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Protein

Putative DNA repair helicase RadD

Gene

radD

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

Functioni

May be a helicase. In combination with RadA is important in repair of double-strand DNA breaks (DSB) (PubMed:25425430, PubMed:25484163).2 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

GO - Molecular functioni

GO - Biological processi

  • cell division Source: EcoCyc
  • double-strand break repair Source: EcoCyc
  • response to drug Source: EcoCyc
  • response to ionizing radiation Source: EcoCyc
  • RNA secondary structure unwinding Source: GO_Central
  • translation Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG12045-MONOMER.
ECOL316407:JW2172-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Putative DNA repair helicase RadD (EC:3.6.4.12)
Gene namesi
Name:radD1 Publication
Synonyms:yejH, yejI, yejJ
Ordered Locus Names:b2184, JW2172
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12045. yejH.

Pathology & Biotechi

Disruption phenotypei

100- to 10000-fold decrease in survival after IR (PubMed:25049088, PubMed:25425430). Double radA-radD deletions have nearly 106-fold lower survival upon IR, and the double mutant is more severely affected by UV radiation than either of the single mutants alone (up to 100 J/m2). The single mutation is more sensitive to dsDNA breaks induced by 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. No effect on RecA-mediated conjugational DNA recombination (PubMed:25425430). In another study double radA-radD deletions are sensitive to CFX but not to UV (up to 40 J/m2) or azidothymidine (AZT) (PubMed:25484163).3 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi37 – 371K → R: Partially complements a radD deletion mutant for survival of ionizing radiation (possible loss of ATPase activity), increases sensitivity to UV of a double radA-radD deletion. Has a dominant negative effect on survival of UV in the presence of wild-type enzyme or ciprofloxacin survival. 1 Publication
Mutagenesisi356 – 586231Missing : Does not complement sensitivity of a double radA-radD deletion to dsDNA breaks. 1 PublicationAdd
BLAST
Mutagenesisi437 – 4371C → A: Does not complement sensitivity of a double radA-radD deletion to dsDNA breaks. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 586586Putative DNA repair helicase RadDPRO_0000169164Add
BLAST

Proteomic databases

PaxDbiP33919.
PRIDEiP33919.

Interactioni

Protein-protein interaction databases

BioGridi4259416. 153 interactions.
IntActiP33919. 5 interactions.
STRINGi511145.b2184.

Structurei

3D structure databases

ProteinModelPortaliP33919.
SMRiP33919. Positions 5-153, 269-355.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini18 – 171154Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini241 – 386146Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Domaini

The C-terminal domain (residues 356-586) is required to alleviate the deleterious effects of UV or ciprofloxacin (CFX) treatment in a double radA-radD mutant; its effect on ionising irradiation (IR) survival in the single radD mutant were not reported (PubMed:25425430).1 Publication

Sequence similaritiesi

Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4105CFI. Bacteria.
COG1061. LUCA.
HOGENOMiHOG000279255.
InParanoidiP33919.
KOiK19789.
OMAiWIYQYHY.
OrthoDBiEOG62G5JD.
PhylomeDBiP33919.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR006935. Helicase/UvrB_N.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR011332. Ribosomal_zn-bd.
[Graphical view]
PfamiPF00271. Helicase_C. 1 hit.
PF04851. ResIII. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
SSF57829. SSF57829. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P33919-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIFTLRPYQQ EAVDATLNHF RRHKTPAVIV LPTGAGKSLV IAELARLARG
60 70 80 90 100
RVLVLAHVKE LVAQNHAKYQ ALGLEADIFA AGLKRKESHG KVVFGSVQSV
110 120 130 140 150
ARNLDAFQGE FSLLIVDECH RIGDDEESQY QQILTHLTKV NPHLRLLGLT
160 170 180 190 200
ATPFRLGKGW IYQFHYHGMV RGDEKALFRD CIYELPLRYM IKHGYLTPPE
210 220 230 240 250
RLDMPVVQYD FSRLQAQSNG LFSEADLNRE LKKQQRITPH IISQIMEFAA
260 270 280 290 300
TRKGVMIFAA TVEHAKEIVG LLPAEDAALI TGDTPGAERD VLIENFKAQR
310 320 330 340 350
FRYLVNVAVL TTGFDAPHVD LIAILRPTES VSLYQQIVGR GLRLAPGKTD
360 370 380 390 400
CLILDYAGNP HDLYAPEVGT PKGKSDNVPV QVFCPACGFA NTFWGKTTAD
410 420 430 440 450
GTLIEHFGRR CQGWFEDDDG HREQCDFRFR FKNCPQCNAE NDIAARRCRE
460 470 480 490 500
CDTVLVDPDD MLKAALRLKD ALVLRCSGMS LQHGHDEKGE WLKITYYDED
510 520 530 540 550
GADVSERFRL QTPAQRTAFE QLFIRPHTRT PGIPLRWITA ADILAQQALL
560 570 580
RHPDFVVARM KGQYWQVREK VFDYEGRFRL AHELRG
Length:586
Mass (Da):66,413
Last modified:November 1, 1997 - v2
Checksum:i2D173250F83333DF
GO

Sequence cautioni

The sequence AAA16381.1 differs from that shown. Reason: Frameshift at position 397. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75245.1.
AP009048 Genomic DNA. Translation: BAE76649.1.
U00008 Genomic DNA. Translation: AAA16381.1. Frameshift.
PIRiG64987.
RefSeqiNP_416689.1. NC_000913.3.
WP_000578061.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75245; AAC75245; b2184.
BAE76649; BAE76649; BAE76649.
GeneIDi945529.
KEGGiecj:JW2172.
eco:b2184.
PATRICi32119723. VBIEscCol129921_2272.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75245.1.
AP009048 Genomic DNA. Translation: BAE76649.1.
U00008 Genomic DNA. Translation: AAA16381.1. Frameshift.
PIRiG64987.
RefSeqiNP_416689.1. NC_000913.3.
WP_000578061.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP33919.
SMRiP33919. Positions 5-153, 269-355.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259416. 153 interactions.
IntActiP33919. 5 interactions.
STRINGi511145.b2184.

Proteomic databases

PaxDbiP33919.
PRIDEiP33919.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75245; AAC75245; b2184.
BAE76649; BAE76649; BAE76649.
GeneIDi945529.
KEGGiecj:JW2172.
eco:b2184.
PATRICi32119723. VBIEscCol129921_2272.

Organism-specific databases

EchoBASEiEB1979.
EcoGeneiEG12045. yejH.

Phylogenomic databases

eggNOGiENOG4105CFI. Bacteria.
COG1061. LUCA.
HOGENOMiHOG000279255.
InParanoidiP33919.
KOiK19789.
OMAiWIYQYHY.
OrthoDBiEOG62G5JD.
PhylomeDBiP33919.

Enzyme and pathway databases

BioCyciEcoCyc:EG12045-MONOMER.
ECOL316407:JW2172-MONOMER.

Miscellaneous databases

PROiP33919.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR006935. Helicase/UvrB_N.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR011332. Ribosomal_zn-bd.
[Graphical view]
PfamiPF00271. Helicase_C. 1 hit.
PF04851. ResIII. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
SSF57829. SSF57829. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  2. "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.
  3. "Automated multiplex sequencing of the E.coli genome."
    Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K., Church G.M.
    Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] OF 1-403.
    Strain: K12 / BHB2600.
  4. "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 / e14.
  5. "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, DOMAIN, DISRUPTION PHENOTYPE, MUTAGENESIS OF LYS-37; CYS-437 AND 356-TYR--GLY-586.
    Strain: K12 / MG1655 / e14.
  6. "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, DISRUPTION PHENOTYPE.
    Strain: K12.

Entry informationi

Entry nameiRADD_ECOLI
AccessioniPrimary (citable) accession number: P33919
Secondary accession number(s): P36926
, P36927, P76449, Q2MAQ7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: November 1, 1997
Last modified: May 11, 2016
This is version 115 of the entry and version 2 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.