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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 head0.2455Least 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 variant0.0003413Least InformativeDirect
Worm Phenotype (WP)cell development variant0.001976Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.003816Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.05706Least InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.039Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.06384Moderately InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.06878Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.2293Moderately InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant0.518Moderately InformativeInherited
Worm Phenotype (WP)apoptosis variant0.8629Moderately InformativeInherited
Worm Phenotype (WP)endocytic transport defect0.00000173InformativeDirect
Worm Phenotype (WP)vulva development variant0.0001121InformativeDirect
Worm Phenotype (WP)tail morphology variant0.0003636InformativeDirect
Worm Phenotype (WP)protein modification variant0.0007031InformativeDirect
Worm Phenotype (WP)VPC competence variant0.007618InformativeInherited
Worm Phenotype (WP)alimentary system development variant0.4949InformativeInherited
Worm Phenotype (WP)coelomocyte uptake defective0.00000009785Highly InformativeDirect
Worm Phenotype (WP)organism UV hypersensitive0.0000006104Highly InformativeDirect
Worm Phenotype (WP)ectopic expression transgene0.0000008878Highly InformativeDirect
Worm Phenotype (WP)transgenerational loss of fertility0.000002271Highly InformativeDirect
Worm Phenotype (WP)vulvaless0.0007636Highly InformativeDirect
Worm Phenotype (WP)gut granule development variant0.002634Highly InformativeInherited
Worm Phenotype (WP)lysosome organization biogenesis variant0.003009Highly 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 variegation0.0000000163InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)larva0.3579Least InformativeInherited
Fly Anatomy (FA)somatic cell0.57Least InformativeInherited
Fly Anatomy (FA)late embryo0.6112Moderately InformativeInherited
Fly Anatomy (FA)embryonic/larval circulatory system0.2638InformativeInherited
Fly Anatomy (FA)embryonic/larval garland cell0.0006619Highly 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 system0.008483Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.1399Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.3727Least InformativeInherited
Xenopus ANatomical entity (XAN)testis0.0004448Moderately 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)Oxidoreductases0.7404Least 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 groups0.0007553Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.001821Moderately InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides0.03789Moderately InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0.1072Moderately 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 incorporate5.029e-16InformativeDirect
Enzyme Commission (EC)DNA helicase0.000000001345InformativeDirect
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0.00000003632InformativeDirect
Enzyme Commission (EC)Protein-tyrosine-phosphatase0.000000435InformativeDirect
Enzyme Commission (EC)Protein-tyrosine kinases0.0001557InformativeDirect
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 kinase0.000002512Highly 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 ]