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Tubby C-terminal domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Tubby C-terminal domain-like [ 54517]
Superfamily:   Tubby C-terminal domain-like [ 54518] (2)
Families:   Transcriptional factor tubby, C-terminal domain [ 54519]
  At5g01750-like [ 143104]


Superfamily statistics
Genomes (722) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 4,455 11,979 3
Proteins 4,363 11,837 3


Functional annotation
General category Information
Detailed category Transcription

Document:
Function annotation of SCOP domain superfamilies

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0Least InformativeDirect
Mammalian Phenotype (MP)cardiovascular system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)abnormal cell death0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal eye morphology0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal neuron morphology0Moderately InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval growth variant0Least InformativeDirect
Worm Phenotype (WP)blast cell physiology variant0.03637Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.0364Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.1489Least InformativeInherited
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.0003508Moderately InformativeDirect
Worm Phenotype (WP)level of transgene expression variant0.005048Moderately InformativeInherited
Worm Phenotype (WP)transgene expression reduced0.0005275InformativeDirect

Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

InterPro annotation
Cross references IPR000007 SSF54518 Protein matches
Abstract

Tubby, an autosomal recessive mutation, mapping to mouse chromosome 7, was recently found to be the result of a splicing defect in a novel gene with unknown function. This mutation maps to the tub gene [PubMed8612280, PubMed8606774]. The mouse tubby mutation is the cause of maturity-onset obesity, insulin resistance and sensory deficits. By contrast with the rapid juvenile-onset weight gain seen in diabetes (db) and obese (ob) mice, obesity in tubby mice develops gradually, and strongly resembles the late-onset obesity observed in the human population. Excessive deposition of adipose tissue culminates in a two-fold increase of body weight. Tubby mice also suffer retinal degeneration and neurosensory hearing loss. The tripartite character of the tubby phenotype is highly similar to human obesity syndromes, such as Alstrom and Bardet-Biedl. Although these phenotypes indicate a vital role for tubby proteins, no biochemical function has yet been ascribed to any family member [PubMed10591637], although it has been suggested that the phenotypic features of tubby mice may be the result of cellular apoptosis triggered by expression of the mutated tub gene. TUB is the founding-member of the tubby-like proteins, the TULPs. TULPs are found in multicellular organisms from both the plant and animal kingdoms. Ablation of members of this protein family cause disease phenotypes that are indicative of their importance in nervous-system function and development [PubMed14708010].

Mammalian TUB is a hydrophilic protein of ~500 residues. The N-terminal portion of the protein is conserved neither in length nor sequence, but, in TUB, contains the nuclear localisation signal and may have transcriptional-activation activity. The C-terminal 250 residues are highly conserved. The C-terminal extremity contains a cysteine residue that might play an important role in the normal functioning of these proteins. The crystal structure of the C-terminal core domain from mouse tubby has been determined to 1.9A resolution. This domain is arranged as a 12-stranded, all anti-parallel, closed beta-barrel that surrounds a central alpha helix, (which is at the extreme carboxyl terminus of the protein) that forms most of the hydrophobic core. Structural analyses suggest that TULPs constitute a unique family of bipartite transcription factors [PubMed10591637].


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 · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) ]

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 3 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 Tubby C-terminal 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 3 hidden Markov models representing the Tubby C-terminal 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 · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Internal database links ]