Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

DNA repair protein RadA

Gene

radA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

DNA-dependent ATPase involved in processing of recombination intermediates, plays a role in repairing DNA breaks. Stimulates the branch migration of RecA-mediated strand transfer reactions, allowing the 3' invading strand to extend heteroduplex DNA faster. Binds ssDNA in the presence of ADP but not other nucleotides, has ATPase activity that is stimulated by ssDNA and various branched DNA structures, but inhibited by SSB. Does not have RecA's homology-searching function (PubMed:26845522). Genetic experiments involving combination of radA mutations with mutations in recA, recB, recG, recJ, recQ, ruvA and ruvC show it plays a role in recombination and recombinational repair, probably involving stabilizing or processing branched DNA or blocked replication forks. Is genetically synergistic to RecG and RuvABC (PubMed:12446634, PubMed:25484163). May be involved in recovery of genetic rearrangements during replication fork breakdown (PubMed:16904387). In combination with RadD is important in recovery from double-strand DNA breaks (DSB) (PubMed:25425430).5 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri11 – 2818C4-typeUniRule annotation1 PublicationAdd
BLAST
Nucleotide bindingi102 – 1098ATPUniRule annotation1 Publication

GO - Molecular functioni

GO - Biological processi

  • recombinational repair Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

DNA damage, DNA repair, Stress response

Keywords - Ligandi

ATP-binding, DNA-binding, Metal-binding, Nucleotide-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:EG11296-MONOMER.
ECOL316407:JW4352-MONOMER.

Protein family/group databases

MEROPSiS16.A04.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA repair protein RadA1 PublicationUniRule annotation (EC:3.6.4.-1 Publication)
Alternative name(s):
Branch migration protein RadA1 Publication
DNA repair protein Sms1 Publication
Gene namesi
Name:radA1 PublicationUniRule annotation
Synonyms:sms1 Publication
Ordered Locus Names:b4389, JW4352
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11296. radA.

Pathology & Biotechi

Disruption phenotypei

Increased sensitivity to methyl methanesulfonate, mitomycin C, phleomycin (PubMed:1327967, PubMed:12446634). Has a modest defect in RecA-mediated conjugational DNA recombination; double radA-radD mutants have wild-type levels (PubMed:25425430, PubMed:12446634). 10- to 1000-fold decrease in survival after ionising irradiation (IR) (PubMed:25049088, PubMed:25425430). Double radA-radD deletions have nearly 106-fold lower survival against IR and the double mutant is more severely affected by UV radiation than either of the single mutants alone. The single mutation is more sensitive to dsDNA breaks induced by ciprofloxacin (CFX), the double radA-radD mutant is inviable upon CFX treatment; the SOS response is slightly induced in the single and more induced in the double mutant (PubMed:25425430). Another group showed very slight sensitivity to CFX, UV and azidothymidine (AZT) in single deletion mutants, a radA-recG deletion is extremely sensitive to CFX and AZT, less so to UV. The SOS response is induced in the radA-recG double mutant, indicating spontaneous DNA damage. AZT sensitivity is suppressed by further recA or recF deletions, suggesting AZT-induced DNA gaps are processed into lethal intermediates in a RecA-dependent fashion mediated by RecF. RuvAB suppresses UV, CFX and AZT sensitivity to vaarying degrees. Similarly, radA-uvrD double deletions are also more sensitive to UV, CFX and AZT. Adding a recF mutation almost completely suppresses AZT and partially suppresses UV and CFX sensitivity, suggesting RadA processes a class of intermediates that accumulates in uvrD mutants (PubMed:25484163).5 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi28 – 281C → Y in radA100; rich medium-grown cells are sensitive to gamma, X-ray and UV radiation as well as methyl methanesulfonate and hydroxyurea, impaired in repair of dsDNA breaks. Decreased resistance to ciprofloxacin (CFX). 4 Publications
Mutagenesisi108 – 1081K → R: Decreased resistance to CFX, semi-dominant to wild-type. 1 Publication
Mutagenesisi228 – 460233Missing : Decreased resistance to CFX. 1 PublicationAdd
BLAST
Mutagenesisi258 – 2581K → R: Decreased resistance to CFX, semi-dominant to wild-type. 1 Publication
Mutagenesisi275 – 460186Missing : Decreased resistance to CFX. 1 PublicationAdd
BLAST
Mutagenesisi372 – 3721S → A: Wild-type resistance to CFX; equivalent to the active site Ser of Lon protease. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 460460DNA repair protein RadAPRO_0000187926Add
BLAST

Proteomic databases

PaxDbiP24554.
PRIDEiP24554.

Expressioni

Inductioni

Part of the serB-radA operon (PubMed:1327967).1 Publication

Interactioni

Protein-protein interaction databases

BioGridi4262780. 144 interactions.
DIPiDIP-10635N.
IntActiP24554. 5 interactions.
STRINGi511145.b4389.

Structurei

3D structure databases

ProteinModelPortaliP24554.
SMRiP24554. Positions 73-280, 286-460.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni357 – 460104Lon-protease-likeUniRule annotation1 PublicationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi258 – 2625RadA KNRFG motifUniRule annotation1 Publication

Domaini

Has a putative N-terminal zinc-finger, a region with homology to RecA with ATPase motifs including the RadA KNRFG motif (approximately residues 60-290), while the C-terminus is homologous to Lon protease (from about residue 290 to the end, the ribosomal S5 domain). In this organism the Lon protease active site Ser-372 is conserved, but not all other bacteria encode Ser at this position (PubMed:1327967, PubMed:8759876). Mutation of Ser-372 has no discernible effect on RadA function, suggesting RadA is not a protease (PubMed:25484163).UniRule annotation2 Publications1 Publication

Sequence similaritiesi

Belongs to the RecA family. RadA subfamily.UniRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri11 – 2818C4-typeUniRule annotation1 PublicationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiENOG4105DNJ. Bacteria.
COG1066. LUCA.
HOGENOMiHOG000218329.
InParanoidiP24554.
KOiK04485.
OMAiFEGERGH.
OrthoDBiEOG6DRPHC.
PhylomeDBiP24554.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.40.50.300. 1 hit.
HAMAPiMF_01498. RadA_bact.
InterProiIPR003593. AAA+_ATPase.
IPR004504. DNA_repair_RadA.
IPR027417. P-loop_NTPase.
IPR020588. RecA_ATP-bd.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
[Graphical view]
SMARTiSM00382. AAA. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
SSF54211. SSF54211. 2 hits.
TIGRFAMsiTIGR00416. sms. 1 hit.
PROSITEiPS50162. RECA_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P24554-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAKAPKRAFV CNECGADYPR WQGQCSACHA WNTITEVRLA ASPMVARNER
60 70 80 90 100
LSGYAGSAGV AKVQKLSDIS LEELPRFSTG FKEFDRVLGG GVVPGSAILI
110 120 130 140 150
GGNPGAGKST LLLQTLCKLA QQMKTLYVTG EESLQQVAMR AHRLGLPTDN
160 170 180 190 200
LNMLSETSIE QICLIAEEEQ PKLMVIDSIQ VMHMADVQSS PGSVAQVRET
210 220 230 240 250
AAYLTRFAKT RGVAIVMVGH VTKDGSLAGP KVLEHCIDCS VLLDGDADSR
260 270 280 290 300
FRTLRSHKNR FGAVNELGVF AMTEQGLREV SNPSAIFLSR GDEVTSGSSV
310 320 330 340 350
MVVWEGTRPL LVEIQALVDH SMMANPRRVA VGLEQNRLAI LLAVLHRHGG
360 370 380 390 400
LQMADQDVFV NVVGGVKVTE TSADLALLLA MVSSLRDRPL PQDLVVFGEV
410 420 430 440 450
GLAGEIRPVP SGQERISEAA KHGFRRAIVP AANVPKKAPE GMQIFGVKKL
460
SDALSVFDDL
Length:460
Mass (Da):49,472
Last modified:March 1, 1992 - v1
Checksum:iC03C8BE5367E7BFF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X63155 Genomic DNA. Translation: CAA44856.1.
U59449 Genomic DNA. Translation: AAC44380.1.
U14003 Genomic DNA. Translation: AAA97285.1.
U00096 Genomic DNA. Translation: AAC77342.1.
AP009048 Genomic DNA. Translation: BAE78378.1.
PIRiJC1417.
RefSeqiNP_418806.1. NC_000913.3.
WP_001029687.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC77342; AAC77342; b4389.
BAE78378; BAE78378; BAE78378.
GeneIDi948912.
KEGGiecj:JW4352.
eco:b4389.
PATRICi32124394. VBIEscCol129921_4537.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X63155 Genomic DNA. Translation: CAA44856.1.
U59449 Genomic DNA. Translation: AAC44380.1.
U14003 Genomic DNA. Translation: AAA97285.1.
U00096 Genomic DNA. Translation: AAC77342.1.
AP009048 Genomic DNA. Translation: BAE78378.1.
PIRiJC1417.
RefSeqiNP_418806.1. NC_000913.3.
WP_001029687.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP24554.
SMRiP24554. Positions 73-280, 286-460.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262780. 144 interactions.
DIPiDIP-10635N.
IntActiP24554. 5 interactions.
STRINGi511145.b4389.

Protein family/group databases

MEROPSiS16.A04.

Proteomic databases

PaxDbiP24554.
PRIDEiP24554.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC77342; AAC77342; b4389.
BAE78378; BAE78378; BAE78378.
GeneIDi948912.
KEGGiecj:JW4352.
eco:b4389.
PATRICi32124394. VBIEscCol129921_4537.

Organism-specific databases

EchoBASEiEB1273.
EcoGeneiEG11296. radA.

Phylogenomic databases

eggNOGiENOG4105DNJ. Bacteria.
COG1066. LUCA.
HOGENOMiHOG000218329.
InParanoidiP24554.
KOiK04485.
OMAiFEGERGH.
OrthoDBiEOG6DRPHC.
PhylomeDBiP24554.

Enzyme and pathway databases

BioCyciEcoCyc:EG11296-MONOMER.
ECOL316407:JW4352-MONOMER.

Miscellaneous databases

PROiP24554.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.40.50.300. 1 hit.
HAMAPiMF_01498. RadA_bact.
InterProiIPR003593. AAA+_ATPase.
IPR004504. DNA_repair_RadA.
IPR027417. P-loop_NTPase.
IPR020588. RecA_ATP-bd.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
[Graphical view]
SMARTiSM00382. AAA. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
SSF54211. SSF54211. 2 hits.
TIGRFAMsiTIGR00416. sms. 1 hit.
PROSITEiPS50162. RECA_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Mutational analysis of the Escherichia coli serB promoter region reveals transcriptional linkage to a downstream gene."
    Neuwald A.F., Berg D.E., Stauffer G.V.
    Gene 120:1-9(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], DOMAIN, DISRUPTION PHENOTYPE, PUTATIVE ZINC FINGER, OPERON.
    Strain: K12.
  2. "Escherichia coli DNA repair genes radA and sms are the same gene."
    Song Y., Sargentini N.J.
    J. Bacteriol. 178:5045-5048(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], DOMAIN, MUTAGENESIS OF CYS-28.
    Strain: K12 / AB1157.
  3. "Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes."
    Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.
    Nucleic Acids Res. 23:2105-2119(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "A mutation (radA100) in Escherichia coli that selectively sensitizes cells grown in rich medium to x- or u.v.-radiation, or methyl methanesulphonate."
    Diver W.P., Sargentini N.J., Smith K.C.
    Int. J. Radiat. Biol. Relat. Stud. Phys. Chem. Med. 42:339-346(1982) [PubMed] [Europe PMC] [Abstract]
    Cited for: ISOLATION OF RADA100 ALLELE, MUTAGENESIS OF CYS-28.
    Strain: K12.
  7. "Role for radA/sms in recombination intermediate processing in Escherichia coli."
    Beam C.E., Saveson C.J., Lovett S.T.
    J. Bacteriol. 184:6836-6844(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF CYS-28.
    Strain: K12 / AB1157.
  8. "Replication arrest-stimulated recombination: Dependence on the RecA paralog, RadA/Sms and translesion polymerase, DinB."
    Lovett S.T.
    DNA Repair 5:1421-1427(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
    Strain: K12 / AB1157.
  9. "Escherichia coli genes and pathways involved in surviving extreme exposure to ionizing radiation."
    Byrne R.T., Chen S.H., Wood E.A., Cabot E.L., Cox M.M.
    J. Bacteriol. 196:3534-3545(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISRUPTION PHENOTYPE.
    Strain: K12 / MG1655 / ATCC 47076.
  10. "Escherichia coli radD (yejH) gene: a novel function involved in radiation resistance and double-strand break repair."
    Chen S.H., Byrne R.T., Wood E.A., Cox M.M.
    Mol. Microbiol. 95:754-768(2015) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE.
  11. "Genetic analysis of Escherichia coli RadA: functional motifs and genetic interactions."
    Cooper D.L., Boyle D.C., Lovett S.T.
    Mol. Microbiol. 95:769-779(2015) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DOMAIN, DISRUPTION PHENOTYPE, MUTAGENESIS OF CYS-28; LYS-108; 228-LEU--LEU-460; LYS-258; 275-GLN--LEU-460 AND SER-372.
    Strain: K12 / AB1157.
  12. "Recombinational branch migration by the RadA/Sms paralog of RecA in Escherichia coli."
    Cooper D.L., Lovett S.T.
    Elife 5:0-0(2016) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ATPASE ACTIVITY, SSDNA-BINDING, MUTAGENESIS OF CYS-28; LYS-108; LYS-258 AND SER-372.

Entry informationi

Entry nameiRADA_ECOLI
AccessioniPrimary (citable) accession number: P24554
Secondary accession number(s): Q2M5S8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 1992
Last sequence update: March 1, 1992
Last modified: June 8, 2016
This is version 140 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.