UniProtKB - P33919 (RADD_ECOLI)
Protein
Putative DNA repair helicase RadD
Gene
radD
Organism
Escherichia coli (strain K12)
Status
Functioni
RadD contains helicase motifs, suggesting it may be a helicase, although that activity has not been observed (Probable). In combination with RadA is important in repair of double-strand DNA breaks (DSB) (PubMed:25425430, PubMed:25484163). Has DNA-independent ATPase activity that is stimulated by single-stranded DNA-binding protein SSB. ATPase is stimulated by a peptide with the last 10 residues of SSB, but not when the peptide's last Phe residue is missing. Binds ssDNA; binding is slightly better in the presence of nucleotides (PubMed:27519413). May be involved in resolution of branched DNA intermediates that result from template switching in postreplication gaps. Binds to DNA structures with 3 branches that resemble replication forks (PubMed:31665437).3 Publications4 Publications
Catalytic activityi
- EC:3.6.4.122 Publications
Cofactori
Zn2+Combined sources1 Publication
Kineticsi
ATPase activity in the presence of KCl in the absence of any nucleic acid substrate.1 Publication
- KM=0.85 µM for ATP1 Publication
- KM=0.63 µM for ATP in the presence of SSB1 Publication
- KM=0.40 µM for ATP in the presence of last 10 residues of SSB1 Publication
pH dependencei
Optimum pH is >7.5.1 Publication
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Metal bindingi | 384 | ZincCombined sources1 Publication | 1 | |
Metal bindingi | 387 | ZincCombined sources1 Publication | 1 | |
Metal bindingi | 411 | ZincCombined sources1 Publication | 1 | |
Metal bindingi | 425 | ZincCombined sources1 Publication | 1 |
GO - Molecular functioni
- ATPase activity Source: EcoCyc
- ATP binding Source: UniProtKB-KW
- DNA helicase activity Source: UniProtKB-EC
- single-stranded DNA binding Source: EcoCyc
- zinc ion binding Source: EcoCyc
GO - Biological processi
- cell division Source: EcoCyc
- double-strand break repair Source: EcoCyc
- response to drug Source: EcoCyc
- response to ionizing radiation Source: EcoCyc
- translation Source: InterPro
Keywordsi
Molecular function | DNA-binding, Helicase, Hydrolase |
Biological process | DNA damage, DNA repair |
Ligand | ATP-binding, Metal-binding, Nucleotide-binding, Zinc |
Enzyme and pathway databases
BioCyci | EcoCyc:EG12045-MONOMER MetaCyc:EG12045-MONOMER |
Names & Taxonomyi
Protein namesi | |
Gene namesi | Name:radD1 Publication Synonyms:yejH, yejI, yejJ Ordered Locus Names:b2184, JW2172 |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
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). Deletion of radD leads to an increase in DNA crossing over, DNA repeat deletion and DNA repeat expansion; double uup-radD deletion increases the phenotypes. Single radD deletion has no effect on cell growth or filamentation, double uup-radD deletions are filamentous and lack defined nucleoids. Single deletion is more sensitive to CFX (PubMed:31665437).4 Publications
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 37 | K → 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. Has no ATPase activity, does not bind ssDNA. 2 Publications | 1 | |
Mutagenesisi | 356 – 586 | Missing : Does not complement sensitivity of a double radA-radD deletion to dsDNA breaks. 1 PublicationAdd BLAST | 231 | |
Mutagenesisi | 437 | C → A: Does not complement sensitivity of a double radA-radD deletion to dsDNA breaks. 1 Publication | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000169164 | 1 – 586 | Putative DNA repair helicase RadDAdd BLAST | 586 |
Proteomic databases
PaxDbi | P33919 |
PRIDEi | P33919 |
Interactioni
Subunit structurei
Protein-protein interaction databases
BioGRIDi | 4259416, 278 interactors 849903, 1 interactor |
IntActi | P33919, 5 interactors |
STRINGi | 511145.b2184 |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | P33919 |
ModBasei | Search... |
PDBe-KBi | Search... |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 18 – 171 | Helicase ATP-binding1 PublicationPROSITE-ProRule annotationAdd BLAST | 154 | |
Domaini | 241 – 386 | Helicase C-terminal1 PublicationPROSITE-ProRule annotationAdd BLAST | 146 |
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 376 – 425 | Zinc finger domain1 PublicationAdd BLAST | 50 | |
Regioni | 429 – 574 | C-terminal domain1 PublicationAdd BLAST | 146 |
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). Crystals have 4 domains; helicase ATP-binding (residues 7-185), helicase C-terminal (residues 187-365), a zinc finger domain (residues 376-425) and the C-terminal domain (429-574) (PubMed:31035307).2 Publications
Phylogenomic databases
eggNOGi | COG1061, Bacteria |
HOGENOMi | CLU_014765_1_0_6 |
InParanoidi | P33919 |
PhylomeDBi | P33919 |
Family and domain databases
InterProi | View protein in InterPro IPR006935, Helicase/UvrB_N IPR014001, Helicase_ATP-bd IPR001650, Helicase_C IPR027417, P-loop_NTPase IPR011332, Ribosomal_zn-bd |
Pfami | View protein in Pfam PF00271, Helicase_C, 1 hit PF04851, ResIII, 1 hit |
SMARTi | View protein in SMART SM00487, DEXDc, 1 hit SM00490, HELICc, 1 hit |
SUPFAMi | SSF52540, SSF52540, 1 hit SSF57829, SSF57829, 1 hit |
PROSITEi | View protein in PROSITE PS51192, HELICASE_ATP_BIND_1, 1 hit PS51194, HELICASE_CTER, 1 hit |
i Sequence
Sequence statusi: Complete.
P33919-1 [UniParc]FASTAAdd to basket
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
Sequence cautioni
The sequence AAA16381 differs from that shown. Reason: Frameshift.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. |
PIRi | G64987 |
RefSeqi | NP_416689.1, NC_000913.3 WP_000578061.1, NZ_LN832404.1 |
Genome annotation databases
EnsemblBacteriai | AAC75245; AAC75245; b2184 BAE76649; BAE76649; BAE76649 |
GeneIDi | 945529 |
KEGGi | ecj:JW2172 eco:b2184 |
PATRICi | fig|1411691.4.peg.52 |
Similar proteinsi
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. |
PIRi | G64987 |
RefSeqi | NP_416689.1, NC_000913.3 WP_000578061.1, NZ_LN832404.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
6JDE | X-ray | 2.80 | A/B | 1-586 | [»] | |
SMRi | P33919 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 4259416, 278 interactors 849903, 1 interactor |
IntActi | P33919, 5 interactors |
STRINGi | 511145.b2184 |
Proteomic databases
PaxDbi | P33919 |
PRIDEi | P33919 |
Genome annotation databases
EnsemblBacteriai | AAC75245; AAC75245; b2184 BAE76649; BAE76649; BAE76649 |
GeneIDi | 945529 |
KEGGi | ecj:JW2172 eco:b2184 |
PATRICi | fig|1411691.4.peg.52 |
Organism-specific databases
EchoBASEi | EB1979 |
Phylogenomic databases
eggNOGi | COG1061, Bacteria |
HOGENOMi | CLU_014765_1_0_6 |
InParanoidi | P33919 |
PhylomeDBi | P33919 |
Enzyme and pathway databases
BioCyci | EcoCyc:EG12045-MONOMER MetaCyc:EG12045-MONOMER |
Miscellaneous databases
PROi | PR:P33919 |
Family and domain databases
InterProi | View protein in InterPro IPR006935, Helicase/UvrB_N IPR014001, Helicase_ATP-bd IPR001650, Helicase_C IPR027417, P-loop_NTPase IPR011332, Ribosomal_zn-bd |
Pfami | View protein in Pfam PF00271, Helicase_C, 1 hit PF04851, ResIII, 1 hit |
SMARTi | View protein in SMART SM00487, DEXDc, 1 hit SM00490, HELICc, 1 hit |
SUPFAMi | SSF52540, SSF52540, 1 hit SSF57829, SSF57829, 1 hit |
PROSITEi | View protein in PROSITE PS51192, HELICASE_ATP_BIND_1, 1 hit PS51194, HELICASE_CTER, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | RADD_ECOLI | |
Accessioni | P33919Primary (citable) accession number: P33919 Secondary accession number(s): P36926 Q2MAQ7 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | February 1, 1994 |
Last sequence update: | November 1, 1997 | |
Last modified: | April 7, 2021 | |
This is version 144 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- PDB cross-references
Index of Protein Data Bank (PDB) cross-references