SUPERFAMILY 1.75 HMM library and genome assignments server


ENTH/VHS domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   alpha-alpha superhelix [ 48370] (24)
Superfamily:   ENTH/VHS domain [ 48464] (4)
Families:   ENTH domain [ 48465]
  VHS domain [ 48468] (5)
  Phosphoinositide-binding clathrin adaptor, N-terminal domain [ 100911] (2)
  RPR domain (SMART 00582 ) [ 109975]


Superfamily statistics
Genomes (446) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 8,577 6,851 14
Proteins 8,552 6,837 14


Functional annotation
General category Processes_IC
Detailed category Transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)developmental process0.00070161Least InformativeInherited
Biological Process (BP)multicellular organismal process0.0014820.9795Least InformativeInherited
Biological Process (BP)single-organism cellular process0.014120.003776Least InformativeInherited
Biological Process (BP)response to stimulus0.052961Least InformativeInherited
Biological Process (BP)regulation of cellular process0.68560.7904Least InformativeInherited
Biological Process (BP)single-organism developmental process0.010371Moderately InformativeInherited
Biological Process (BP)organ development0.1311Moderately InformativeInherited
Biological Process (BP)signal transduction0.00076590.1688Moderately InformativeInherited
Biological Process (BP)embryonic organ development9.241e-080.0002605InformativeDirect
Biological Process (BP)embryo development ending in birth or egg hatching9.656e-070.01302InformativeInherited

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) localization 3.749e-15 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.7904 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.003776 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.5842 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.9795 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular localization 0 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.0007966 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.6262 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.6617 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) system process 0.011 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.1931 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.8013 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.1335 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.7064 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.4471 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.2035 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.4315 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.583 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.2723 Moderately Informative Inherited
Biological Process (BP) organic substance transport 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.1567 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.1688 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.1242 Moderately Informative Inherited
Biological Process (BP) gene expression 0.2067 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.1043 Moderately Informative Inherited
Biological Process (BP) embryonic organ development 0.0002605 Informative Direct
Biological Process (BP) vesicle-mediated transport 3.434e-11 Informative Direct
Biological Process (BP) secretion by cell 2.718e-10 Informative Direct
Biological Process (BP) membrane organization 3.653e-08 Informative Direct
Biological Process (BP) protein transport 1.019e-07 Informative Direct
Biological Process (BP) transmission of nerve impulse 3.883e-05 Informative Direct
Biological Process (BP) RNA processing 0.0003149 Informative Direct
Biological Process (BP) negative regulation of developmental process 0.08164 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.1315 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.1356 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.1802 Informative Inherited
Biological Process (BP) protein localization to organelle 0.9027 Informative Inherited
Biological Process (BP) dephosphorylation 0.05477 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.996 Informative Inherited
Biological Process (BP) organelle localization 0.06863 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.007367 Informative Inherited
Biological Process (BP) positive regulation of protein metabolic process 0.0112 Informative Inherited
Biological Process (BP) transmembrane transport 0.286 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.001951 Informative Inherited
Biological Process (BP) protein complex assembly 0.7355 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.1279 Informative Inherited
Biological Process (BP) protein catabolic process 0.1437 Informative Inherited
Biological Process (BP) proteolysis 0.264 Informative Inherited
Biological Process (BP) cytoskeleton organization 0.4142 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.8611 Informative Inherited
Biological Process (BP) cell-cell signaling 0.002115 Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.06485 Informative Inherited
Biological Process (BP) cytoplasmic transport 1 Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.001673 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.01302 Informative Inherited
Biological Process (BP) actin filament-based process 0.01243 Informative Inherited
Biological Process (BP) synaptic vesicle localization 0 Highly Informative Direct
Biological Process (BP) regulation of neurotransmitter levels 7.331e-15 Highly Informative Direct
Biological Process (BP) vesicle organization 8.283e-14 Highly Informative Direct
Biological Process (BP) neurotransmitter transport 3.31e-10 Highly Informative Direct
Biological Process (BP) establishment of vesicle localization 6.911e-06 Highly Informative Direct
Biological Process (BP) autophagy 7.707e-06 Highly Informative Direct
Biological Process (BP) regulation of protein catabolic process 6.796e-05 Highly Informative Direct
Biological Process (BP) mRNA processing 6.896e-05 Highly Informative Direct
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 8.528e-05 Highly Informative Direct
Biological Process (BP) signal release 0.0002366 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 0.02225 Highly Informative Inherited
Biological Process (BP) protein dephosphorylation 0.002344 Highly Informative Inherited
Biological Process (BP) protein import 0.03514 Highly Informative Inherited
Biological Process (BP) ubiquitin-dependent protein catabolic process 0.05002 Highly Informative Inherited
Biological Process (BP) regulation of vesicle-mediated transport 0.002075 Highly Informative Inherited
Biological Process (BP) Golgi vesicle transport 0.06294 Highly Informative Inherited
Molecular Function (MF) binding 1.347e-05 Least Informative Direct
Molecular Function (MF) anion binding 1.614e-06 Moderately Informative Direct
Molecular Function (MF) lipid binding 1.826e-11 Informative Direct
Molecular Function (MF) enzyme binding 0.0205 Informative Inherited
Molecular Function (MF) cytoskeletal protein binding 0.3883 Informative Inherited
Molecular Function (MF) protein complex binding 0.02868 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 0.04404 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.4569 Least Informative Inherited
Cellular Component (CC) protein complex 0.03251 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1043 Least Informative Inherited
Cellular Component (CC) membrane 0.02455 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) vesicle 3.5e-07 Moderately Informative Direct
Cellular Component (CC) endomembrane system 2.628e-06 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 6.515e-06 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0.6399 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.7047 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.9408 Moderately Informative Inherited
Cellular Component (CC) endosome 2.842e-08 Informative Direct
Cellular Component (CC) cell cortex 5.539e-08 Informative Direct
Cellular Component (CC) coated vesicle 3.055e-07 Informative Direct
Cellular Component (CC) nuclear DNA-directed RNA polymerase complex 3.183e-06 Informative Direct
Cellular Component (CC) nucleoplasm part 0.0008025 Informative Direct
Cellular Component (CC) actin cytoskeleton 0.001982 Informative Inherited
Cellular Component (CC) coated pit 0 Highly Informative Direct
Cellular Component (CC) clathrin-coated vesicle 0 Highly Informative Direct
Cellular Component (CC) cortical cytoskeleton 5.136e-09 Highly Informative Direct
Cellular Component (CC) trans-Golgi network 5.371e-08 Highly Informative Direct
Cellular Component (CC) endosomal part 0.0001124 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 0.5595 Highly Informative Inherited

Document: GO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal homeostasis0.9693Least InformativeInherited
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0.4836Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal circulating glucose level0.05372InformativeInherited
Mammalian Phenotype (MP)decreased body size0.07419InformativeInherited
Mammalian Phenotype (MP)abnormal total tissue mass0.7322InformativeInherited
Mammalian Phenotype (MP)postnatal growth retardation1.468e-05Highly InformativeDirect
Mammalian Phenotype (MP)decreased birth weight0.0007168Highly InformativeDirect
Mammalian Phenotype (MP)hypoglycemia0.0009177Highly InformativeDirect
Mammalian Phenotype (MP)decreased body weight0.02393Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.0006634Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.1134Least InformativeInherited
Worm Phenotype (WP)endocytic transport defect0.005458Moderately InformativeInherited
Worm Phenotype (WP)chemical response variant0.005993Moderately InformativeInherited
Worm Phenotype (WP)drug resistant0.1295InformativeInherited
Worm Phenotype (WP)coelomocyte uptake defective4.753e-06Highly InformativeDirect
Worm Phenotype (WP)aldicarb resistant0.0002594Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)intracellular transport0.0006977InformativeDirect

Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processProtein transport0Moderately InformativeDirect
Biological processEndocytosis0InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Cellular componentCoated pit0Highly InformativeDirect
DomainZinc-finger2.426e-06Moderately InformativeDirect
DomainCoiled coil6.32e-05Moderately InformativeDirect
DomainSH3 domain0InformativeDirect
Molecular functionZinc0.0006408Least InformativeDirect
Molecular functionLipid-binding0InformativeDirect
Molecular functionActin-binding1.071e-06InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationAcetylation0.0005041Least InformativeDirect
Post-translational modificationUbl conjugation4.695e-08Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008942 SSF48464 Protein matches
Abstract

This entry represents domains with a multi-helical, alpha-alpha 2-layered structural fold as found in: the ENTH domain of Epsin; the VHS domain of Hrs, Tom1, and ADP-ribosylation factors; the RPR domain of PCF11 protein; and the N-terminal domain of phosphoinositide-binding clathrin adaptor.

The epsin NH2-terminal homology (ENTH) domain is a membrane interacting module composed of a superhelix of alpha-helices. It is present at the NH2-terminus of proteins that often contain consensus sequences for binding to clathrin coat components and their accessory factors, and therefore function as endocytic adaptors. ENTH domain containing proteins have additional roles in signalling and actin regulation and may have yet other actions in the nucleus. The ENTH domain is structurally similar to the VHS domain.

The ENTH domain is approximately 150 amino acids long. The ENTH domain forms a compact globular structure, composed of eight alpha-helices connected by loops of varying length. Three helical hairpins that are stacked consecutively with a right-handed twist determine the general topology of the domain. This stacking gives the ENTH domain a rectangular appearance when viewed face on. The most highly conserved amino acids fall roughly into two classes: internal residues that are involved in packing and therefore are necessary for structural integrity, and solvent accessible residues that may be involved in protein-protein interactions [PubMed11911874].

VHS domains are found at the N-termini of select proteins involved in intracellular membrane trafficking. The domain consists of eight helices arranged in a superhelix. The surface of the domain has two main features: a basic patch on one side due to several conserved positively charged residues on helix 3 and a negatively charged ridge on the opposite side, formed by residues on helix 2. Comparison of the two VHS domains and the ENTH domain reveals a conserved surface, composed of helices 2 and 4, that is utilised for protein-protein interactions. In addition, VHS domain-containing proteins are also often localized to membranes. It has therefore been suggested that the conserved positively charged surface of helix 3 in VHS and ENTH domains plays a role in membrane binding [PubMed10985773].


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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 10 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 ENTH/VHS domain 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 10 hidden Markov models representing the ENTH/VHS domain 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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]