canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain. PDZ domains usually bind to short specific peptide sequences located at the C-terminal end of their partner proteins known as PDZ binding motifs. These domains can also interact with internal peptide motifs and certain lipids, and can take part in a head-to-tail oligomerization with other PDZ domains. The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. The canonical PDZ domain contains 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 767924059   26 QVQENSPAQQAGLEPYFDFIITIGHSRLNKENDtLKALLKANVEKPVKLEVFNMKTMRVREVEVVPSNMWGGQGLLGASV 105
Cdd:pfam04495  49 DVHENSPAAKAGLQPYSDYIIGTPKGLLKGEDD-LYTLVEDHEDRPLRLYVYNSETDTVREVTITPNRNWGGEGALGCGL 127

GRASP55/65 PDZ-like domain; GRASP55 (Golgi re-assembly stacking protein of 55 kDa) and GRASP65 (a 65 kDa) protein are highly homologous. GRASP55 is a component of the Golgi stacking machinery. GRASP65, an N-ethylmaleimide- sensitive membrane protein required for the stacking of Golgi cisternae in a cell-free system. This region appears to be related to the PDZ domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767924059   26 QVQENSPAQQAGLEPYFDFIITIGHSRLNKENDtLKALLKANVEKPVKLEVFNMKTMRVREVEVVPSNMWGGQGLLGASV 105
Cdd:pfam04495  49 DVHENSPAAKAGLQPYSDYIIGTPKGLLKGEDD-LYTLVEDHEDRPLRLYVYNSETDTVREVTITPNRNWGGEGALGCGL 127

Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, protein turnover, chaperones, Transcription];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767924059  26 QVQENSPAQQAGLEPYfDFIITIGHSRLNKENDtLKALLKANVEKPVKLEVfnmktMR---VREVEVVP-SNMWGGQGLL 101
Cdd:COG0750  134 EVVPGSPAAKAGLQPG-DRIVAINGQPVTSWDD-LVDIIRASPGKPLTLTV-----ERdgeELTLTVTPrLVEEDGVGRI 206

                         90       100       110
                 ....*....|....*....|....*....|
gi 767924059 102 GASVRFC----------SFRRASEQVWHVL 121
Cdd:COG0750  207 GVSPSGEvvtvrygpleALGAGVKETWDMI 236

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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767924059   16 GMHPARSVF-QQVQENSPAQQAGLEPYfDFIITIGHSRLNKENDTLKALLKANVEKPVKLEVF-NMKTMRVR-------E 86
Cdd:TIGR02037 252 GLEKQRGALvAQVLPGSPAEKAGLKAG-DVITSVNGKPISSFADLRRAIGTLKPGKKVTLGILrKGKEKTITvtlgaspE 330

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 767924059   87 VEVVPSNMWggQGLLGASVRFCSFRRASEQVWH----VLDVEPSSPAALAGLRP 136
Cdd:TIGR02037 331 EQASSSNPF--LGLTVANLSPEIRKELRLKGDVkgvvVTKVVSGSPAARAGLQP 382

envelope glycoprotein D; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767924059 151 PPSYHKKPPGTPPPSALPLGAPPPDALPPGPTPEDSPSLETGSRQSDYMEALLQAP----GSSMEDPLPGPGSPSHSAPD 226
Cdd:PHA03264 255 PPYFEESKGYEPPPAPSGGSPAPPGDDRPEAKPEPGPVEDGAPGRETGGEGEGPEPagrdGAAGGEPKPGPPRPAPDADR 334

                         90
                 ....*....|....*..
gi 767924059 227 PDGLPHFMETPLQPPPP 243
Cdd:PHA03264 335 PEGWPSLEAITFPPPTP 351

GRASP55/65 PDZ-like domain; GRASP55 (Golgi re-assembly stacking protein of 55 kDa) and GRASP65 (a 65 kDa) protein are highly homologous. GRASP55 is a component of the Golgi stacking machinery. GRASP65, an N-ethylmaleimide- sensitive membrane protein required for the stacking of Golgi cisternae in a cell-free system. This region appears to be related to the PDZ domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767924059   26 QVQENSPAQQAGLEPYFDFIITIGHSRLNKENDtLKALLKANVEKPVKLEVFNMKTMRVREVEVVPSNMWGGQGLLGASV 105
Cdd:pfam04495  49 DVHENSPAAKAGLQPYSDYIIGTPKGLLKGEDD-LYTLVEDHEDRPLRLYVYNSETDTVREVTITPNRNWGGEGALGCGL 127

Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, protein turnover, chaperones, Transcription];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767924059  26 QVQENSPAQQAGLEPYfDFIITIGHSRLNKENDtLKALLKANVEKPVKLEVfnmktMR---VREVEVVP-SNMWGGQGLL 101
Cdd:COG0750  134 EVVPGSPAAKAGLQPG-DRIVAINGQPVTSWDD-LVDIIRASPGKPLTLTV-----ERdgeELTLTVTPrLVEEDGVGRI 206

                         90       100       110
                 ....*....|....*....|....*....|
gi 767924059 102 GASVRFC----------SFRRASEQVWHVL 121
Cdd:COG0750  207 GVSPSGEvvtvrygpleALGAGVKETWDMI 236

Predicted metalloprotease, contains C-terminal PDZ domain [General function prediction only];

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767924059  19 PARSVFQQVQENSPAQQAGLEPYfDFIITIGHSRLNKENdtLKALLK-ANVEKPVKLEVFNMKtmRVREVEVVP 91
Cdd:COG3975  493 GGGLVVTSVLWGSPAYKAGLSAG-DELLAIDGLRVTADN--LDDALAaYKPGDPIELLVFRRD--ELRTVTVTL 561

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 767924059  26 QVQENSPAQQAGLEPYfDFIITIGHSRLNKENDTLKAlLKANVEKPVKLEVfnmktMR---VREVEVVPSNM---WGGQG 99
Cdd:cd23081    5 EVVANSPAAEAGLKPG-DRILKIDGQKVRTWEDIVRI-VRENPGKPLTLKI-----ERdgkILTVTVTPELVeveGKGVG 77

                 ...
gi 767924059 100 LLG 102
Cdd:cd23081   78 RIG 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 767924059  25 QQVQENSPAQQAGLEPYfDFIITIGHSRLNKENDTLKALLKANVEKPVKLEVfnmktMR---VREVEVVP 91
Cdd:COG0265  206 ARVEPGSPAAKAGLRPG-DVILAVDGKPVTSARDLQRLLASLKPGDTVTLTV-----LRggkELTVTVTL 269

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        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767924059    12 SVDSGMHPARSVF-QQVQENSPAQQAGLEPYfDFIITIGHSRLNKENDTLKALLKANVEKPVKLEV 76
Cdd:smart00228  17 SLVGGKDEGGGVVvSSVVPGSPAAKAGLRVG-DVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLTV 81

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
                 ....*....|....*....|....*....|....*....|....*....|....
gi 767924059  23 VFQQVQENSPAQQAGLEPYfDFIITIGHSRLNKENDTLKALLKANVEKPVKLEV 76
Cdd:cd06781   33 YVAQVQSNSPAEKAGLKKG-DVITKLDGKKVESSSDLRQILYSHKVGDTVKVTI 85