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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 0 117
Proteins 37,943 0 112


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 eye0.4377Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.424Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of vision0.3342InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.000003399Least InformativeDirect
Mammalian Phenotype (MP)abnormal nervous system physiology0.1534Moderately InformativeInherited
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.3606Moderately InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.7764Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.8288Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.8996Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal behavior1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cochlear hair cell morphology0.01122InformativeInherited
Mammalian Phenotype (MP)abnormal behavioral response to xenobiotic0.08983InformativeInherited
Mammalian Phenotype (MP)abnormal neural tube morphology0.5482InformativeInherited
Mammalian Phenotype (MP)craniorachischisis0.0001196Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cochlear hair cell stereociliary bundle morphology0.000263Highly 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 variant0.05863Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.09453Least InformativeInherited
Worm Phenotype (WP)cell development variant0.1165Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.1558Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.3267Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.4233Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.5097Least InformativeInherited
Worm Phenotype (WP)protein expression variant0.0009954Moderately InformativeDirect
Worm Phenotype (WP)chemical response variant0.0223Moderately InformativeInherited
Worm Phenotype (WP)nervous system morphology variant0.07534Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.3342Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.6265Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.7463Moderately InformativeInherited
Worm Phenotype (WP)aldicarb response variant0.000002894InformativeDirect
Worm Phenotype (WP)drug resistant0.000848InformativeDirect
Worm Phenotype (WP)organelle organization biogenesis variant0.02265InformativeInherited
Worm Phenotype (WP)cell number increased0.2366InformativeInherited
Worm Phenotype (WP)epithelial system development variant0.5825InformativeInherited
Worm Phenotype (WP)oocyte morphology variant0.9219InformativeInherited
Worm Phenotype (WP)cell polarity variant0.000001853Highly InformativeDirect
Worm Phenotype (WP)presynaptic region morphology variant0.000007798Highly InformativeDirect
Worm Phenotype (WP)body muscle dystrophy0.00003175Highly InformativeDirect
Worm Phenotype (WP)body elongation variant0.0003284Highly InformativeDirect
Worm Phenotype (WP)cell division polarity variant0.000373Highly InformativeDirect
Worm Phenotype (WP)ovulation variant0.0004556Highly InformativeDirect
Worm Phenotype (WP)endomitotic oocytes0.0005909Highly InformativeDirect
Worm Phenotype (WP)cytoskeleton organization biogenesis variant0.005772Highly InformativeInherited
Worm Phenotype (WP)epithelial development variant0.008254Highly InformativeInherited
Worm Phenotype (WP)cell number decreased0.03787Highly 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 defective0.0008501InformativeDirect

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 structure0.5437Least InformativeInherited
Zebrafish Anatomy (ZA)nervous system0.6085Least InformativeInherited
Zebrafish Anatomy (ZA)compound organ0.6859Least InformativeInherited
Zebrafish Anatomy (ZA)cell0.9628Least InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.4791Moderately InformativeInherited
Zebrafish Anatomy (ZA)central nervous system0.9541Moderately InformativeInherited
Zebrafish Anatomy (ZA)spinal cord0.01229Highly InformativeInherited
Zebrafish Anatomy (ZA)ventricular system0.08182Highly 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 organ0.0001923Least 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 groups0.01203Least 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)Phosphoric monoester hydrolases0.0008453Moderately InformativeDirect
Enzyme Commission (EC)Acyltransferases0.2967Moderately InformativeInherited
Enzyme Commission (EC)Serine endopeptidases0InformativeDirect
Enzyme Commission (EC)Protein-tyrosine-phosphatase0.0000000009842InformativeDirect
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0.00001552InformativeDirect
Enzyme Commission (EC)Non-specific serine/threonine protein kinase0.0003943InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen. The oxygen incorporate0.00114InformativeInherited
Enzyme Commission (EC)Metalloendopeptidases0.2938InformativeInherited
Enzyme Commission (EC)With NADH or NADPH as one donor, and incorporation of one atom of oxygen0.00000217Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processApoptosis0Moderately InformativeDirect
Biological processDifferentiation0Moderately InformativeDirect
Biological processProtein transport0.000000000002052Moderately InformativeDirect
Biological processLipid metabolism1Moderately InformativeInherited
Biological processWnt signaling pathway0InformativeDirect
Biological processNeurogenesis0.00000000000004546InformativeDirect
Biological processStress response0.0000008326InformativeDirect
Biological processChemotaxis0.00003811InformativeDirect
Biological processCell adhesion0.00006631InformativeDirect
Biological processSteroid metabolism0.002093InformativeInherited
Biological processExocytosis0Highly InformativeDirect
Biological processCilium biogenesis/degradation0.00000000000258Highly InformativeDirect
Biological processHearing0.000000001303Highly InformativeDirect
Biological processOsteogenesis0.0000004136Highly InformativeDirect
Biological processNeurotransmitter transport0.000001947Highly InformativeDirect
Biological processCholesterol metabolism0.0001005Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCytoplasm1Least InformativeInherited
Cellular componentCytoskeleton0Moderately InformativeDirect
Cellular componentCell junction0Moderately InformativeDirect
Cellular componentCell projection0Moderately InformativeDirect
Cellular componentCell membrane0Moderately InformativeDirect
Cellular componentEndosome0.0000008727Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0.00004822Moderately InformativeDirect
Cellular componentPeriplasm0.00000000136InformativeDirect
Cellular componentSynapse1InformativeInherited
Cellular componentTight junction0Highly InformativeDirect
Cellular componentSynaptosome0.00001163Highly InformativeDirect
Coding sequence diversityAlternative splicing0.00000000000002715Least InformativeDirect
DiseaseDeafness0.0005711InformativeDirect
DomainRepeat0Least InformativeDirect
DomainTransmembrane1Least InformativeInherited
DomainCoiled coil0.00003042Moderately InformativeDirect
DomainSH3 domain0InformativeDirect
DomainSH3-binding0.0008277InformativeDirect
DomainLIM domain0Highly InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionLipid-binding0.000000001213Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationKinase1Moderately InformativeInherited
Post-translational modificationActin-binding0InformativeDirect
Post-translational modificationCalmodulin-binding0InformativeDirect
Post-translational modificationGTPase activation0InformativeDirect
Post-translational modificationGuanine-nucleotide releasing factor0InformativeDirect
Post-translational modificationSerine protease0InformativeDirect
Post-translational modificationSerine/threonine-protein kinase0.00000009532InformativeDirect
Post-translational modificationGrowth factor binding0.0000000000001352Highly InformativeDirect
Post-translational modificationSignal transduction inhibitor0.000001643Highly InformativeDirect
Post-translational modificationCytokine0.00003695Highly InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect

Document: KW 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) · UniProtKB KeyWords (KW) ]

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 79 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 79 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) · UniProtKB KeyWords (KW) · Internal database links ]