SUPERFAMILY 1.75 HMM library and genome assignments server

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 (2,683) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 8,054 20,294 2
Proteins 8,041 20,278 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) positive regulation of biological process 0.00007648 Least Informative Direct
Biological Process (BP) localization 0.0002641 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) developmental process 0.1195 Least Informative Inherited
Biological Process (BP) response to stimulus 0.2617 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.372 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.003069 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.01807 Least Informative Inherited
Biological Process (BP) positive regulation of molecular function 0 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.000000000000003707 Moderately Informative Direct
Biological Process (BP) regulation of phosphorus metabolic process 0.0000000000001712 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0.0000000007784 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.00003753 Moderately Informative Direct
Biological Process (BP) response to endogenous stimulus 0.2671 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.03691 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.7777 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.002616 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.001671 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.01166 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.761 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.8041 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.001084 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.006195 Moderately Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0 Informative Direct
Biological Process (BP) positive regulation of phosphate metabolic process 0 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0 Informative Direct
Biological Process (BP) positive regulation of catabolic process 0 Informative Direct
Biological Process (BP) regulation of nucleoside metabolic process 0 Informative Direct
Biological Process (BP) positive regulation of hydrolase activity 0.0000000003477 Informative Direct
Biological Process (BP) single-organism behavior 0.0003163 Informative Direct
Biological Process (BP) protein localization to organelle 0.04816 Informative Inherited
Biological Process (BP) response to oxidative stress 0.06369 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.4424 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.133 Informative Inherited
Biological Process (BP) sensory organ development 0.263 Informative Inherited
Biological Process (BP) organ morphogenesis 0.2734 Informative Inherited
Biological Process (BP) positive regulation of GTPase activity 0 Highly Informative Direct
Biological Process (BP) response to nerve growth factor 0.000000000417 Highly Informative Direct
Biological Process (BP) cellular response to reactive oxygen species 0.00007439 Highly Informative Direct
Biological Process (BP) small GTPase mediated signal transduction 0.0007391 Highly Informative Direct
Biological Process (BP) cellular response to growth factor stimulus 0.00131 Highly Informative Inherited
Biological Process (BP) cell fate commitment 0.001832 Highly Informative Inherited
Biological Process (BP) regulation of Ras GTPase activity 1 Highly Informative Inherited
Biological Process (BP) eye morphogenesis 0.002562 Highly Informative Inherited
Molecular Function (MF) binding 0.1228 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.000002673 Moderately Informative Direct
Molecular Function (MF) enzyme activator activity 0 Informative Direct
Molecular Function (MF) lipid binding 0.000000002089 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 0.1232 Informative Inherited
Molecular Function (MF) GTPase activator activity 0.0000000001578 Highly Informative Direct
Molecular Function (MF) small GTPase regulator activity 0.04099 Highly Informative Inherited
Molecular Function (MF) phosphatidylinositol binding 0.2405 Highly Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.5531 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.1175 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.6294 Least Informative Inherited
Cellular Component (CC) membrane 0.6145 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.2978 Least Informative Inherited
Cellular Component (CC) cytoskeleton 0.04844 Moderately Informative Inherited
Cellular Component (CC) cell projection 0.008762 Moderately Informative Inherited
Cellular Component (CC) bounding membrane of organelle 0.03564 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 0.0000000000005759 Informative Direct
Cellular Component (CC) cell junction 0.000001089 Informative Direct
Cellular Component (CC) cell leading edge 0.0007003 Informative Direct
Cellular Component (CC) synapse 0.003897 Informative Inherited
Cellular Component (CC) endosome 0.001585 Informative Inherited
Cellular Component (CC) adherens junction 0.000000000009077 Highly Informative Direct
Cellular Component (CC) trans-Golgi network 0.0002709 Highly Informative Direct
Cellular Component (CC) endosomal part 0.0006902 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

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system0Least InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)pollen development stage0.0003282Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)L mature pollen stage0.00003075InformativeDirect
Plant structure DEvelopment stage (PDE)M germinated pollen stage0.000179InformativeDirect

Document: AP 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 transport0.0000006854Moderately InformativeDirect
Biological processDNA recombination0InformativeDirect
Biological processER-Golgi transport0Highly InformativeDirect
Cellular componentGolgi apparatus0.000000000000001597Moderately InformativeDirect
Cellular componentEndosome0.0001326Moderately InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainCoiled coil0.00007377Moderately InformativeDirect
DomainANK repeat0InformativeDirect
DomainSH3 domain0.0005107InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationGTPase activation0InformativeDirect
Post-translational modificationPhosphoprotein0.000003713Least InformativeDirect

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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · 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 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]