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Rad51 N-terminal domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   SAM domain-like [ 47768] (16)
Superfamily:   Rad51 N-terminal domain-like [ 47794] (3)
Families:   DNA repair protein Rad51, N-terminal domain [ 47795]
  NusA extra C-terminal domains [ 109873]
  Hypothetical protein AF1548, C-terminal domain [ 116936]


Superfamily statistics
Genomes (1,914) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,410 15,274 12
Proteins 2,544 9,585 12


Functional annotation
General category Information
Detailed category DNA replication/repair

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) heterocycle metabolic process 0.00000000001998 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.00000000002739 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00000000007593 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.000000000533 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0000000006877 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.000001018 Least Informative Direct
Biological Process (BP) primary metabolic process 0.000001112 Least Informative Direct
Biological Process (BP) response to stimulus 0.0001058 Least Informative Direct
Biological Process (BP) biological regulation 0.5457 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.9031 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.5122 Least Informative Inherited
Biological Process (BP) reproduction 0.000000000395 Moderately Informative Direct
Biological Process (BP) response to stress 0.00000006069 Moderately Informative Direct
Biological Process (BP) organelle organization 0.0001472 Moderately Informative Direct
Biological Process (BP) regulation of nitrogen compound metabolic process 0.0149 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.02237 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.08872 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.6415 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.001562 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.08781 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.02833 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.007876 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 0.08945 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.04708 Moderately Informative Inherited
Biological Process (BP) cellular response to DNA damage stimulus 0 Informative Direct
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) cell cycle process 0.000000000000195 Informative Direct
Biological Process (BP) single organism reproductive process 0.0000000000117 Informative Direct
Biological Process (BP) organelle fission 0.000000001657 Informative Direct
Biological Process (BP) response to radiation 0.0000005668 Informative Direct
Biological Process (BP) response to nitrogen compound 0.0002285 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.0003472 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.0004793 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0.01893 Informative Inherited
Biological Process (BP) meiotic cell cycle process 0 Highly Informative Direct
Biological Process (BP) DNA recombination 0 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.000000005856 Highly Informative Direct
Biological Process (BP) chromosome organization 0.00000001986 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.000001004 Highly Informative Direct
Biological Process (BP) cellular response to abiotic stimulus 0.00003376 Highly Informative Direct
Biological Process (BP) cellular response to organonitrogen compound 0.00003792 Highly Informative Direct
Biological Process (BP) response to alcohol 0.00005265 Highly Informative Direct
Biological Process (BP) DNA replication 0.004776 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 0.00000000006895 Least Informative Direct
Molecular Function (MF) small molecule binding 0 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) ribonucleoside binding 0 Informative Direct
Molecular Function (MF) ribonucleotide binding 0 Informative Direct
Molecular Function (MF) purine nucleoside binding 0 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0 Informative Direct
Molecular Function (MF) purine nucleotide binding 0 Informative Direct
Molecular Function (MF) ATPase activity 0 Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) ATP binding 0 Highly Informative Direct
Molecular Function (MF) single-stranded DNA binding 0 Highly Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.000000002047 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.00002424 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0001005 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.0000000005732 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.0000003553 Moderately Informative Direct
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) nuclear chromosome 0 Highly Informative Direct
Cellular Component (CC) condensed chromosome 0.0000008158 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.000005136 Highly Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
Biological processTranscription regulation0.01901Moderately InformativeInherited
Biological processDNA recombination0InformativeDirect
Biological processMeiosis0.0000000000001097InformativeDirect
Biological processTranscription termination0.000000000000002853Highly InformativeDirect
Cellular componentNucleus0.0000000008303Least InformativeDirect
Cellular componentCytoplasm1Least InformativeInherited
Cellular componentCytoskeleton0.0003673Moderately InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0.00008197Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)biopolymer biosynthesis0Moderately InformativeDirect
UniPathway (UP)poly-(R)-3-hydroxybutanoate biosynthesis0Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR010995 SSF47794 Protein matches
Abstract

This entry represents an alpha-helical bundle domain, which has a SAM domain-like fold. This compact domain consists of a 4-5 helical bundle of two orthogonally packed alpha-hairpins, and contains one classic and one pseudo HhH (helix-hairpin-helix) motif. This domain is found at N-terminal of the DNA repair protein Rad1, at the C-terminal of the transcription elongation protein NusA, and at the C-terminal of the hypothetical protein AF1548.

Human Rad51 protein is a homologue of Escherichia coli RecA protein, and functions in DNA repair and recombination [PubMed10390347]. In higher eukaryotes, Rad51 protein is essential for cell viability. The N-terminal region of Rad51 is highly conserved among eukaryotic Rad51 proteins but is absent from RecA, suggesting a Rad51-specific function for this region. The-terminal domain is involved in interactions with DNA and proteins; DNA binding may be regulated via phosphorylation within the N-terminal domain.

NusA (N utilisation substance A) from Escherichia coli is an essential transcription factor that associates with the RNA polymerase (RNAP) core enzyme, where it modulates transcriptional pausing, termination and anti-termination [PubMed15987884]. The C-terminal of NusA consists of two repeat units, and is responsible for the interaction of NisA with the C-terminal of RNAP, and with its interaction with protein N from phage lambda during anti-termination [PubMed15365170].


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) · UniProtKB UniPathway (UP) ]

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 6 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 Rad51 N-terminal domain-like 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 6 hidden Markov models representing the Rad51 N-terminal domain-like 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) · UniProtKB UniPathway (UP) · Internal database links ]