SUPERFAMILY 1.75 HMM library and genome assignments server


GYF domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   GYF/BRK domain-like [ 55276] (2)
Superfamily:   GYF domain [ 55277]
Families:   GYF domain [ 55278] (2)


Superfamily statistics
Genomes (455) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 1,636 1,261 3
Proteins 1,619 1,252 3


Functional annotation
General category General
Detailed category Ligand binding

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) single-organism cellular process 0.7403 Least Informative Inherited
Biological Process (BP) developmental process 0.265 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.4249 Least Informative Inherited
Biological Process (BP) response to stimulus 0.6405 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.1755 Least Informative Inherited
Biological Process (BP) system process 0.0005743 Moderately Informative Direct
Biological Process (BP) homeostatic process 0.0009387 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.003495 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.1266 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.001319 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.0823 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.07685 Moderately Informative Inherited
Biological Process (BP) response to DNA damage stimulus 4.243e-06 Informative Direct
Biological Process (BP) enzyme linked receptor protein signaling pathway 3.565e-08 Informative Direct
Biological Process (BP) central nervous system development 4.846e-05 Informative Direct
Biological Process (BP) cell cycle process 4.007e-05 Informative Direct
Biological Process (BP) growth 8.554e-06 Informative Direct
Biological Process (BP) single-organism behavior 3.822e-07 Informative Direct
Biological Process (BP) generation of neurons 0.000499 Informative Direct
Biological Process (BP) regulation of cell cycle 3.124e-05 Informative Direct
Biological Process (BP) cell cycle checkpoint 7.534e-11 Highly Informative Direct
Biological Process (BP) tissue homeostasis 2.054e-12 Highly Informative Direct
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 8.613e-10 Highly Informative Direct
Biological Process (BP) locomotory behavior 7.956e-10 Highly Informative Direct
Biological Process (BP) post-embryonic development 9.468e-09 Highly Informative Direct
Biological Process (BP) adult behavior 5.605e-11 Highly Informative Direct
Biological Process (BP) neuromuscular process 4.735e-13 Highly Informative Direct
Biological Process (BP) negative regulation of mitotic cell cycle phase transition 1.7e-11 Highly Informative Direct
Biological Process (BP) regulation of G1/S transition of mitotic cell cycle 3.281e-14 Highly Informative Direct

Document: GO 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)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Moderately InformativeDirect
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP 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)
Cellular componentNucleus0.00014Least InformativeDirect
Post-translational modificationPhosphoprotein5.074e-06Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR003169 SSF55277 Protein matches
Abstract

The glycine-tyrosine-phenylalanine (GYF) domain is an around 60-amino acid domain which contains a conserved GP[YF]xxxx[MV]xxWxxx[GN]YF motif. It was identified in the human intracellular protein termed CD2 binding protein 2 (CD2BP2), which binds to a site containing two tandem PPPGHR segments within the cytoplasmic region of CD2. Binding experiments and mutational analyses have demonstrated the critical importance of the GYF tripeptide in ligand binding. A GYF domain is also found in several other eukaryotic proteins of unknown function [PubMed9843987]. It has been proposed that the GYF domain found in these proteins could also be involved in proline-rich sequence recognition [PubMed10404223]. Resolution of the structure of the CD2BP2 GYF domain by NMR spectroscopy revealed a compact domain with a beta-beta-alpha-beta-beta topology, where the single alpha-helix is tilted away from the twisted, anti-parallel beta-sheet. The conserved residues of the GYF domain create a contiguous patch of predominantly hydrophobic nature which forms an integral part of the ligand-binding site [PubMed10404223]. There is limited homology within the C-terminal 20-30 amino acids of various GYF domains, supporting the idea that this part of the domain is structurally but not functionally important [PubMed12426371].


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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · 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 2 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 GYF 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 2 hidden Markov models representing the GYF 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]