Allosteric Activation of DegS, a Stress Sensor PDZ Protease

Sohn, Jungsan; Grant, Robert A.; Sauer, Robert T.

doi:10.1016/j.cell.2007.08.044

Cited by 113 publications

(217 citation statements)

References 40 publications

Supporting

Mentioning

200

Contrasting

Order By: Relevance

“…Recent study showed that ligand binding to PDZ1 induces an allosteric activation of DegP (39). Similar PDZ-ligand-dependent activation has also been reported for DegS, a DegP homolog (9,10). RseP and DegP are similar in that they have tandem PDZ domains, but the roles of these domains appear to be different between these two enzymes.…”

Section: Discussionmentioning

confidence: 72%

A Pair of Circularly Permutated PDZ Domains Control RseP, the S2P Family Intramembrane Protease of Escherichia coli

Inaba

Suzuki

Maegawa

et al. 2008

Journal of Biological Chemistry

View full text Add to dashboard Cite

TheE pathway of extracytoplasmic stress responses in Escherichia coli is activated through sequential cleavages of the anti-E protein, RseA, by membrane proteases DegS and RseP. Without the first cleavage by DegS, RseP is unable to cleave full-length RseA. We previously showed that a PDZ-like domain in the RseP periplasmic region is essential for this negative regulation of RseP. We now isolated additional deregulated RseP mutants. Many of the mutations affected a periplasmic region that is N-terminal to the previously defined PDZ domain. We expressed these regions and determined their crystal structures. Consistent with a recent prediction, our results indicate that RseP has tandem, circularly permutated PDZ domains (PDZ-N and PDZ-C). Strikingly, almost all the strong mutations have been mapped around the ligand binding cleft region in PDZ-N. These results together with those of an in vitro reaction reproducing the two-step RseA cleavage suggest that the proteolytic function of RseP is controlled by ligand binding to PDZ-N.

show abstract

Section: Discussionmentioning

confidence: 72%

A Pair of Circularly Permutated PDZ Domains Control RseP, the S2P Family Intramembrane Protease of Escherichia coli

Inaba

Suzuki

Maegawa

et al. 2008

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…DegS is a DegP paralog that contains a protease domain and one PDZ domain and functions as a stable trimer (16)(17)(18). Substrates bind and activate DegS in a positively cooperative reaction that involves a transition from a proteolytically inactive trimer to an active trimer and is fit well by the concerted Monod-WymanChangeux model of allostery (19,20).…”

Section: Discussionmentioning

confidence: 93%

Cage assembly of DegP protease is not required for substrate-dependent regulation of proteolytic activity or high-temperature cell survival

Kim

Sauer

2012

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

DegP, a member of the highly conserved HtrA family, performs quality-control degradation of misfolded proteins in the periplasm of Gram-negative bacteria and is required for high-temperature survival of Escherichia coli. Substrate binding transforms DegP from an inactive oligomer containing two trimers into active polyhedral cages, typically containing four or eight trimers. Although these observations suggest a causal connection, we show that cage assembly and proteolytic activation can be uncoupled. Indeed, DegP variants that remain trimeric, hexameric, or dodecameric in the presence or absence of substrate still display robust and positively cooperative substrate degradation in vitro and, most importantly, sustain high-temperature bacterial growth as well as the wild-type enzyme. Our results support a model in which substrate binding converts inactive trimers into proteolytically active trimers, and simultaneously leads to cage assembly by enhancing binding of PDZ1 domains in one trimer to PDZ2′ domains in neighboring trimers. Thus, both processes depend on substrate binding, but they can be uncoupled without loss of biological function. We discuss potential coupling mechanisms and why cage formation may have evolved if it is not required for DegP proteolysis. macromolecular assembly | periplasmic degradation | protein quality control | stress survival E fficient proteolytic removal of misfolded and/or damaged proteins is essential for intracellular protein-quality control, but degradation of the wrong proteins can waste cellular resources and destroy essential proteins. Thus, controlling the activity and specificity of intracellular proteases is critical for maintaining viability. The DegP protease is a member of the HtrA family, functions in the periplasm of Gram-negative bacteria, is essential for survival of Escherichia coli at high temperatures, and its expression is increased substantially following heat shock or other stresses that result in protein misfolding (1-6).The fundamental structural unit of DegP is a trimer (7), which is stabilized by contacts between trypsin-like protease domains, each of which contains a conventional Ser-His-Asp catalytic triad and has two attached PDZ domains ( Fig. 1 A and B). In the absence of substrate, two DegP trimers stack face-to-face in an inactive hexamer with malformed active sites (Fig. 1C, Left) (7). Intriguingly, when protein substrates are added, DegP assembles into cage-like polyhedrons (Fig. 1C) that can contain 4, 6, 8, or more trimers (8-10). Packing between PDZ1 domains in one trimer and PDZ2′ domains in neighboring trimers stabilize these cages (Fig. 1D). The active sites are inside these cages and can degrade unfolded substrates that were trapped by assembly or subsequently diffuse into the chamber through openings at the cage vertices.The best model substrates for DegP contain a hydrophobic Cterminal residue, which binds in a pocket in the PDZ1 domain, and a hydrophobic residue at the P1 position of the scissile peptide bond, which binds in the active...

show abstract

“…For example, the PDZ domain of Par6 alters its binding affinity for ligand upon binding of Cdc42 to the semi-Crib motif, which is immediately N-terminal to the PDZ domain, and augments its ␤-sheet (18). In a reverse sense, "PDZ proteases" are regulated by ligand-induced changes in PDZ structure (20). PDZ function has also been shown to be regulated by redox events within the PDZ domain (44), and this redox potential can be allosterically regulated by binding to yet another PDZ domain (45).…”

Section: Discussionmentioning

confidence: 99%

Phosphorylation of a PDZ Domain Extension Modulates Binding Affinity and Interdomain Interactions in Postsynaptic Density-95 (PSD-95) Protein, a Membrane-associated Guanylate Kinase (MAGUK)

Zhang

Petit

King

et al. 2011

Journal of Biological Chemistry

View full text Add to dashboard Cite

Postsynaptic density-95 is a multidomain scaffolding protein that recruits glutamate receptors to postsynaptic sites and facilitates signal processing and connection to the cytoskeleton. It is the leading member of the membrane-associated guanylate kinase family of proteins, which are defined by the PSD-95/ Discs large/ZO-1 (PDZ)-Src homology 3 (SH3)-guanylate kinase domain sequence. We used NMR to show that phosphorylation of conserved tyrosine 397, which occurs in vivo and is located in an atypical helical extension (␣3), initiates a rapid equilibrium of docked and undocked conformations. Undocking reduced ligand binding affinity allosterically and weakened the interaction of PDZ3 with SH3 even though these domains are separated by a ϳ25-residue linker. Additional phosphorylation at two linker sites further disrupted the interaction, implicating ␣3 and the linker in tuning interdomain communication. These experiments revealed a novel mode of regulation by a detachable PDZ element and offer a first glimpse at the dynamic interaction of PDZ and SH3-guanylate kinase domains in membrane-associated guanylate kinases.Phosphorylation is one of the most common modifications made to proteins. Depending on the protein substrate, it can regulate the gain or loss of activity through a variety of mechanisms. Most mechanisms studied to date appear to work via a change in steric geometry at the active site or a global conformational change in the protein (1-3), although a few recent examples indicate modulation of protein dynamics that can yield a graded response (4, 5). In some cases, phosphorylation simply provides a protein-protein recognition site (6). Overall, the extent of structural characterization of phosphorylation mechanisms is limited given the ubiquity of this post-translational signaling mechanism and the large diversity of effects observed upon phosphorylation. A greater understanding of how phosphorylation(s) modulates protein activity is essential for a mechanistic understanding of signal transduction.Many phosphorylated proteins are multidomain, modular proteins (2-4). One class of such proteins that shape signal transduction is the scaffolding proteins, which are frequently phosphorylated (7). Membrane-associated guanylate kinase (MAGUK) 2 family proteins are multidomain scaffolding proteins that play roles in ion channel clustering, intracellular trafficking, signal transduction, and cell-cell adhesion (8 -10). Malfunction of MAGUKs is associated with central nervous system disorders (11). The defining MAGUK signature is the PDZ-SH3-guanylate kinase "supradomain" architecture. The best known MAGUK protein is postsynaptic density-95 (PSD-95), which is found on the cytoplasmic side of postsynaptic terminals. PSD-95 is a non-catalytic scaffolding protein that clusters glutamate receptors and assembles macromolecular complexes for signal integration in the postsynapse at excitatory neurons (8,12). It consists of three PDZ domains, an SH3 domain, and a non-catalytic guanylate kinase (GK) domain (see Fig. 1A). ...

show abstract

Allosteric Activation of DegS, a Stress Sensor PDZ Protease

Cited by 113 publications

References 40 publications

A Pair of Circularly Permutated PDZ Domains Control RseP, the S2P Family Intramembrane Protease of Escherichia coli

A Pair of Circularly Permutated PDZ Domains Control RseP, the S2P Family Intramembrane Protease of Escherichia coli

Cage assembly of DegP protease is not required for substrate-dependent regulation of proteolytic activity or high-temperature cell survival

Phosphorylation of a PDZ Domain Extension Modulates Binding Affinity and Interdomain Interactions in Postsynaptic Density-95 (PSD-95) Protein, a Membrane-associated Guanylate Kinase (MAGUK)

Contact Info

Product

Resources

About