PDZ domain; This entry represents the PDZ domain from a wide variety of proteins.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1799133700  79 VLSVIPGSPVDEA-LYAGDINLSIDGINIYNYGGLRDF---KNRGNITLKVQR 127
Cdd:pfam17820   2 VTAVVPGSPAERAgLRVGDVILAVNGKPVRSLEDVARLlqgSAGESVTLTVRR 54

Superfamily II DNA and RNA helicase [Replication, recombination and repair];

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1799133700   3 TKKFSQLGVCSWINQQLETMQIKTATPVQAACIPKIL 39
Cdd:COG0513     1 MMSFADLGLSPPLLKALAELGYTTPTPIQAQAIPLIL 37

PDZ domain of Golgi-associated PDZ and coiled-coil motif-containing protein (GOPC), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of GOPC and related domains. GOPC, also known as PIST (PDZ domain protein interacting specifically with TC10), FIG (fused in glioblastoma), and CAL (CFTR-associated ligand), regulates the trafficking of a wide array of proteins, including small GTPases, receptors, and cell surface molecules such as cadherin 23 and CFTR. It may regulate CFTR chloride currents and acid-sensing ASIC3 currents by modulating cell surface expression of both channels, and may play a role in autophagy. Interaction partners of the GOPC PDZ domains include: FZD5, FZD8, ASIC3, CFTR, MUC3, ARFRP1, Ggamma13, neuroligin, and Stargazin. 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 GOPC-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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133700  55 TVVINKTSSQHFGCHIT--ISNGIAKVLSVI-PGSPVD--EALYAGDINLSIDGINiynyggLRDFKN----------RG 119
Cdd:cd06800     2 KVLLSKEPHEGLGISITggKEHGVPILISEIhEGQPADrcGGLYVGDAILSVNGID------LRDAKHkeavtilsqqRG 75

                  ....*...
gi 1799133700 120 NITLKVQR 127
Cdd:cd06800    76 EITLEVVY 83

Superfamily II DNA and RNA helicase [Replication, recombination and repair];

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1799133700   3 TKKFSQLGVCSWINQQLETMQIKTATPVQAACIPKIL 39
Cdd:COG0513     1 MMSFADLGLSPPLLKALAELGYTTPTPIQAQAIPLIL 37

PDZ domain of Golgi-associated PDZ and coiled-coil motif-containing protein (GOPC), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of GOPC and related domains. GOPC, also known as PIST (PDZ domain protein interacting specifically with TC10), FIG (fused in glioblastoma), and CAL (CFTR-associated ligand), regulates the trafficking of a wide array of proteins, including small GTPases, receptors, and cell surface molecules such as cadherin 23 and CFTR. It may regulate CFTR chloride currents and acid-sensing ASIC3 currents by modulating cell surface expression of both channels, and may play a role in autophagy. Interaction partners of the GOPC PDZ domains include: FZD5, FZD8, ASIC3, CFTR, MUC3, ARFRP1, Ggamma13, neuroligin, and Stargazin. 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 GOPC-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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133700  55 TVVINKTSSQHFGCHIT--ISNGIAKVLSVI-PGSPVD--EALYAGDINLSIDGINiynyggLRDFKN----------RG 119
Cdd:cd06800     2 KVLLSKEPHEGLGISITggKEHGVPILISEIhEGQPADrcGGLYVGDAILSVNGID------LRDAKHkeavtilsqqRG 75

                  ....*...
gi 1799133700 120 NITLKVQR 127
Cdd:cd06800    76 EITLEVVY 83

PDZ domain 1 of Zonula Occludens-1 (ZO-1), homologs ZO-2 and ZO-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of ZO-1, -2, -3 and related domains. Zonula occludens proteins (ZO-1, ZO-2, ZO-3) are multi-PDZ domain proteins involved in the maintenance and biogenesis of multi-protein networks at the cytoplasmic surface of intercellular contacts in epithelial and endothelial cells. They have three N-terminal PDZ domains, PDZ1-3, followed by a Src homology-3 (SH3) domain and a guanylate kinase (GuK)-like domain. Among protein-protein interactions for all ZO proteins is the binding of the first PDZ domain (PDZ1) to the C-termini of claudins, and the homo- and hetero-dimerization of ZO-proteins via their second PDZ domain (PDZ2), which takes place by symmetrical domain swapping of the first two beta-strands of PDZ2. At the cell level, ZO-1 and ZO-2 are involved in polarity maintenance, gene transcription, cell proliferation, and tumor cell metastasis. 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 ZO family PDZ1 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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133700  55 TVVINKTSSQHFGchITISNGIAK----------VLS-VIPGSPVDEALYAGDINLSIDGINIYN------YGGLRDFKN 117
Cdd:cd06727     2 TVTLHRAPGFGFG--IAVSGGRDNphfqsgdtsiVISdVLKGGPAEGKLQENDRVVSVNGVSMENvehsfaVQILRKCGK 79

                  ....*..
gi 1799133700 118 RGNITLK 124
Cdd:cd06727    80 TANITVK 86

Predicted secreted protein YlbL, contains PDZ domain [Signal transduction mechanisms];

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1799133700  69 HITISNGIaKVLSVIPGSPVDEALYAGDINLSIDGINIYNYGGLRDF-KNRG---NITLKVQR 127
Cdd:COG3480   133 GYPVTEGV-YVASVLEGSPADGVLQPGDVITAVDGKPVTTAEDLRDAlAAKKpgdTVTLTVTR 194

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
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1799133700  81 SVIPGSPVDEA-LYAGDINLSIDGINIYNYGGLRDF--KNRGN-ITLKVQR 127
Cdd:cd23081     5 EVVANSPAAEAgLKPGDRILKIDGQKVRTWEDIVRIvrENPGKpLTLKIER 55

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1799133700  77 AKVLSVIPGSPVDEA-LYAGDINLSIDGINIYNYGGLRDFKNRGNI----TLKVQR 127
Cdd:COG0265   203 VLVARVEPGSPAAKAgLRPGDVILAVDGKPVTSARDLQRLLASLKPgdtvTLTVLR 258

DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

                          10        20
                  ....*....|....*....|....*
gi 1799133700  15 INQQLETMQIKTATPVQAACIPKIL 39
Cdd:cd00268     1 LLKALKKLGFEKPTPIQAQAIPLIL 25