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Conserved domains on  [gi|193787027|dbj|BAG51850|]
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unnamed protein product [Homo sapiens]

Protein Classification

PDZ domain-containing protein( domain architecture ID 650)

PDZ domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PDZ_canonical super family cl49608
canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs ...
 3-50 9.27e-08

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.


The actual alignment was detected with superfamily member pfam04495:

Pssm-ID: 483948 [Multi-domain]  Cd Length: 138  Bit Score: 49.96  E-value: 9.27e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 193787027    3 LGVSAE--QPAGGAE-GFHLHgDVEPSSPAALAGLRPYTDYVVGSD-QILQE 50
Cdd:pfam04495  28 LGLSLRwcSFAKALEnVWHVL-DVHENSPAAKAGLQPYSDYIIGTPkGLLKG 78
 
Name Accession Description Interval E-value
GRASP55_65 pfam04495
GRASP55/65 PDZ-like domain; GRASP55 (Golgi re-assembly stacking protein of 55 kDa) and GRASP65 ...
 3-50 9.27e-08

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.


Pssm-ID: 427981 [Multi-domain]  Cd Length: 138  Bit Score: 49.96  E-value: 9.27e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 193787027    3 LGVSAE--QPAGGAE-GFHLHgDVEPSSPAALAGLRPYTDYVVGSD-QILQE 50
Cdd:pfam04495  28 LGLSLRwcSFAKALEnVWHVL-DVHENSPAAKAGLQPYSDYIIGTPkGLLKG 78
PDZ_NHERF-like cd06768
PDZ domains of the Na+/H+ exchange regulatory cofactor (NHERF) family (NHERF1-4), and related ...
 16-42 7.18e-03

PDZ domains of the Na+/H+ exchange regulatory cofactor (NHERF) family (NHERF1-4), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the Na+/H+ exchange regulatory cofactor (NHERF) family of multi-PDZ-domain-containing scaffolding proteins (NHERF1-4), and related domains. The NHERF family includes NHERF1 (also known as EBP50), NHERF2 (also known as E3KARP; TKA-1; SIP-1), NHERF3 (also known as CAP70; CLAMP; Napi-Cap-1; PDZD1) and NHERF4 (also known as IKEPP; PDZK2; Napi-Cap-2). NHERF1 and NHERF2 have tandem PDZ domains (PDZ1-2); NHERF3 and NHERF4 have four PDZ domains (PDZ1-4). NHERFs are involved in the regulation of multiple receptors or transporters, such as type II sodium-phosphate cotransporter (Npt2a), purinergic P2Y1 receptor P2Y1R, the beta2-adrenergic receptor (beta2-AR), parathyroid hormone receptor type 1 (PTHR), the lysophosphatidic acid receptors (LPARs), sodium-hydrogen exchanger 3 (NHE3), and cystic fibrosis transmembrane conductance regulator (CFTR). NHERF-PDZ1 domain interaction partners include Npt2a, purinergic P2Y1 receptor, beta2-AR, CFTR, PTHR, NH3, G-protein-coupled receptor kinase 6 (GRK6A), platelet-derived growth factor receptor (PDGFR), B1 subunit of the H+ATPase, cholesterol, receptor for activated C-kinase RACK1, aquaporin 9, among others. The NHERF PDZ2 domain interacts with fewer proteins: NHERF1 PDZ2 binds Npt2a, PTHR, beta-catenin, aquaporin 9, and RACK1; NHERF2 PDZ2 binds LPA2, P2Y1R, and NHE3, cGMP-dependent protein kinase type II (cGKII). NHERF4 PDZ1 and PDZ4 bind the epithelial Ca(2+) channels TRPV5 and TRPV6. NHERF2/NHERF3 heterodimerization is mediated by PDZ domains of NHERF2 and the C-terminal PDZ domain recognition motif of NHERF3. NHERF4 regulates several transporters mediating influx of xenobiotics and nutrients in the small intestine. 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 NHERF-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.


Pssm-ID: 467249 [Multi-domain]  Cd Length: 80  Bit Score: 34.72  E-value: 7.18e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 193787027  16 GFHLH----------GDVEPSSPAALAGLRPYtDYVV 42
Cdd:cd06768   13 GFNLHaekgrpghfiREVDPGSPAERAGLKDG-DRLV 48
 
Name Accession Description Interval E-value
GRASP55_65 pfam04495
GRASP55/65 PDZ-like domain; GRASP55 (Golgi re-assembly stacking protein of 55 kDa) and GRASP65 ...
 3-50 9.27e-08

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.


Pssm-ID: 427981 [Multi-domain]  Cd Length: 138  Bit Score: 49.96  E-value: 9.27e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 193787027    3 LGVSAE--QPAGGAE-GFHLHgDVEPSSPAALAGLRPYTDYVVGSD-QILQE 50
Cdd:pfam04495  28 LGLSLRwcSFAKALEnVWHVL-DVHENSPAAKAGLQPYSDYIIGTPkGLLKG 78
PDZ_NHERF-like cd06768
PDZ domains of the Na+/H+ exchange regulatory cofactor (NHERF) family (NHERF1-4), and related ...
 16-42 7.18e-03

PDZ domains of the Na+/H+ exchange regulatory cofactor (NHERF) family (NHERF1-4), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the Na+/H+ exchange regulatory cofactor (NHERF) family of multi-PDZ-domain-containing scaffolding proteins (NHERF1-4), and related domains. The NHERF family includes NHERF1 (also known as EBP50), NHERF2 (also known as E3KARP; TKA-1; SIP-1), NHERF3 (also known as CAP70; CLAMP; Napi-Cap-1; PDZD1) and NHERF4 (also known as IKEPP; PDZK2; Napi-Cap-2). NHERF1 and NHERF2 have tandem PDZ domains (PDZ1-2); NHERF3 and NHERF4 have four PDZ domains (PDZ1-4). NHERFs are involved in the regulation of multiple receptors or transporters, such as type II sodium-phosphate cotransporter (Npt2a), purinergic P2Y1 receptor P2Y1R, the beta2-adrenergic receptor (beta2-AR), parathyroid hormone receptor type 1 (PTHR), the lysophosphatidic acid receptors (LPARs), sodium-hydrogen exchanger 3 (NHE3), and cystic fibrosis transmembrane conductance regulator (CFTR). NHERF-PDZ1 domain interaction partners include Npt2a, purinergic P2Y1 receptor, beta2-AR, CFTR, PTHR, NH3, G-protein-coupled receptor kinase 6 (GRK6A), platelet-derived growth factor receptor (PDGFR), B1 subunit of the H+ATPase, cholesterol, receptor for activated C-kinase RACK1, aquaporin 9, among others. The NHERF PDZ2 domain interacts with fewer proteins: NHERF1 PDZ2 binds Npt2a, PTHR, beta-catenin, aquaporin 9, and RACK1; NHERF2 PDZ2 binds LPA2, P2Y1R, and NHE3, cGMP-dependent protein kinase type II (cGKII). NHERF4 PDZ1 and PDZ4 bind the epithelial Ca(2+) channels TRPV5 and TRPV6. NHERF2/NHERF3 heterodimerization is mediated by PDZ domains of NHERF2 and the C-terminal PDZ domain recognition motif of NHERF3. NHERF4 regulates several transporters mediating influx of xenobiotics and nutrients in the small intestine. 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 NHERF-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.


Pssm-ID: 467249 [Multi-domain]  Cd Length: 80  Bit Score: 34.72  E-value: 7.18e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 193787027  16 GFHLH----------GDVEPSSPAALAGLRPYtDYVV 42
Cdd:cd06768   13 GFNLHaekgrpghfiREVDPGSPAERAGLKDG-DRLV 48
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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