P27296 · DING_ECOLI
- ProteinATP-dependent DNA helicase DinG
- GenedinG
- StatusUniProtKB reviewed (Swiss-Prot)
- Organism
- Amino acids716 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
DNA-dependent ATPase and 5'-3' DNA helicase (PubMed:12748189, PubMed:17416902, PubMed:25059658, PubMed:37537265).
Can also unwind DNA:RNA hybrid duplexes (PubMed:17416902).
Is active on D-loops, R-loops, and on forked structures (PubMed:17416902, PubMed:37537265).
Unwinds G-quadruplex DNA in a 5'-3' direction; unwinding efficiency differs on different substrates (PubMed:25059658, PubMed:37537265).
Does not appear to unwind replication forks or Holliday junctions (PubMed:25059658).
Translocates on single-stranded (ss)DNA with a 5'-3' polarity (PubMed:25059658).
In vitro at high concentrations also unwinds in a 3'-5' direction (PubMed:25059658).
May be involved in recombinational DNA repair and the resumption of replication after DNA damage (PubMed:17416902).
The [4Fe-4S] cluster is redox active at cellular potentials and is involved in DNA-mediated charge-transport signaling between DNA repair proteins from distinct pathways (PubMed:24738733).
DinG cooperates at long-range with endonuclease III, a base excision repair enzyme, using DNA charge transport to redistribute to regions of DNA damage (PubMed:24738733).
Binds 10-11 nucleotides of ssDNA in a positively-charged groove across the helicase domains (PubMed:30520735).
Can also unwind DNA:RNA hybrid duplexes (PubMed:17416902).
Is active on D-loops, R-loops, and on forked structures (PubMed:17416902, PubMed:37537265).
Unwinds G-quadruplex DNA in a 5'-3' direction; unwinding efficiency differs on different substrates (PubMed:25059658, PubMed:37537265).
Does not appear to unwind replication forks or Holliday junctions (PubMed:25059658).
Translocates on single-stranded (ss)DNA with a 5'-3' polarity (PubMed:25059658).
In vitro at high concentrations also unwinds in a 3'-5' direction (PubMed:25059658).
May be involved in recombinational DNA repair and the resumption of replication after DNA damage (PubMed:17416902).
The [4Fe-4S] cluster is redox active at cellular potentials and is involved in DNA-mediated charge-transport signaling between DNA repair proteins from distinct pathways (PubMed:24738733).
DinG cooperates at long-range with endonuclease III, a base excision repair enzyme, using DNA charge transport to redistribute to regions of DNA damage (PubMed:24738733).
Binds 10-11 nucleotides of ssDNA in a positively-charged groove across the helicase domains (PubMed:30520735).
Catalytic activity
- Couples ATP hydrolysis with the unwinding of duplex DNA at the replication fork by translocating in the 5'-3' direction. This creates two antiparallel DNA single strands (ssDNA). The leading ssDNA polymer is the template for DNA polymerase III holoenzyme which synthesizes a continuous strand.
- ATP + H2O = ADP + H+ + phosphate
Cofactor
Protein has several cofactor binding sites:
Note: ATP-dependent DNA helicase activity requires divalent cations (Mg2+, Ca2+ or Mn2+) but is not detected in the presence of Zn2+ (PubMed:12748189).
Activity regulation
ATPase activity is 15-fold stimulated by single-stranded DNA (ssDNA). Reduction of the [4Fe-4S] cluster reversibly switches off helicase activity. Remains fully active after exposure to 100-fold excess of hydrogen peroxide, but the [4Fe-4S] cluster can be efficiently modified by nitric oxide (NO), forming the DinG-bound dinitrosyl iron complex with the concomitant inactivation of helicase activity (PubMed:19074432).
Helicase activity on G-quadruplex DNA is inhibited by porphyrin derivatives meso-tetra (N-methyl-4-pyridyl) porphine tetra tosylate (T4) and N-methyl mesoporphyrin IX (NMM) (PubMed:25059658).
Helicase activity on forked duplexes is not inhibited by T4 or NMM (PubMed:25059658).
G-quadruplex ligands such as Pyridostatin, PhenDC3, BRACO-19 and Netropsin can alter recognition and unwinding of G-quadruplex DNAs; the effect is both ligand- and G-quadruplex DNA-specific (PubMed:37537265).
Helicase activity on G-quadruplex DNA is inhibited by porphyrin derivatives meso-tetra (N-methyl-4-pyridyl) porphine tetra tosylate (T4) and N-methyl mesoporphyrin IX (NMM) (PubMed:25059658).
Helicase activity on forked duplexes is not inhibited by T4 or NMM (PubMed:25059658).
G-quadruplex ligands such as Pyridostatin, PhenDC3, BRACO-19 and Netropsin can alter recognition and unwinding of G-quadruplex DNAs; the effect is both ligand- and G-quadruplex DNA-specific (PubMed:37537265).
Features
Showing features for binding site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 26 | ATP (UniProtKB | ChEBI) | ||||
Sequence: I | ||||||
Binding site | 31 | ATP (UniProtKB | ChEBI) | ||||
Sequence: Q | ||||||
Binding site | 60 | ATP (UniProtKB | ChEBI) | ||||
Sequence: K | ||||||
Binding site | 61 | ATP (UniProtKB | ChEBI) | ||||
Sequence: T | ||||||
Binding site | 120 | [4Fe-4S] cluster (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 194 | [4Fe-4S] cluster (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 199 | [4Fe-4S] cluster (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 205 | [4Fe-4S] cluster (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 599 | ATP (UniProtKB | ChEBI) | ||||
Sequence: D | ||||||
Binding site | 656 | ATP (UniProtKB | ChEBI) | ||||
Sequence: R | ||||||
Binding site | 659 | ATP (UniProtKB | ChEBI) | ||||
Sequence: R |
GO annotations
Aspect | Term | |
---|---|---|
Molecular Function | 4 iron, 4 sulfur cluster binding | |
Molecular Function | 5'-3' DNA helicase activity | |
Molecular Function | ATP binding | |
Molecular Function | ATP hydrolysis activity | |
Molecular Function | DNA binding | |
Molecular Function | DNA helicase activity | |
Molecular Function | DNA/RNA helicase activity | |
Molecular Function | isomerase activity | |
Molecular Function | metal ion binding | |
Biological Process | DNA duplex unwinding | |
Biological Process | DNA repair | |
Biological Process | G-quadruplex DNA unwinding | |
Biological Process | SOS response |
Keywords
- Molecular function
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameATP-dependent DNA helicase DinG
- EC number
- Alternative names
Gene names
Organism names
- Organism
- Strains
- Taxonomic lineageBacteria > Pseudomonadota > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Escherichia
Accessions
- Primary accessionP27296
Proteomes
Phenotypes & Variants
Disruption phenotype
Knockout results in a slight reduction of UV resistance (PubMed:12748189).
Knockout mutants are sensitive to very high levels of chain-terminating nucleoside analog 3' azidothymidine (AZT) (PubMed:26544712).
Knockout mutants are sensitive to very high levels of chain-terminating nucleoside analog 3' azidothymidine (AZT) (PubMed:26544712).
Features
Showing features for mutagenesis.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Mutagenesis | 117 | Significant decrease in helicase activity, small decrease in ssDNA binding. | ||||
Sequence: R → A | ||||||
Mutagenesis | 120 | Abolishes iron-sulfur-binding. | ||||
Sequence: C → S | ||||||
Mutagenesis | 194 | Abolishes iron-sulfur-binding. | ||||
Sequence: C → S | ||||||
Mutagenesis | 199 | Abolishes iron-sulfur-binding. | ||||
Sequence: C → S | ||||||
Mutagenesis | 205 | Abolishes iron-sulfur-binding. | ||||
Sequence: C → S | ||||||
Mutagenesis | 211 | Significant decrease in helicase activity, small decrease in ssDNA binding. | ||||
Sequence: R → A | ||||||
Mutagenesis | 615 | Loss of helicase activity, loss of ssDNA binding. | ||||
Sequence: F → A | ||||||
Mutagenesis | 618 | Loss of helicase activity, loss of ssDNA binding. | ||||
Sequence: I → A | ||||||
Mutagenesis | 636 | Loss of helicase activity, loss of ssDNA binding. | ||||
Sequence: Y → A | ||||||
Mutagenesis | 638 | Loss of helicase activity, loss of ssDNA binding. | ||||
Sequence: F → A | ||||||
Mutagenesis | 673 | Loss of helicase activity, loss of ssDNA binding. | ||||
Sequence: R → A |
PTM/Processing
Features
Showing features for chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000101996 | 1-716 | ATP-dependent DNA helicase DinG | |||
Sequence: MALTAALKAQIAAWYKALQEQIPDFIPRAPQRQMIADVAKTLAGEEGRHLAIEAPTGVGKTLSYLIPGIAIAREEQKTLVVSTANVALQDQIYSKDLPLLKKIIPDLKFTAAFGRGRYVCPRNLTALASTEPTQQDLLAFLDDELTPNNQEEQKRCAKLKGDLDTYKWDGLRDHTDIAIDDDLWRRLSTDKASCLNRNCYYYRECPFFVARREIQEAEVVVANHALVMAAMESEAVLPDPKNLLLVLDEGHHLPDVARDALEMSAEITAPWYRLQLDLFTKLVATCMEQFRPKTIPPLAIPERLNAHCEELYELIASLNNILNLYMPAGQEAEHRFAMGELPDEVLEICQRLAKLTEMLRGLAELFLNDLSEKTGSHDIVRLHRLILQMNRALGMFEAQSKLWRLASLAQSSGAPVTKWATREEREGQLHLWFHCVGIRVSDQLERLLWRSIPHIIVTSATLRSLNSFSRLQEMSGLKEKAGDRFVALDSPFNHCEQGKIVIPRMRVEPSIDNEEQHIAEMAAFFRKQVESKKHLGMLVLFASGRAMQRFLDYVTDLRLMLLVQGDQPRYRLVELHRKRVANGERSVLVGLQSFAEGLDLKGDLLSQVHIHKIAFPPIDSPVVITEGEWLKSLNRYPFEVQSLPSASFNLIQQVGRLIRSHGCWGEVVIYDKRLLTKNYGKRLLDALPVFPIEQPEVPEGIVKKKEKTKSPRRRRR |
Proteomic databases
Expression
Induction
DNA damage-inducible. Transcriptionally regulated by LexA.
Interaction
Subunit
Binary interactions
Type | Entry 1 | Entry 2 | Number of experiments | Intact | |
---|---|---|---|---|---|
BINARY | P27296 | ssb P0AGE0 | 2 | EBI-1114590, EBI-1118620 |
Protein-protein interaction databases
Chemistry
Structure
Family & Domains
Features
Showing features for region, domain, motif.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Region | 1-114 | HD1 domain N-terminus | ||||
Sequence: MALTAALKAQIAAWYKALQEQIPDFIPRAPQRQMIADVAKTLAGEEGRHLAIEAPTGVGKTLSYLIPGIAIAREEQKTLVVSTANVALQDQIYSKDLPLLKKIIPDLKFTAAFG | ||||||
Domain | 17-294 | Helicase ATP-binding | ||||
Sequence: ALQEQIPDFIPRAPQRQMIADVAKTLAGEEGRHLAIEAPTGVGKTLSYLIPGIAIAREEQKTLVVSTANVALQDQIYSKDLPLLKKIIPDLKFTAAFGRGRYVCPRNLTALASTEPTQQDLLAFLDDELTPNNQEEQKRCAKLKGDLDTYKWDGLRDHTDIAIDDDLWRRLSTDKASCLNRNCYYYRECPFFVARREIQEAEVVVANHALVMAAMESEAVLPDPKNLLLVLDEGHHLPDVARDALEMSAEITAPWYRLQLDLFTKLVATCMEQFRPKT | ||||||
Region | 115-216 | [4Fe-4S] domain | ||||
Sequence: RGRYVCPRNLTALASTEPTQQDLLAFLDDELTPNNQEEQKRCAKLKGDLDTYKWDGLRDHTDIAIDDDLWRRLSTDKASCLNRNCYYYRECPFFVARREIQE | ||||||
Region | 217-261 | HD1 domain middle | ||||
Sequence: AEVVVANHALVMAAMESEAVLPDPKNLLLVLDEGHHLPDVARDAL | ||||||
Motif | 248-251 | DEAH box | ||||
Sequence: DEGH | ||||||
Region | 262-438 | Arch domain | ||||
Sequence: EMSAEITAPWYRLQLDLFTKLVATCMEQFRPKTIPPLAIPERLNAHCEELYELIASLNNILNLYMPAGQEAEHRFAMGELPDEVLEICQRLAKLTEMLRGLAELFLNDLSEKTGSHDIVRLHRLILQMNRALGMFEAQSKLWRLASLAQSSGAPVTKWATREEREGQLHLWFHCVGI | ||||||
Region | 439-491 | HD1 domain middle | ||||
Sequence: RVSDQLERLLWRSIPHIIVTSATLRSLNSFSRLQEMSGLKEKAGDRFVALDSP | ||||||
Region | 492-716 | HD2 domain | ||||
Sequence: FNHCEQGKIVIPRMRVEPSIDNEEQHIAEMAAFFRKQVESKKHLGMLVLFASGRAMQRFLDYVTDLRLMLLVQGDQPRYRLVELHRKRVANGERSVLVGLQSFAEGLDLKGDLLSQVHIHKIAFPPIDSPVVITEGEWLKSLNRYPFEVQSLPSASFNLIQQVGRLIRSHGCWGEVVIYDKRLLTKNYGKRLLDALPVFPIEQPEVPEGIVKKKEKTKSPRRRRR |
Domain
Has 4 domains; the discontinous helicase 1 (HD1), helicase 2 (HD2), arch and Fe-S cluster domains (PubMed:30520735).
The arch domain sits above the other domains and contacts the Fe-S cluster domain above the ssDNA-binding surface (PubMed:30520735).
Addition of an ATP analog to a DinG-ssDNA crystal induces changes in the relative orientation of the domains; HD1 remains tightly bound while HD2 slides along the DNA, upon ATP hydrolysis HD1 slides while HD2 remains tightly bound, thus the enzyme translocates in a 5'-3' direction along the ssDNA (Probable) (PubMed:30520735).
The arch domain sits above the other domains and contacts the Fe-S cluster domain above the ssDNA-binding surface (PubMed:30520735).
Addition of an ATP analog to a DinG-ssDNA crystal induces changes in the relative orientation of the domains; HD1 remains tightly bound while HD2 slides along the DNA, upon ATP hydrolysis HD1 slides while HD2 remains tightly bound, thus the enzyme translocates in a 5'-3' direction along the ssDNA (Probable) (PubMed:30520735).
Sequence similarities
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length716
- Mass (Da)81,440
- Last updated1994-06-01 v3
- Checksum63E6767E8EAA67D2
Sequence caution
Features
Showing features for sequence conflict.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Sequence conflict | 513 | in Ref. 2; AAA23685 | ||||
Sequence: N → H |
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
L02123 EMBL· GenBank· DDBJ | AAA53655.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
M81935 EMBL· GenBank· DDBJ | AAA23685.1 EMBL· GenBank· DDBJ | Genomic DNA | Different initiation | |
U00096 EMBL· GenBank· DDBJ | AAC73886.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
AP009048 EMBL· GenBank· DDBJ | BAA35465.1 EMBL· GenBank· DDBJ | Genomic DNA |