
(B) Interactions near the active site of the 3GDV structure. The O1P oxygen of Mis^201 (2F[o]-F[c] electron density contoured at 1.6 σ) accepts hydrogen bonds from the -NH groups of the oxyanion hole. Packing interactions between the pyrrolidine ring of Pro^198 and the aromatic ring of Tyr^162 help to stabilize the hydrogen bond between backbone carbonyl oxygen and -NH groups of these amino acids and therefore stabilize the functional active site.
(C) The peptide-bound 1SOZ structure (Wilken et al., 2004) and our peptide-bound 3GCO structure have very similar conformations near the active site, except for the modification of Ser^201 in 3CGO and the His^198→Pro sequence change. In the 3GCO structure, Leu^218 and Ser^219 in the S1-specificity pocket move to some degree to accommodate the isopropyl moiety of Mis^201, which mimics the P1 side chain of a substrate.

Figure 5.
Figure 5. Models for DegS Activation
(A) The inhibition-relief model posits an equilibrium between free inactive trimers (open squares) and free active trimers (open circles). OMP peptides bind to both states (shaded circles or squares) and shift the equilibrium toward the active form because they bind more tightly to this conformation than the inactive conformation.
(B) The peptide-activation model posits that different OMP peptides stabilize slightly different DegS conformations, in which the precise activity depends on the identity of the penultimate side-chain of the bound peptide.

The above figures are reprinted by permission from Cell Press: Structure (2009, 17, 1411-1421) copyright 2009.

Figures were selected by an automated process.