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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 (504) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 9,801 23,171 14
Proteins 9,768 23,099 14


Functional annotation
General category Processes_IC
Detailed category Transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) biological regulation 0.7437 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.273 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.4269 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.7866 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.9863 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.7615 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.9329 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) cellular localization 0.000000007416 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0006592 Moderately Informative Direct
Biological Process (BP) cellular component assembly 0.0008614 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.2728 Moderately Informative Inherited
Biological Process (BP) single-organism transport 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.7809 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.4654 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.02853 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.07937 Moderately Informative Inherited
Biological Process (BP) protein complex biogenesis 0.1638 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.1648 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 0.1459 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.8109 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.01092 Moderately Informative Inherited
Biological Process (BP) gene expression 0.03481 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.05412 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.2509 Moderately Informative Inherited
Biological Process (BP) single organism signaling 0.01492 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.004096 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.851 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.1688 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.928 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.169 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.02744 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.2111 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.02645 Moderately Informative Inherited
Biological Process (BP) cell communication 0.04529 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.3887 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.4433 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.6193 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.7921 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.2165 Moderately Informative Inherited
Biological Process (BP) vesicle-mediated transport 0 Informative Direct
Biological Process (BP) protein transport 0.000000000000003734 Informative Direct
Biological Process (BP) secretion by cell 0.00000000000005545 Informative Direct
Biological Process (BP) intracellular transport 0.000000007407 Informative Direct
Biological Process (BP) single-organism cellular localization 0.0000004743 Informative Direct
Biological Process (BP) cellular protein complex assembly 0.000004746 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.0003081 Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 0.02743 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.2083 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.2697 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.3978 Informative Inherited
Biological Process (BP) protein localization to organelle 0.01754 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.9077 Informative Inherited
Biological Process (BP) organelle localization 0.0788 Informative Inherited
Biological Process (BP) transmembrane transport 0.2467 Informative Inherited
Biological Process (BP) proteolysis 0.01127 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.04917 Informative Inherited
Biological Process (BP) regulation of cell differentiation 0.2792 Informative Inherited
Biological Process (BP) regulation of proteolysis 0.1262 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 0.1978 Informative Inherited
Biological Process (BP) positive regulation of catalytic activity 0.208 Informative Inherited
Biological Process (BP) positive regulation of cellular protein metabolic process 0.2792 Informative Inherited
Biological Process (BP) actin cytoskeleton organization 0.005475 Informative Inherited
Biological Process (BP) supramolecular fiber organization 0.001337 Informative Inherited
Biological Process (BP) transcription, DNA-templated 0.006743 Informative Inherited
Biological Process (BP) regulation of neurotransmitter levels 0 Highly Informative Direct
Biological Process (BP) vesicle organization 0.000000001246 Highly Informative Direct
Biological Process (BP) autophagy 0.000000005938 Highly Informative Direct
Biological Process (BP) mRNA processing 0.00000003073 Highly Informative Direct
Biological Process (BP) cell-cell signaling 0.00000004177 Highly Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 0.0000001429 Highly Informative Direct
Biological Process (BP) establishment of organelle localization 0.0001076 Highly Informative Direct
Biological Process (BP) actin filament organization 0.0001216 Highly Informative Direct
Biological Process (BP) transcription from RNA polymerase II promoter 0.0001705 Highly Informative Direct
Biological Process (BP) protein dephosphorylation 0.0009916 Highly Informative Direct
Biological Process (BP) cellular protein catabolic process 0.007173 Highly Informative Inherited
Biological Process (BP) modification-dependent macromolecule catabolic process 0.03618 Highly Informative Inherited
Biological Process (BP) protein import 0.001583 Highly Informative Inherited
Biological Process (BP) positive regulation of proteolysis 0.002886 Highly Informative Inherited
Biological Process (BP) positive regulation of hydrolase activity 0.02668 Highly Informative Inherited
Biological Process (BP) Golgi vesicle transport 0.8071 Highly Informative Inherited
Molecular Function (MF) binding 0.00000006436 Least Informative Direct
Molecular Function (MF) anion binding 0.000004057 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.1975 Moderately Informative Inherited
Molecular Function (MF) phospholipid binding 0.000000000000003188 Informative Direct
Molecular Function (MF) RNA binding 0.00001124 Informative Direct
Molecular Function (MF) enzyme binding 0.01113 Informative Inherited
Molecular Function (MF) macromolecular complex binding 0.02426 Informative Inherited
Molecular Function (MF) protein domain specific binding 0.0006149 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.0000321 Least Informative Direct
Cellular Component (CC) membrane 0.005053 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.00596 Least Informative Inherited
Cellular Component (CC) protein complex 0.01006 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) endomembrane system 0 Moderately Informative Direct
Cellular Component (CC) vesicle 0.000000000000003036 Moderately Informative Direct
Cellular Component (CC) whole membrane 0.000000009284 Moderately Informative Direct
Cellular Component (CC) plasma membrane 0.7356 Moderately Informative Inherited
Cellular Component (CC) transferase complex 0.07774 Moderately Informative Inherited
Cellular Component (CC) cytoskeleton 0.007555 Moderately Informative Inherited
Cellular Component (CC) membrane protein complex 0.04101 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.2824 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.1135 Moderately Informative Inherited
Cellular Component (CC) cytoplasmic vesicle part 0.00000000009106 Informative Direct
Cellular Component (CC) membrane region 0.00000001416 Informative Direct
Cellular Component (CC) cytoplasmic region 0.0000004177 Informative Direct
Cellular Component (CC) endosome 0.000002662 Informative Direct
Cellular Component (CC) Golgi apparatus 0.000004584 Informative Direct
Cellular Component (CC) transferase complex, transferring phosphorus-containing groups 0.0002745 Informative Direct
Cellular Component (CC) plasma membrane region 0.01946 Informative Inherited
Cellular Component (CC) actin cytoskeleton 0.004441 Informative Inherited
Cellular Component (CC) nucleoplasm part 0.04277 Informative Inherited
Cellular Component (CC) membrane coat 0.0000000009678 Highly Informative Direct
Cellular Component (CC) cortical cytoskeleton 0.00000858 Highly Informative Direct
Cellular Component (CC) coated vesicle 0.000009628 Highly Informative Direct
Cellular Component (CC) presynapse 0.0001767 Highly Informative Direct
Cellular Component (CC) Golgi subcompartment 0.0007999 Highly Informative Direct

Document: GO 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
Biological processmRNA processing0.000005509InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Cellular componentCoated pit0Highly InformativeDirect
Coding sequence diversityAlternative splicing0.0009572Least InformativeDirect
DomainZinc-finger0.0000008047Moderately InformativeDirect
DomainCoiled coil0.00003711Moderately InformativeDirect
DomainSH3 domain0InformativeDirect
Molecular functionLipid-binding0Moderately InformativeDirect
Post-translational modificationActin-binding0.000001837InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation0.000000000000004662Moderately InformativeDirect
Post-translational modificationIsopeptide bond0.000009431Moderately 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-coverage) · 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-coverage) · UniProtKB KeyWords (KW) · Internal database links ]