1U3B,3SUZ,1U37,2YT7


Conserved Protein Domain Family
PDZ1_APBA1_3-like

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cd06720: PDZ1_APBA1_3-like 
PDZ domain 1 of amyloid-beta A4 precursor protein-binding family A member 1 (APBA1), APBA2, APBA3, and related domains
PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of APBA1, APBA2, APBA3, and related domains. The APBA/X11/Mint protein family includes three members: neuron specific APBA1 (also known as X11alpha and Mint1) and APBA2 (also known as X11beta and Mint2), and the ubiquitously expressed APBA3 (also known as (X12gamma and Mint3). They are involved in regulating neuronal signaling, trafficking and plasticity. They contain two PDZ domains (PDZ1 and PDZ2) which bind a variety of proteins: Arf GTPases (APBA1 and APBA2 PDZ2) and neurexin (APBA1 and APBA2 PDZ1 and 2), which are involved in vesicle docking and exocytosis; alpha1B subunit of N-type Ca2+ channel (APBA1 PDZ1) that is involved in ion channels; KIF17 (APBA1 PDZ1) that is involved in transport and traffic; and Alzheimer's disease related proteins such as APP (APBA3 PDZ2), CCS (APBA1 PDZ2), NF-kappa-B/p65 (APBA2 PDZ2), presenilin-1 (APBA1 and APBA2 PDZ1 and PDZ2). 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 APBA1,2,3-like family domain is a canonical PDZ domain containing 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.
Statistics
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PSSM-Id: 467203
Aligned: 29 rows
Threshold Bit Score: 129.302
Created: 20-Jun-2007
Updated: 27-Apr-2023
Structure
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Program:
Drawing:
Aligned Rows:
 
peptide binding
Conserved site includes 13 residues -Click on image for an interactive view with Cn3D
Feature 1:peptide binding site [polypeptide binding site]
Evidence:
  • Comment:based on canonical PDZ domains with structure
  • Comment:PDZ domains specifically recognize and bind to short C-terminal peptide motifs, but can also recognize internal peptide motifs and certain lipids
  • Structure:1U3B: PDZ domain 1 of human APBA1 (in autoinhibited conformation) binds APBA1 C-terminal peptide; contacts at 4A
  • Comment:in this autoinhibited conformation the C-terminal tail of APBA1 folds back and inserts into the target-binding groove of the first PDZ domain; the binding of this tail occludes the binding of other target peptides
  • Structure:3SUZ: PDZ domain 1 of Rattus norvegicus APBA2 binds its C-terminal self-binding motif extension (PLYI); contacts at 4A

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                    #######             #  #                             #   #  ##       
1U3B_A          3 KDVFIEKQKGeILGVVIVESGWGSILPTVIIANMMhGGPAEKSGKLNIGDQIMSINGTSLVGLPLSTCQSIIKGLKNQsR 82   human
O17583        800 KEVVVPKKAGePLGIVVVESGWGSMLPTVVLAHMNpVGPAAHSNKLNIGDQIININGISLVGLPLSAAQTQIKNMKTAtA 879  Caenorhabditi...
NP_727440    1957 KEVVVPKAKGeILGVVIVESGWGSMLPTVVIANLMsSGAAARCGQLNIGDQLIAINGLSLVGLPLSTCQTYIKNTKNQtV 2036 fruit fly
EEC20174      347 KEVVVPKQKGeILGMVIVESGWGSMLPTVVVANMAhNGPAARCSQLNIGDQIIAINGVSLVGLPLSTCQAYVKNTKHQnV 426  black-legged ...
ELU02867      159 KEVIAPKLKGePLGVVIVESGWGSMVPTVVLANMNpAGAAARCGQLNIGDQIMSVNGVSLVGLPLSSCQNYIKATKNQtV 238  Capitella teleta
EFX71305      192 KEVIVPKARNeILGVVIVESGWGSMLPTVVIANLApAGAAARCGQLNIGDQIIAINGISLVGLPLSTCQTYIKNAKSAtV 271  Daphnia pulex
XP_002110545  127 KKVVVRKKRNeNLGIMIIPSGWGSLIPAPVIAHINkFGPAALGGQLNVGDHLMFVNGISLVALPIDKCKAIIKVHCQAtE 206  Trichoplax ad...
XP_012557201  642 REVVVVKKVGdPLGIMLLESGWGSMLPTVFVAHIAnYSATAQCQKISVGDHILACDGTSLVGLSLSECTTILKNFRNSnK 721  Hydra vulgaris
XP_019855699  460 REITFAKPKGdILGLVVIDSGYGSVIPSCIVAHMNkTGAAGRSNLLNVGDQILSINGVSLVGMPLRVAIDQIKKCRNLtL 539  Amphimedon qu...
XP_014158662  502 TQVTLRKTPDeSLGFMITETSRSSLLPCVFVSHIYpGGAASRSHLLHVGDTILAVNGVSLVGLPFKESLKLFKDLSVGtE 581  Sphaeroforma ...
Feature 1               
1U3B_A         83 VKLNIV 88   human
O17583        880 VRMTVV 885  Caenorhabditis elegans
NP_727440    2037 VKFTVV 2042 fruit fly
EEC20174      427 VKLTVV 432  black-legged tick
ELU02867      239 VKLNVV 244  Capitella teleta
EFX71305      272 VKLTVV 277  Daphnia pulex
XP_002110545  207 VTLEIV 212  Trichoplax adhaerens
XP_012557201  722 VTFRVV 727  Hydra vulgaris
XP_019855699  540 VKMTTC 545  Amphimedon queenslandica
XP_014158662  582 INLTVV 587  Sphaeroforma arctica JP610

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