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ArfGap/RecO-like zinc finger superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   ArfGap/RecO-like zinc finger [ 57862]
Superfamily:   ArfGap/RecO-like zinc finger [ 57863] (2)
Families:   Pyk2-associated protein beta ARF-GAP domain [ 57864]
  RecO C-terminal domain-like [ 118303]


Superfamily statistics
Genomes (2,691) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 8,167 27,804 2
Proteins 8,154 27,748 2


Functional annotation
General category General
Detailed category Ion 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) response to stimulus 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.3757 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) biological regulation 0.6867 Least Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.1276 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.5371 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.7681 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.03804 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.09352 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.2885 Moderately Informative Inherited
Biological Process (BP) cell communication 0.3977 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) single organism signaling 0.4288 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.07318 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 0.368 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.7976 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.06625 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.00304 Moderately Informative Inherited
Biological Process (BP) animal organ development 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.02202 Moderately Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.0002344 Informative Direct
Biological Process (BP) protein transport 0.0007428 Informative Direct
Biological Process (BP) regulation of intracellular signal transduction 0.01005 Informative Inherited
Biological Process (BP) positive regulation of catalytic activity 0.04154 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 0.002935 Informative Inherited
Biological Process (BP) protein localization to organelle 0.4397 Informative Inherited
Biological Process (BP) intracellular transport 0.002934 Informative Inherited
Biological Process (BP) animal organ morphogenesis 0.2939 Informative Inherited
Biological Process (BP) regulation of GTPase activity 0.00000004342 Highly Informative Direct
Biological Process (BP) positive regulation of hydrolase activity 0.0002658 Highly Informative Direct
Biological Process (BP) response to growth factor 0.002279 Highly Informative Inherited
Biological Process (BP) cell-cell signaling 0.07215 Highly Informative Inherited
Biological Process (BP) Golgi vesicle transport 0.007933 Highly Informative Inherited
Biological Process (BP) sensory organ morphogenesis 0.002312 Highly Informative Inherited
Molecular Function (MF) binding 0.01081 Least Informative Inherited
Molecular Function (MF) molecular function regulator 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.0000000000047 Moderately Informative Direct
Molecular Function (MF) enzyme activator activity 0 Informative Direct
Molecular Function (MF) phospholipid binding 0.00000000000002122 Informative Direct
Molecular Function (MF) enzyme binding 0.2243 Informative Inherited
Molecular Function (MF) GTPase regulator activity 0 Highly Informative Direct
Molecular Function (MF) small GTPase binding 0.00004888 Highly Informative Direct
Molecular Function (MF) phosphatidylinositol phosphate binding 0.007644 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.000227 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.7607 Least Informative Inherited
Cellular Component (CC) membrane 0.008445 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) endomembrane system 0.0001472 Moderately Informative Direct
Cellular Component (CC) vesicle 0.0007787 Moderately Informative Direct
Cellular Component (CC) bounding membrane of organelle 0.02083 Moderately Informative Inherited
Cellular Component (CC) whole membrane 0.3748 Moderately Informative Inherited
Cellular Component (CC) cell projection 0.1938 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 0.0000001433 Informative Direct
Cellular Component (CC) cytoplasmic vesicle part 0.01345 Informative Inherited
Cellular Component (CC) endosome 0.08128 Informative Inherited
Cellular Component (CC) ruffle 0.00001138 Highly Informative Direct
Cellular Component (CC) endosome membrane 0.00005662 Highly Informative Direct
Cellular Component (CC) cell-substrate adherens junction 1 Highly Informative Inherited

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processDNA damage0Moderately InformativeDirect
Biological processProtein transport0.00000006657Moderately InformativeDirect
Biological processDNA recombination0InformativeDirect
Biological processDNA repair0InformativeDirect
Biological processER-Golgi transport0Highly InformativeDirect
Cellular componentGolgi apparatus0.000000000000005165Moderately InformativeDirect
Cellular componentEndosome0.00009761Moderately InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainCoiled coil0.0001237Moderately InformativeDirect
DomainANK repeat0InformativeDirect
DomainSH3 domain0.00008699InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationGTPase activation0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001164 SSF57863 Protein matches
Abstract

This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins [PubMed9446556]. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins.

The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved [PubMed10601011]. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis [PubMed10102276].

The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs [PubMed7637788]. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.


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 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 ArfGap/RecO-like 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 2 hidden Markov models representing the ArfGap/RecO-like 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 · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · Internal database links ]