Evidence for PDZ domains in bacteria, yeast, and plants

Ponting, Chris P.

doi:10.1002/pro.5560060225

Cited by 221 publications

(188 citation statements)

References 43 publications

(35 reference statements)

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“…Bacterial PDZ domains are homologous to the metazoan PDZ domains (23,24,26); however, their topology is different (20), and thus they are designated "PDZ-like" domains.…”

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confidence: 99%

Role of the PDZ Domains in Escherichia coli DegP Protein

et al. 2007

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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.PDZ domains represent a common protein interaction motif, and their name was derived from the first three proteins in which such domains were identified, namely PSD-95, Drosophila melanogaster Disc large protein, and zonula occludens protein 1. Bacterial PDZ domains are homologous to the metazoan PDZ domains (23,24,26); however, their topology is different (20), and thus they are designated "PDZ-like" domains.PDZ domains are approximately 90 residues long and have a common structure consisting of six ␤-strands and two ␣-helices, which fold in an overall six-stranded ␤-sandwich. The C-terminal ends of a protein substrate (7) usually bind in a groove of the domain formed between one of the ␣-helices and the adjacent ␤-strand, which thus serves as an extra ␤-strand added to the ␤-sheet (8). In this manner, the C-terminal peptide backbone participates in an extensive hydrogen-bonding pattern with the main chain atoms of the PDZ domain ␤-strand. The terminal carboxylate group is also stabilized by a series of hydrogen bonds with the highly conserved "carboxylate-binding loop" (3). However, the side chain of the C-terminal residue and the side chain of the residue at position Ϫ2 are the structures that are most critical for the specificity of substrate recognition by the PDZ domain, rather than the extensive hydrogen bonds with the main chain of the PDZ domain ␤-strand (29). In this context, ...

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“…Bacterial PDZ domains are homologous to the metazoan PDZ domains (23,24,26); however, their topology is different (20), and thus they are designated "PDZ-like" domains.…”

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confidence: 99%

Role of the PDZ Domains in Escherichia coli DegP Protein

et al. 2007

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“…Nma111p belongs to the HtrA family of serine proteases and consists of two tandem HtrA repeats, each completed with two PDZ domains (Clausen et al, 2002;Pallen and Wren, 1997;Ponting, 1997). Whereas the N-terminal HtrA repeat harbours a complete catalytic triad characteristic for serine proteases, the second repeat lacks two of the three active-site residues (Pallen and Wren, 1997).…”

Section: The N-terminal Htra Repeat Of Nma111p Is Required For Apoptomentioning

confidence: 99%

“…The serine protease Nma111p belongs to the family of HtrA (high temperature requirement A) proteins, which are defined by a characteristic combination of a catalytic serine-protease domain with at least one PDZ (postsynaptic density 95/disc large/zona occludens) domain (Clausen et al, 2002;Pallen and Wren, 1997;Ponting, 1997;Vande Walle et al, 2008). Nma111p harbours an internal duplication of the HtrA-like sequence, with the N-terminal repeat retaining the catalytic triad residues of HtrA-like serine proteases (Clausen et al, 2002;Pallen and Wren, 1997;Ponting, 1997).…”

Section: Introductionmentioning

confidence: 99%

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Nuclear localisation is crucial for the proapoptotic activity of the HtrA-like serine protease Nma111p

Walter

Henderson

Yelton

et al. 2009

Journal of Cell Science

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Programmed cell death is induced by the activation of a subset of intracellular proteins in response to specific extra- and intracellular signals. In the yeast Saccharomyces cerevisiae, Nma111p functions as a nuclear serine protease that is necessary for apoptosis under cellular stress conditions, such as elevated temperature or treatment of cells with hydrogen peroxide to induce cell death. We have examined the role of nuclear protein import in the function of Nma111p in apoptosis. Nma111p contains two small clusters of basic residues towards its N-terminus, both of which are necessary for efficient translocation into the nucleus. Nma111p does not shuttle between the nucleus and cytoplasm during either normal growth conditions or under environmental stresses that induce apoptosis. The N-terminal half of Nma111p is sufficient to provide the apoptosis-inducing activity of the protein, and the nuclear-localisation signal (NLS) sequences and catalytic serine 235 are both necessary for this function. We provide compelling evidence that intranuclear Nma111p activity is necessary for apoptosis in yeast.

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“…4a) 8 Table S1). Interestingly, the Ctp DUF3340 domain shows sequence similarity with the 9 mammalian interphotoreceptor retinoid binding protein (IRBP) (Keiler and Sauer 1995) and 10 might be ancestral to it (Ponting 1997 Supplementary Fig. 4).…”

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confidence: 99%