Nas2 N_terminal domain; Nas2 is a proteosome assembly chaperone. Nas2 bivalently binds the proteasome Rpt5 subunit. The Nas2 N-terminal helical domain masks the Rpt1-interacting surface of Rpt5.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119508441   23 IQDLMRRKEEIEAEIKANYDVLESQkGIGMNEPLVDCEGYPRADVDLYQVRTARHNIICLQNDHKALMKQVEEALHQLHA 102
Cdd:pfam18265   1 LKELMAKKDEIEAELEELSDVLDSH-GVGMDGPLVDEEGFPRSDIDVYQVRLARHRIICLRNDYKALMKQIEEALHELHS 79

Nas2 N_terminal domain; Nas2 is a proteosome assembly chaperone. Nas2 bivalently binds the proteasome Rpt5 subunit. The Nas2 N-terminal helical domain masks the Rpt1-interacting surface of Rpt5.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119508441   23 IQDLMRRKEEIEAEIKANYDVLESQkGIGMNEPLVDCEGYPRADVDLYQVRTARHNIICLQNDHKALMKQVEEALHQLHA 102
Cdd:pfam18265   1 LKELMAKKDEIEAELEELSDVLDSH-GVGMDGPLVDEEGFPRSDIDVYQVRLARHRIICLRNDYKALMKQIEEALHELHS 79

circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and related domains; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ResP (also known as Site-2 protease RseP, and YaeL), and related domains. RseP is involved in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmE) protein RseA; it cleaves the peptide bond between the critical alanine and cysteine in the transmembrane region of RseA, releasing the cytoplasmic domain of RseA with its associated sigmaE. RseP contains two tandem-arranged periplasmic PDZ domains (PDZ-N/PDZ1 and PDZ-C/PDZ2) which act to negatively regulate protease action on intact RseA; they serve as a size-exclusion filter which prevents the access of an intact RseA into the active site of RseP. PDZ domains usually bind in sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This RseP family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119508441 138 VNSISPGSPASIAGLQVDDEIVEFGSVNTQNFQSVQNvgTVVQHSeGKPLNVTVIRRGEKHQLRLIPTRWA----GKGLL 213
Cdd:cd23081    3 VGEVVANSPAAEAGLKPGDRILKIDGQKVRTWEDIVR--IVRENP-GKPLTLKIERDGKILTVTVTPELVEvegkGVGRI 79

                 .
gi 119508441 214 G 214
Cdd:cd23081   80 G 80

Peptidase family M50;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119508441  124 LASNSPVLPQAFARVNSISPGSPASIAGLQVDDEIVefgSVNTQNFQSVQNVGTVVQHSEGKPLNVTVIRRGEKHQLRLI 203
Cdd:pfam02163  83 LLFLSGVPPPAPPVIGGVAPGSPAAKAGLKPGDVIL---SINGKKITSWQDLVEALAKSPGKPITLTVERGGQTLTVTIT 159

                          90
                  ....*....|.
gi 119508441  204 PTRWAGKGLLG 214
Cdd:pfam02163 160 PKSSEESKFIG 170

periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures. [Protein fate, Protein folding and stabilization, Protein fate, Degradation of proteins, peptides, and glycopeptides]

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 119508441  136 ARVNSISPGSPASIAGLQVDDEIVEFGSVNTQNFQSVQN-VGTvvqHSEGKPLNVTVIRRGEKHQL 200
Cdd:TIGR02037 259 ALVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRaIGT---LKPGKKVTLGILRKGKEKTI 321

Nas2 N_terminal domain; Nas2 is a proteosome assembly chaperone. Nas2 bivalently binds the proteasome Rpt5 subunit. The Nas2 N-terminal helical domain masks the Rpt1-interacting surface of Rpt5.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119508441   23 IQDLMRRKEEIEAEIKANYDVLESQkGIGMNEPLVDCEGYPRADVDLYQVRTARHNIICLQNDHKALMKQVEEALHQLHA 102
Cdd:pfam18265   1 LKELMAKKDEIEAELEELSDVLDSH-GVGMDGPLVDEEGFPRSDIDVYQVRLARHRIICLRNDYKALMKQIEEALHELHS 79

circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and related domains; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ResP (also known as Site-2 protease RseP, and YaeL), and related domains. RseP is involved in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmE) protein RseA; it cleaves the peptide bond between the critical alanine and cysteine in the transmembrane region of RseA, releasing the cytoplasmic domain of RseA with its associated sigmaE. RseP contains two tandem-arranged periplasmic PDZ domains (PDZ-N/PDZ1 and PDZ-C/PDZ2) which act to negatively regulate protease action on intact RseA; they serve as a size-exclusion filter which prevents the access of an intact RseA into the active site of RseP. PDZ domains usually bind in sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This RseP family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119508441 138 VNSISPGSPASIAGLQVDDEIVEFGSVNTQNFQSVQNvgTVVQHSeGKPLNVTVIRRGEKHQLRLIPTRWA----GKGLL 213
Cdd:cd23081    3 VGEVVANSPAAEAGLKPGDRILKIDGQKVRTWEDIVR--IVRENP-GKPLTLKIERDGKILTVTVTPELVEvegkGVGRI 79

                 .
gi 119508441 214 G 214
Cdd:cd23081   80 G 80

Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones];

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 119508441 136 ARVNSISPGSPASIAGLQVDDEIVEFGSVNTQNFQSVQNVgtVVQHSEGKPLNVTVIRRGEKHQLRLIPTR 206
Cdd:COG0265  203 VLVARVEPGSPAAKAGLRPGDVILAVDGKPVTSARDLQRL--LASLKPGDTVTLTVLRGGKELTVTVTLGE 271

circularly permuted PDZ domain 2 (PDZ-C) of Escherichia coli Regulator of sigma-E protease (RseP) and related domains; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ResP (also known as Site-2 protease RseP, and YaeL) and related domains. RseP is involved in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmaE) protein RseA; it cleaves the peptide bond between the critical alanine and cysteine in the transmembrane region of RseA, releasing the cytoplasmic domain of RseA with it associated sigmaE. RseP contains two tandem-arranged periplasmic PDZ domains (PDZ-N/PDZ1 and PDZ-C/PDZ2) which act to negatively regulate protease action on intact RseA; they serve as a size-exclusion filter which prevents the access of an intact RseA into the active site of RseP. PDZ domains usually bind in sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This RseP family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 119508441 141 ISPGSPASIAGLQVDDEIVEfgsVNTQNFQSVQNVGTVVQHSEGKPLNVTVIRRGEKHQLRLIP 204
Cdd:cd23083    6 VQPNSAAEKAGLQAGDRIVK---VDGQPLTQWQTFVMAVRDNPGKPLALEIERQGSPLSLTLIP 66

circularly permuted PDZ domain of DegS serine endoprotease; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Escherichia coli DegS and related domains. DegS (also known as Site-1 protease DegS, S1P protease DegS, and Site-1-type intramembrane protease) participates in the activation of the sigma(E) extracytoplasmic stress response. Initially, there is an accumulation of misfolded membrane proteins (OMPs) in the periplasm which bind by their YXF motif to the DegS PDZ domain, activating DegS-catalyzed cleavage of the RseA periplasmic domain and making RseA a substrate for cleavage by another membrane protease RseP. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This DegS family PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 119508441 136 ARVNSISPGSPASIAGLQVDDEIVEFGSVNTQNFQSVQNVGTVVQhsEGKPLNVTVIRRGE 196
Cdd:cd06777   27 ALVKGVSPDSPAAKAGIQVGDIILQFDNKPVISVLELMDLVAEIR--PGTVIPVVVLRDGK 85

Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 119508441   138 VNSISPGSPASIAGLQVDDEIVEFGSVNTQNFQSVQNVgtVVQHSEGKPLNVTVIRRG 195
Cdd:smart00228  30 VSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAV--DLLKKAGGKVTLTVLRGG 85

circularly permuted PDZ domain of high-temperature requirement factor A (HtrA) family serine proteases and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of HtrA family serine proteases including human HtrA1, HtrA2 (mitochondrial), HtrA3, and HtrA4, and related domains. These proteases are key enzymes associated with pregnancy. Their diverse biological functions include cell growth proliferation, migration and apoptosis. They are also implicated in disorders including Alzheimer's, Parkinson's, arthritis and cancer. HtrA1 (also known as high-temperature requirement A serine peptidase 1, L56, and serine protease 11) substrates include extracellular matrix proteins, proteoglycans, and insulin-like growth factor (IGF)-binding proteins. HtrA1 also inhibits signaling by members of the transforming growth factor beta (TGF-beta) family. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This HtrA-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119508441 143 PGSPASIAGLQVDDEIVefgSVNTQNFQSVQNVGTVVQhsEGKPLNVTVIRRGEKHQLRLIP 204
Cdd:cd06785   40 PGSPAQRAGLKDGDVII---SINGKPVKSSSDVYEAVK--SGSSLLVVVRRGNEDLLLTVTP 96

serine endoprotease DegS;

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 119508441 137 RVNSISPGSPASIAGLQVDDEIVefgSVNTQNFQSVQNvgTVVQHSEGKP---LNVTVIRRGEK 197
Cdd:PRK10898 282 VVNEVSPDGPAAKAGIQVNDLII---SVNNKPAISALE--TMDQVAEIRPgsvIPVVVMRDDKQ 340

circularly permuted PDZ domain of Bacillus subtilis HtrA-type serine proteases HtrA, HtrB, and YyxA and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Bacillus subtilis HtrA/YkdA, HtrB/YvtA and YyxA/YycK, and related domains. HtrA-type serine proteases participate in folding and degradation of aberrant proteins, and in processing and maturation of native proteins. HtrA, HtrB, and YyxA have a single transmembrane domain at the N-terminus and a PDZ domain at the C-terminus. Expression of htrA and htrB genes is induced both by heat shock and by secretion stress (by a common) mechanism; yyxA is neither heat shock nor secretion stress inducible. HtrA and HtrB may have overlapping cellular functions; YyxA may have a cellular function distinct from the other two proteases or have the same function but under different conditions. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This BsHtrA-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 119508441 138 VNSISPGSPASIAGLQVDDEIVEFGSVNTQNFQSVQNVgtVVQHSEGKPLNVTVIRRGEKHQLRL 202
Cdd:cd06781   34 VAQVQSNSPAEKAGLKKGDVITKLDGKKVESSSDLRQI--LYSHKVGDTVKVTIYRDGKEKTLNI 96

periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures. [Protein fate, Protein folding and stabilization, Protein fate, Degradation of proteins, peptides, and glycopeptides]

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 119508441  136 ARVNSISPGSPASIAGLQVDDEIVEFGSVNTQNFQSVQN-VGTvvqHSEGKPLNVTVIRRGEKHQL 200
Cdd:TIGR02037 259 ALVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRaIGT---LKPGKKVTLGILRKGKEKTI 321

C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, protein turnover, chaperones];

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 119508441 137 RVNSISPGSPASIAGLQVDDEIVEFGSVNTQNfQSVQNVGTVVQHSEGKPLNVTVIRRGEK 197
Cdd:COG0793   74 VVVSVIPGSPAEKAGIKPGDIILAIDGKSVAG-LTLDDAVKLLRGKAGTKVTLTIKRPGEG 133

permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping serine proteases and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Deg/HtrA-type serine proteases that participate in folding and degradation of aberrant proteins, and in processing and maturation of native proteins. Typically, these proteases have an N-terminal serine protease domain and at least one C-terminal PDZ domain that recognizes substrates, and in some cases activates the protease function. An exception is yeast Nma11p which has two protease domains and four PDZ domains; its N-terminal half is comprised of a protease domain, followed by two PDZ domains, and its C-terminal half has a similar domain arrangement. HtrA-type proteases include the human HtrA1-4 and MBTPS2, tricorn protease, DegS, DegP and C-terminal processing peptidase, cyanobacterial serine proteases Hhoa, HhoB, and HtrA, and yeast Nma11p. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-termini of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This Deg/HtrA family PDZ domain is a circularly permuted PDZ domain which places beta-strand A at the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 119508441 138 VNSISPGSPASIAGLQVDDEIVefgSVNTQNFQSVQNVGTVV-QHSEGKPLNVTVIRRGEKHQLRL 202
Cdd:cd06779   29 VAEVIPGSPAAKAGLKEGDVIL---SVNGKPVTSFNDLRAALdTKKPGDSLNLTILRDGKTLTVTV 91

circularly permuted second PDZ domain (PDZ2) of Escherichia coli periplasmic serine endoprotease DegP and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Escherichia coli DegP (also known as heat shock protein DegP and Protease Do), and related domains. DegP belongs to the HtrA family of housekeeping proteases. It acts as a protease, degrading transiently denatured and unfolded or misfolded proteins which accumulate in the periplasm following heat shock or other stress conditions, and as a molecular chaperone at low temperatures. DegP has two PDZ domains in addition to the protease domain; its PDZ1 domain is responsible for the identifying the distinct substrate sequences that affect degradation (degron) of the substrate sequence, and its PDZ2 domain is responsible for the combining with other DegP monomers to form a stable oligomer structure. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This DegP family PDZ domain 2 is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 119508441 138 VNSISPGSPASIAGLQVDDEIVEFgsvntqNFQSVQNVGTVVQHSEGKPLNVTV-IRRGEKHQLRLIP 204
Cdd:cd23084   22 VTEVDPGSPAAQSGLKKGDVIIGV------NRQPVKSIAELRKVLKSKPSAVLLqIKRGDSSRYLALP 83

PDZ domain 7 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ7 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

                         10        20        30
                 ....*....|....*....|....*....|..
gi 119508441 138 VNSISPGSPASIAGLQVDDEIVEFGSVNTQNF 169
Cdd:cd06685   32 VNAIRPGGPADLSGLQPYDRILQVNHVRTRDF 63

PDZ domain of Drosophila melanogaster PDZ and LIM domain protein Zasp52 (also known as Zasp), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Drosophila melanogaster Zasp52 and related domains. Drosophila melanogaster Zasp52 (also known as Z band alternatively spliced PDZ-motif protein or Zasp) colocalizes with integrins at myotendinous junctions and with alpha-actinin at Z-disks and is required for muscle attachment as well as Z-disk assembly and maintenance. The Zasp52 actin-binding site includes the extended PDZ domain and the ZM region. The Zasp52-PDZ domain is required for myofibril assembly. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Zasp52-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

                         10        20        30
                 ....*....|....*....|....*....|.
gi 119508441 138 VNSISPGSPASIAGLQVDDEIVEFGSVNTQN 168
Cdd:cd23068   29 IQKVNPGSPADKAGLRRGDVILRINGTDTSN 59

PDZ domain 3 of multi-PDZ-domain protein 1 (MUPP1) and PATJ (protein-associated tight junction) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of MUPP1 and PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 119508441 138 VNSISPGSPASIAG-LQVDDEIVEFGSVNTQNFQSVQNVgTVVQHSeGKPLNVTVIR 193
Cdd:cd06791   35 VKSIIPGSAADQDGrIQVNDQIIAVDGVNLQGFTNQEAV-EVLRNT-GQVVHLTLAR 89

periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures. [Protein fate, Protein folding and stabilization, Protein fate, Degradation of proteins, peptides, and glycopeptides]

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 119508441  138 VNSISPGSPASIAGLQVDDEIVefgSVNTQNFQSVQNVGTVVqHSEGKPLNVTV-IRRGE 196
Cdd:TIGR02037 366 VTKVVSGSPAARAGLQPGDVIL---SVNQQPVSSVAELRKVL-ARAKKGGRVALlILRGG 421

PDZ domain of rhophilin-1, rhophilin-2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of rhophilin-1, rhophilin-2, and related domains. Rhophilin-1 (RHPN1, also known as GTP-Rho-binding protein 1) and rhophilin-2 (RHPN2, also known as GTP-Rho-binding protein 2) are Rho-GTP binding proteins involved in cytoskeletal dynamics. Rhophilin-2 inhibits RhoA's activity to induce F-actin stress fibers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This rhophilin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 119508441 127 NSPVLpqafarVNSISPGSPASIAGLQVDDEIVEFGSVNT 166
Cdd:cd06712   20 DSPVQ------VASVDPGSCAAEAGLKEGDYIVSVGGVDC 53