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PDZ domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   PDZ domain-like [ 50155]
Superfamily:   PDZ domain-like [ 50156] (6)
Families:   PDZ domain [ 50157] (46)
  Tail specific protease PDZ domain [ 68933] (2)
  HtrA-like serine proteases [ 74933] (4)
  Interleukin 16 [ 50172]
  EpsC C-terminal domain-like [ 159046]
  MTH1368 C-terminal domain-like [ 159049]


Superfamily statistics
Genomes (3,127) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 56,247 278,199 117
Proteins 37,943 201,025 112


Functional annotation
General category Regulation
Detailed category Signal transduction

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds1Least InformativeInherited
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Protein-serine/threonine kinases0Moderately InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or red0.0003073Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.0004756Moderately InformativeDirect
Enzyme Commission (EC)Protein-tyrosine-phosphatase0.0000000007522InformativeDirect
Enzyme Commission (EC)With NADH or NADPH as one donor, and incorporation0.0000003399InformativeDirect
Enzyme Commission (EC)Metalloendopeptidases0.3199InformativeInherited
Enzyme Commission (EC)Nitric-oxide synthase0.0000000000001896Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)genetic disease0.4853Moderately InformativeInherited
Disease Ontology (DO)autosomal recessive disease0.2182InformativeInherited

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the eye0.3802Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.6198Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of vision0.4438InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.000003416Least InformativeDirect
Mammalian Phenotype (MP)abnormal nervous system physiology0.1526Moderately InformativeInherited
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.3603Moderately InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.7771Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.8283Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.9003Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal behavior1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cochlear hair cell morphology0.01121InformativeInherited
Mammalian Phenotype (MP)abnormal behavioral response to xenobiotic0.08969InformativeInherited
Mammalian Phenotype (MP)abnormal neural tube morphology0.5499InformativeInherited
Mammalian Phenotype (MP)craniorachischisis0.0001188Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cochlear hair cell stereociliary bundle morphology0.0002626Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell morphology variant0.03576Least InformativeInherited
Worm Phenotype (WP)cell development variant0.07949Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.09868Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.1046Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.3339Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.5193Least InformativeInherited
Worm Phenotype (WP)chemical response variant0.02406Moderately InformativeInherited
Worm Phenotype (WP)nervous system morphology variant0.05256Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.6987Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.7356Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.7421Moderately InformativeInherited
Worm Phenotype (WP)aldicarb response variant0.000002926InformativeDirect
Worm Phenotype (WP)drug resistant0.0008202InformativeDirect
Worm Phenotype (WP)organelle organization biogenesis variant0.02213InformativeInherited
Worm Phenotype (WP)cell number increased0.2432InformativeInherited
Worm Phenotype (WP)epithelial system development variant0.5872InformativeInherited
Worm Phenotype (WP)oocyte morphology variant0.9227InformativeInherited
Worm Phenotype (WP)cell polarity variant0.000002487Highly InformativeDirect
Worm Phenotype (WP)presynaptic region morphology variant0.000007673Highly InformativeDirect
Worm Phenotype (WP)body muscle dystrophy0.00003778Highly InformativeDirect
Worm Phenotype (WP)body elongation variant0.0003253Highly InformativeDirect
Worm Phenotype (WP)cell division polarity variant0.000369Highly InformativeDirect
Worm Phenotype (WP)ovulation variant0.0004436Highly InformativeDirect
Worm Phenotype (WP)endomitotic oocytes0.0005863Highly InformativeDirect
Worm Phenotype (WP)cytoskeleton organization biogenesis variant0.00576Highly InformativeInherited
Worm Phenotype (WP)epithelial development variant0.008307Highly InformativeInherited
Worm Phenotype (WP)cell number decreased0.03827Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)cell polarity defective0.0008403InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)multi-tissue structure0.5481Least InformativeInherited
Zebrafish Anatomy (ZA)nervous system0.6016Least InformativeInherited
Zebrafish Anatomy (ZA)compound organ0.6913Least InformativeInherited
Zebrafish Anatomy (ZA)cell0.9696Least InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.4965Moderately InformativeInherited
Zebrafish Anatomy (ZA)central nervous system0.8707Moderately InformativeInherited
Zebrafish Anatomy (ZA)spinal cord0.01231Highly InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)cavitated compound organ0.0001701Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Transferring phosphorus-containing groups0.01164Least InformativeInherited
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Protein-serine/threonine kinases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptidases)0Moderately InformativeDirect
Enzyme Commission (EC)Aminoacyltransferases0.0005159Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.0008376Moderately InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0InformativeDirect
Enzyme Commission (EC)Protein-tyrosine-phosphatase0.0000000009831InformativeDirect
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0.0000141InformativeDirect
Enzyme Commission (EC)Non-specific serine/threonine protein kinase0.0003997InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen. The oxygen incorporate0.001272InformativeInherited
Enzyme Commission (EC)Metalloendopeptidases0.3004InformativeInherited
Enzyme Commission (EC)With NADH or NADPH as one donor, and incorporation of one atom of oxygen0.0000002236Highly InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR001478 SSF50156 Protein matches
Abstract

PDZ domains are found in diverse signaling proteins in bacteria, yeasts, plants, insects and vertebrates [PubMed9041651, PubMed9204764]. PDZ domains can occur in one or multiple copies and are nearly always found in cytoplasmic proteins. They bind either the carboxyl-terminal sequences of proteins or internal peptide sequences [PubMed9204764]. In most cases, interaction between a PDZ domain and its target is constitutive, with a binding affinity of 1 to 10 żM. However, agonist-dependent activation of cell surface receptors is sometimes required to promote interaction with a PDZ protein. PDZ domain proteins are frequently associated with the plasma membrane, a compartment where high concentrations of phosphatidylinositol 4,5-bisphosphate (PIP2) are found. Direct interaction between PIP2 and a subset of class II PDZ domains (syntenin, CASK, Tiam-1) has been demonstrated.

PDZ domains consist of 80 to 90 amino acids comprising six beta-strands (betaA to betaF) and two alpha-helices, A and B, compactly arranged in a globular structure. Peptide binding of the ligand takes place in an elongated surface groove as an antiparallel beta-strand interacts with the betaB strand and the B helix. The structure of PDZ domains allows binding to a free carboxylate group at the end of a peptide through a carboxylate-binding loop between the betaA and betaB strands.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 176 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a PDZ domain-like domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 176 hidden Markov models representing the PDZ domain-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]