scholarly journals Role of the PDZ Domains in Escherichia coli DegP Protein

2007 ◽  
Vol 189 (8) ◽  
pp. 3176-3186 ◽  
Author(s):  
Jack Iwanczyk ◽  
Daniela Damjanovic ◽  
Joel Kooistra ◽  
Vivian Leong ◽  
Ahmad Jomaa ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Protease Activity ◽  
Pdz Domain ◽  
Structural Features ◽  
Periplasmic Protein ◽  
Pdz Domains ◽  
Protease Domain ◽  
Interaction Domains ◽  
And Function

ABSTRACT PDZ domains are modular protein interaction domains that are present in metazoans and bacteria. These domains possess unique structural features that allow them to interact with the C-terminal residues of their ligands. The Escherichia coli essential periplasmic protein DegP contains two PDZ domains attached to the C-terminal end of the protease domain. In this study we examined the role of each PDZ domain in the protease and chaperone activities of this protein. Specifically, DegP mutants with either one or both PDZ domains deleted were generated and tested to determine their protease and chaperone activities, as well as their abilities to sequester unfolded substrates. We found that the PDZ domains in DegP have different roles; the PDZ1 domain is essential for protease activity and is responsible for recognizing and sequestering unfolded substrates through C-terminal tags, whereas the PDZ2 domain is mostly involved in maintaining the hexameric cage of DegP. Interestingly, neither of the PDZ domains was required for the chaperone activity of DegP. In addition, we found that the loops connecting the protease domain to PDZ1 and connecting PDZ1 to PDZ2 are also essential for the protease activity of the hexameric DegP protein. New insights into the roles of the PDZ domains in the structure and function of DegP are provided. These results imply that DegP recognizes substrate molecules targeted for degradation and substrate molecules targeted for refolding in different manners and suggest that the substrate recognition mechanisms may play a role in the protease-chaperone switch, dictating whether the substrate is degraded or refolded.

Structure and function of Escherichia coli DnaB protein: Role of the N-terminal domain in helicase activity

Biochemistry ◽  
1994 ◽  
Vol 33 (37) ◽  
pp. 11307-11314 ◽  
Author(s):  
Subhasis B. Biswas ◽  
Pei-Hua Chen ◽  
Esther E. Biswas
Keyword(s):  
Escherichia Coli ◽  
Structure And Function ◽  
Helicase Activity ◽  
Terminal Domain ◽  
And Function

scholarly journals Identification of PDZ Domain Containing Proteins Interacting with 1.2 and PMCA4b

2013 ◽  
Vol 2013 ◽  
pp. 1-16 ◽  
Author(s):  
Doreen Korb ◽  
Priscilla Y. Tng ◽  
Vladimir M. Milenkovic ◽  
Nadine Reichhart ◽  
Olaf Strauss ◽  
...  
Keyword(s):  
Pdz Domain ◽  
Pdz Domains ◽  
Hek 293 ◽  
Zonula Occludens ◽  
C Terminus ◽  
293 Cells ◽  
Interaction Partners ◽  
Voltage Dependent ◽  
Interaction Domains ◽  
Zonula Occludens 1

PDZ (PSD-95/Disc large/Zonula occludens-1) protein interaction domains bind to cytoplasmic protein C-termini of transmembrane proteins. In order to identify new interaction partners of the voltage-gated L-type Ca2+ channel 1.2 and the plasma membrane Ca2+ ATPase 4b (PMCA4b), we used PDZ domain arrays probing for 124 PDZ domains. We confirmed this by GST pull-downs and immunoprecipitations. In PDZ arrays, strongest interactions with 1.2 and PMCA4b were found for the PDZ domains of SAP-102, MAST-205, MAGI-1, MAGI-2, MAGI-3, and ZO-1. We observed binding of the 1.2 C-terminus to PDZ domains of NHERF1/2, Mint-2, and CASK. PMCA4b was observed to interact with Mint-2 and its known interactions with Chapsyn-110 and CASK were confirmed. Furthermore, we validated interaction of 1.2 and PMCA4b with NHERF1/2, CASK, MAST-205 and MAGI-3 via immunoprecipitation. We also verified the interaction of 1.2 and nNOS and hypothesized that nNOS overexpression might reduce Ca2+ influx through 1.2. To address this, we measured Ca2+ currents in HEK 293 cells co-expressing 1.2 and nNOS and observed reduced voltage-dependent 1.2 activation. Taken together, we conclude that 1.2 and PMCA4b bind promiscuously to various PDZ domains, and that our data provides the basis for further investigation of the physiological consequences of these interactions.

scholarly journals Sphingomyelin metabolism controls the shape and function of the Golgi cisternae

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Felix Campelo ◽  
Josse van Galen ◽  
Gabriele Turacchio ◽  
Seetharaman Parashuraman ◽  
Michael M Kozlov ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Structural Organization ◽  
Structural Features ◽  
Membrane Curvature ◽  
Eukaryotic Cells ◽  
Golgi Cisterna ◽  
Golgi Membranes ◽  
And Function ◽  
Flat Cisternae

The flat Golgi cisterna is a highly conserved feature of eukaryotic cells, but how is this morphology achieved and is it related to its function in cargo sorting and export? A physical model of cisterna morphology led us to propose that sphingomyelin (SM) metabolism at the trans-Golgi membranes in mammalian cells essentially controls the structural features of a Golgi cisterna by regulating its association to curvature-generating proteins. An experimental test of this hypothesis revealed that affecting SM homeostasis converted flat cisternae into highly curled membranes with a concomitant dissociation of membrane curvature-generating proteins. These data lend support to our hypothesis that SM metabolism controls the structural organization of a Golgi cisterna. Together with our previously presented role of SM in controlling the location of proteins involved in glycosylation and vesicle formation, our data reveal the significance of SM metabolism in the structural organization and function of Golgi cisternae.

scholarly journals Activity and Function of the PRMT8 Protein Arginine Methyltransferase in Neurons

Life ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1132
Author(s):  
Rui Dong ◽  
Xuejun Li ◽  
Kwok-On Lai
Keyword(s):  
Potential Role ◽  
Neurological Diseases ◽  
Structural Features ◽  
Protein Arginine Methyltransferases ◽  
Synapse Maturation ◽  
Membrane Bound ◽  
And Function ◽  
Neuronal Functions ◽  
Mammalian Protein

Among the nine mammalian protein arginine methyltransferases (PRMTs), PRMT8 is unusual because it has restricted expression in the nervous system and is the only membrane-bound PRMT. Emerging studies have demonstrated that this enzyme plays multifaceted roles in diverse processes in neurons. Here we will summarize the unique structural features of PRMT8 and describe how it participates in various neuronal functions such as dendritic growth, synapse maturation, and synaptic plasticity. Recent evidence suggesting the potential role of PRMT8 function in neurological diseases will also be discussed.

Mechanism and role of PDZ domains in signaling complex assembly

2001 ◽  
Vol 114 (18) ◽  
pp. 3219-3231 ◽  
Author(s):  
Baruch Z. Harris ◽  
Wendell A. Lim
Keyword(s):  
Cell Signaling ◽  
Pdz Domain ◽  
Photoreceptor Cells ◽  
Protein Recognition ◽  
Pdz Domains ◽  
Peptide Motifs ◽  
Signaling Complex ◽  
Multicellular Organisms ◽  
Drosophila Photoreceptor

PDZ domains are protein-protein recognition modules that play a central role in organizing diverse cell signaling assemblies. These domains specifically recognize short C-terminal peptide motifs, but can also recognize internal sequences that structurally mimic a terminus. PDZ domains can therefore be used in combination to bind an array of target proteins or to oligomerize into branched networks. Several PDZ-domain-containing proteins play an important role in the transport, localization and assembly of supramolecular signaling complexes. Examples of such PDZ-mediated assemblies exist in Drosophila photoreceptor cells and at mammalian synapses. The predominance of PDZ domains in metazoans indicates that this highly specialized scaffolding module probably evolved in response to the increased signaling needs of multicellular organisms.

scholarly journals Steric clashes with bound OMP peptides activate the DegS stress-response protease

2015 ◽  
Vol 112 (11) ◽  
pp. 3326-3331 ◽  
Author(s):  
Anna K. de Regt ◽  
Tania A. Baker ◽  
Robert T. Sauer
Keyword(s):  
Outer Membrane Proteins ◽  
Pdz Domain ◽  
Peptide Binding ◽  
Structural Rearrangement ◽  
Signaling Cascade ◽  
Pdz Domains ◽  
Protease Domain ◽  
Allosteric Activation ◽  
Steric Clash ◽  
Envelope Stress

Escherichia coli senses envelope stress using a signaling cascade initiated when DegS cleaves a transmembrane inhibitor of a transcriptional activator for response genes. Each subunit of the DegS trimer contains a protease domain and a PDZ domain. During stress, unassembled outer-membrane proteins (OMPs) accumulate in the periplasm and their C-terminal peptides activate DegS by binding to its PDZ domains. In the absence of stress, autoinhibitory interactions, mediated by the L3 loop, stabilize inactive DegS, but it is not known how this autoinhibition is reversed during activation. Here, we show that OMP peptides initiate a steric clash between the PDZ domain and the L3 loop that results in a structural rearrangement of the loop and breaking of autoinhibitory interactions. Many different L3-loop sequences are compatible with activation but those that relieve the steric clash reduce OMP activation dramatically. Our results provide a compelling molecular mechanism for allosteric activation of DegS by OMP-peptide binding.

scholarly journals The function and dynamics of the apical scaffolding protein E3KARP are regulated by cell-cycle phosphorylation

2015 ◽  
Vol 26 (20) ◽  
pp. 3615-3627 ◽  
Author(s):  
Cécile Sauvanet ◽  
Damien Garbett ◽  
Anthony Bretscher
Keyword(s):  
Pdz Domain ◽  
Duplication Event ◽  
Scaffolding Protein ◽  
Gene Duplication Event ◽  
Pdz Domains ◽  
Tail Region ◽  
Dynamics And Function ◽  
And Function

We examine the dynamics and function of the apical scaffolding protein E3KARP/NHERF2, which consists of two PDZ domains and a tail containing an ezrin-binding domain. The exchange rate of E3KARP is greatly enhanced during mitosis due to phosphorylation at Ser-303 in its tail region. Whereas E3KARP can substitute for the function of the closely related scaffolding protein EBP50/NHERF1 in the formation of interphase microvilli, E3KARP S303D cannot. Moreover, the S303D mutation enhances the in vivo dynamics of the E3KARP tail alone, whereas in vitro the interaction of E3KARP with active ezrin is unaffected by S303D, implicating another factor regulating dynamics in vivo. A-Raf is found to be required for S303 phosphorylation in mitotic cells. Regulation of the dynamics of EBP50 is known to be dependent on its tail region but modulated by PDZ domain occupancy, which is not the case for E3KARP. Of interest, in both cases, the mechanisms regulating dynamics involve the tails, which are the most diverged region of the paralogues and probably evolved independently after a gene duplication event that occurred early in vertebrate evolution.

scholarly journals Phosphorylation-induced changes in the PDZ domain of Dishevelled 3

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Miroslav Jurásek ◽  
Jitender Kumar ◽  
Petra Paclíková ◽  
Alka Kumari ◽  
Konstantinos Tripsianes ◽  
...  
Keyword(s):  
Pdz Domain ◽  
Phosphorylation Sites ◽  
Pdz Domains ◽  
Recognition Motif ◽  
Regulation Mechanisms ◽  
Binding Groove ◽  
Dynamics Simulations ◽  
Induced Changes ◽  
Insight Into

AbstractThe PDZ domain of Dishevelled 3 protein belongs to a highly abundant protein recognition motif which typically binds short C-terminal peptides. The affinity of the PDZ towards the peptides could be fine-tuned by a variety of post-translation modifications including phosphorylation. However, how phosphorylations affect the PDZ structure and its interactions with ligands remains elusive. Combining molecular dynamics simulations, NMR titration, and biological experiments, we explored the role of previously reported phosphorylation sites and their mimetics in the Dishevelled PDZ domain. Our observations suggest three major roles for phosphorylations: (1) acting as an on/off PDZ binding switch, (2) allosterically affecting the binding groove, and (3) influencing the secondary binding site. Our simulations indicated that mimetics had similar but weaker effects, and the effects of distinct sites were non-additive. This study provides insight into the Dishevelled regulation by PDZ phosphorylation. Furthermore, the observed effects could be used to elucidate the regulation mechanisms in other PDZ domains.

scholarly journals Structure of Myo7b/USH1C complex suggests a general PDZ domain binding mode by MyTH4-FERM myosins

2017 ◽  
Vol 114 (19) ◽  
pp. E3776-E3785 ◽  
Author(s):  
Jianchao Li ◽  
Yunyun He ◽  
Meredith L. Weck ◽  
Qing Lu ◽  
Matthew J. Tyska ◽  
...  
Keyword(s):  
Molecular Basis ◽  
Common Property ◽  
Pdz Domain ◽  
Binding Mode ◽  
Pdz Domains ◽  
Unconventional Myosin ◽  
Binding Partners ◽  
Interaction Mode ◽  
Similar Mode ◽  
And Function

Unconventional myosin 7a (Myo7a), myosin 7b (Myo7b), and myosin 15a (Myo15a) all contain MyTH4-FERM domains (myosin tail homology 4-band 4.1, ezrin, radixin, moesin; MF) in their cargo binding tails and are essential for the growth and function of microvilli and stereocilia. Numerous mutations have been identified in the MyTH4-FERM tandems of these myosins in patients suffering visual and hearing impairment. Although a number of MF domain binding partners have been identified, the molecular basis of interactions with the C-terminal MF domain (CMF) of these myosins remains poorly understood. Here we report the high-resolution crystal structure of Myo7b CMF in complex with the extended PDZ3 domain of USH1C (a.k.a., Harmonin), revealing a previously uncharacterized interaction mode both for MyTH4-FERM tandems and for PDZ domains. We predicted, based on the structure of the Myo7b CMF/USH1C PDZ3 complex, and verified that Myo7a CMF also binds to USH1C PDZ3 using a similar mode. The structure of the Myo7b CMF/USH1C PDZ complex provides mechanistic explanations for >20 deafness-causing mutations in Myo7a CMF. Taken together, these findings suggest that binding to PDZ domains, such as those from USH1C, PDZD7, and Whirlin, is a common property of CMFs of Myo7a, Myo7b, and Myo15a.

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