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FYVE/PHD zinc finger superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   FYVE/PHD zinc finger [ 57902]
Superfamily:   FYVE/PHD zinc finger [ 57903] (3)
Families:   FYVE, a phosphatidylinositol-3-phosphate binding domain [ 57904] (6)
  PHD domain [ 57911] (13)
  variant PHD-like domain [ 118346]


Superfamily statistics
Genomes (563) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 41,327 0 26
Proteins 34,656 0 26


Functional annotation
General category Information
Detailed category DNA replication/repair

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring one-carbon groups0.0000000006577Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.008364Least InformativeInherited
Enzyme Commission (EC)Acting on ester bonds0.2911Least InformativeInherited
Enzyme Commission (EC)Oxidoreductases0.067Least InformativeInherited
Enzyme Commission (EC)Acting on paired donors, with incorporation or red0Moderately InformativeDirect
Enzyme Commission (EC)Methyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0.0000000268Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0.0000003973Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.0005085Moderately InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as accep0.0831Moderately InformativeInherited
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect
Enzyme Commission (EC)Histone acetyltransferase0InformativeDirect
Enzyme Commission (EC)Protein-tyrosine-phosphatase0.0000000008157InformativeDirect
Enzyme Commission (EC)With 2-oxoglutarate as one donor, and incorporatio0Highly InformativeDirect
Enzyme Commission (EC)1-phosphatidylinositol-3-phosphate 5-kinase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.2785Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.5352Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cardiovascular system morphology0.3262Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.4704Moderately InformativeInherited
Phenotypic Abnormality (PA)Hypoplastic male external genitalia0.0009163Highly InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.000323Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.003684Least InformativeInherited
Worm Phenotype (WP)cell development variant0.004048Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.05688Least InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.04008Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.0636Moderately InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.06798Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.2255Moderately InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant0.5221Moderately InformativeInherited
Worm Phenotype (WP)apoptosis variant0.9144Moderately InformativeInherited
Worm Phenotype (WP)endocytic transport defect0.00000179InformativeDirect
Worm Phenotype (WP)cell fate specification variant0.0000243InformativeDirect
Worm Phenotype (WP)vulva development variant0.0001046InformativeDirect
Worm Phenotype (WP)tail morphology variant0.0003508InformativeDirect
Worm Phenotype (WP)protein modification variant0.000713InformativeDirect
Worm Phenotype (WP)alimentary system development variant0.4868InformativeInherited
Worm Phenotype (WP)multivulva0.000000007247Highly InformativeDirect
Worm Phenotype (WP)coelomocyte uptake defective0.00000009285Highly InformativeDirect
Worm Phenotype (WP)organism UV hypersensitive0.0000006602Highly InformativeDirect
Worm Phenotype (WP)ectopic expression transgene0.0000008656Highly InformativeDirect
Worm Phenotype (WP)transgenerational loss of fertility0.000002259Highly InformativeDirect
Worm Phenotype (WP)vulvaless0.000759Highly InformativeDirect
Worm Phenotype (WP)gut granule development variant0.002514Highly InformativeInherited
Worm Phenotype (WP)lysosome organization biogenesis variant0.003032Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)modifier of variegation0.00000002055InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)larva0.3515Least InformativeInherited
Fly Anatomy (FA)somatic cell0.557Least InformativeInherited
Fly Anatomy (FA)embryo0.662Least InformativeInherited
Fly Anatomy (FA)late embryo0.6197Moderately InformativeInherited
Fly Anatomy (FA)circulatory system0.4696InformativeInherited
Fly Anatomy (FA)embryonic/larval garland cell0.0006986Highly InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0.008864Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.1383Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.3762Least InformativeInherited
Xenopus ANatomical entity (XAN)testis0.0004482Moderately 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)portion of meristem tissue0.4074Least InformativeInherited
Plant ANatomical entity (PAN)shoot axis0.675Least InformativeInherited
Plant ANatomical entity (PAN)shoot apical meristem0.000005463Highly InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0.7379Least InformativeInherited
Enzyme Commission (EC)Transferring phosphorus-containing groups1Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Acyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0.0003041Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.001839Moderately InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides0.03863Moderately InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0.1076Moderately InformativeInherited
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect
Enzyme Commission (EC)Histone acetyltransferase0InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen. The oxygen incorporate2.506e-16InformativeDirect
Enzyme Commission (EC)DNA helicase0.000000001744InformativeDirect
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0.0000001736InformativeDirect
Enzyme Commission (EC)Protein-tyrosine-phosphatase0.000000427InformativeDirect
Enzyme Commission (EC)Protein-tyrosine kinases0.0001624InformativeDirect
Enzyme Commission (EC)With 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors0Highly InformativeDirect
Enzyme Commission (EC)Non-specific protein-tyrosine kinase0.000002757Highly 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 processTranscription regulation0Moderately InformativeDirect
Biological processUbl conjugation pathway0Moderately InformativeDirect
Biological processCell cycle0.0000004072Moderately InformativeDirect
Biological processProtein transport0.000003236Moderately InformativeDirect
Biological processNeurogenesis0InformativeDirect
Biological processBiological rhythms0.000000002693InformativeDirect
Biological processAutophagy0.00000000364InformativeDirect
Biological processMeiosis0.00000001248InformativeDirect
Biological processEndocytosis0.000005151InformativeDirect
Biological processExocytosis0.0000000000001487Highly InformativeDirect
Biological processGrowth regulation0.00000000000255Highly InformativeDirect
Biological processNeurotransmitter transport0.0000008604Highly InformativeDirect
Biological processFlowering0.000001283Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentCytoplasm1Least InformativeInherited
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentCytoskeleton0.000000000002712Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0.000000000004832Moderately InformativeDirect
Cellular componentCell junction0.0000000009497Moderately InformativeDirect
Cellular componentChromosome0.00000000000001354InformativeDirect
Cellular componentCentromere0.000144Highly InformativeDirect
Coding sequence diversityAlternative splicing0Least InformativeDirect
Coding sequence diversityChromosomal rearrangement0.0000001648InformativeDirect
DiseaseTumor suppressor0.00001579Moderately InformativeDirect
DiseaseMental retardation0.0002883InformativeDirect
DomainRepeat0.000000000000002154Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainCoiled coil0.000000000000001851Moderately InformativeDirect
DomainBromodomain0Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionLipid-binding0.00003079Moderately InformativeDirect
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationDNA-binding0.000000000000003094Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.000001177Moderately InformativeDirect
Post-translational modificationOxidoreductase0.3801Moderately InformativeInherited
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationActin-binding0.000005068InformativeDirect
Post-translational modificationGuanine-nucleotide releasing factor0.00003294InformativeDirect
Post-translational modificationHelicase0.0001815InformativeDirect
Post-translational modificationMethyltransferase0.0002598InformativeDirect
Post-translational modificationDioxygenase0Highly InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationAcetylation0.0000000000001315Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0Moderately InformativeDirect
Post-translational modificationCitrullination0.00000001084Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011011 SSF57903 Protein matches
Abstract

The FYVE zinc finger domain is conserved from yeast to man, and is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. It functions in the membrane recruitment of cytosolic proteins by binding to phosphatidylinositol 3-phosphate (PI3P), which is found mainly on endosomes [PubMed11911884, PubMed12665246].

The plant homeodomain (PHD) zinc finger domain has a C4HC3-type motif, and is widely distributed in eukaryotes, being found in many chromatin regulatory factors [PubMed14679290].

Both the FYVE and the PHD zinc finger motifs display strikingly similar dimetal(zinc)-bound alpha+beta folds.

More information about these proteins can be found at Protein of the Month: Zinc Fingers.


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) · Human Phenotype (HP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · 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 22 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 FYVE/PHD zinc finger 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 22 hidden Markov models representing the FYVE/PHD zinc finger 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) · Human Phenotype (HP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]