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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 41,327 117,615 26
Proteins 34,656 97,856 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 head0.06859Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.1604Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal ocular adnexa morphology0.00002607Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the upper urinary tract0.1368Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.2662Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.6317Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal testis morphology0.2068InformativeInherited
Phenotypic Abnormality (PA)Abnormal leukocyte morphology0.3042InformativeInherited
Phenotypic Abnormality (PA)Abnormal ureter physiology0.0009403Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal lymphocyte morphology0.1787Highly InformativeInherited

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.000001188Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.000001292Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.001562Least InformativeInherited
Worm Phenotype (WP)cell development variant0.002367Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.04704Least InformativeInherited
Worm Phenotype (WP)endocytic transport variant0.00001177Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.003395Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.0366Moderately InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.06921Moderately InformativeInherited
Worm Phenotype (WP)body region morphology variant0.07069Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.1964Moderately InformativeInherited
Worm Phenotype (WP)metabolic pathway variant0.4408Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.5902Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.6887Moderately InformativeInherited
Worm Phenotype (WP)apoptosis variant0.835Moderately InformativeInherited
Worm Phenotype (WP)coelomic system physiology variant0.000000000001042InformativeDirect
Worm Phenotype (WP)endocytic transport defect0.000009721InformativeDirect
Worm Phenotype (WP)protein modification variant0.00004341InformativeDirect
Worm Phenotype (WP)cell fate specification variant0.00006311InformativeDirect
Worm Phenotype (WP)vulva development variant0.0001099InformativeDirect
Worm Phenotype (WP)tail morphology variant0.0003596InformativeDirect
Worm Phenotype (WP)alimentary system development variant0.4905InformativeInherited
Worm Phenotype (WP)protein methylation variant0.00000000004265Highly InformativeDirect
Worm Phenotype (WP)coelomocyte uptake defective0.00000001435Highly InformativeDirect
Worm Phenotype (WP)organism UV hypersensitive0.0000005588Highly InformativeDirect
Worm Phenotype (WP)transgenerational loss of fertility0.000003099Highly InformativeDirect
Worm Phenotype (WP)vulvaless0.0007988Highly InformativeDirect
Worm Phenotype (WP)ectopic expression transgene0.0009904Highly InformativeDirect
Worm Phenotype (WP)gut granule development variant0.002756Highly InformativeInherited
Worm Phenotype (WP)lysosome organization biogenesis variant0.006186Highly 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 variegation0.00000002304InformativeDirect

Document: FP 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)urogenital system0.04971Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.1556Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.381Least InformativeInherited
Xenopus ANatomical entity (XAN)testis0.0004291Moderately 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 tissue0.4077Least InformativeInherited
Plant ANatomical entity (PAN)shoot axis0.6752Least InformativeInherited
Plant ANatomical entity (PAN)shoot apical meristem0.000005488Highly InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0.6423Least InformativeInherited
Enzyme Commission (EC)Transferring phosphorus-containing groups1Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Aminoacyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0.0006842Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.001554Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases0.001789Moderately InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0.1044Moderately InformativeInherited
Enzyme Commission (EC)Transferring groups other than amino-acyl groups1Moderately 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 incorporate0.000000000000001515InformativeDirect
Enzyme Commission (EC)DNA helicase0.000000001401InformativeDirect
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0.00000004952InformativeDirect
Enzyme Commission (EC)Protein-tyrosine-phosphatase0.0000004188InformativeDirect
Enzyme Commission (EC)Protein-tyrosine kinases0.0001542InformativeDirect
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 kinase0.000002421Highly InformativeDirect

Document: EC 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) ]

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 41 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 41 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) · Internal database links ]