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Protein

DNA polymerase IV

Gene

dinB

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

Functioni

Poorly processive, error-prone DNA polymerase involved in translesion repair and untargeted mutagenesis (PubMed:10488344, PubMed:10801133). Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by Pol IV. Exhibits no 3'-5' exonuclease (proofreading) activity (PubMed:10488344). Overexpression of Pol IV results in increased frameshift mutagenesis. It is required for stationary-phase adaptive mutation, which provides the bacterium with flexibility in dealing with environmental stress, enhancing long-term survival and evolutionary fitness. Not seen to be involved in translesion snythesis even when stimulated by the beta slding-clamp and clamp-loading complex, which do however increase non-targeted DNA polymerase efficiency 3,000-fold, may be due to targeting to stalled replication forks on nondamaged DNA (PubMed:10801133, PubMed:16168375). Involved in translesional synthesis, in conjunction with the beta clamp from PolIII (PubMed:14592985, PubMed:14729336).1 Publication9 Publications

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

Cofactori

Mg2+By similarityNote: Binds 2 magnesium ions per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi8MagnesiumBy similarity1
Sitei13Substrate discriminationBy similarity1
Metal bindingi103MagnesiumBy similarity1
Active sitei104By similarity1

GO - Molecular functioni

  • damaged DNA binding Source: InterPro
  • DNA-directed DNA polymerase activity Source: EcoCyc
  • magnesium ion binding Source: UniProtKB-UniRule

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, DNA-directed DNA polymerase, Mutator protein, Nucleotidyltransferase, Transferase
Biological processDNA damage, DNA repair, DNA replication
LigandMagnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:G6115-MONOMER
MetaCyc:G6115-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase IV (EC:2.7.7.7)
Short name:
Pol IV
Alternative name(s):
Translesion synthesis polymerase IV1 Publication
Short name:
TSL polymerase IV
Gene namesi
Name:dinB
Synonyms:dinP
Ordered Locus Names:b0231, JW0221
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13141 dinB

Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi8D → A or H: Loss of function. 1 Publication1
Mutagenesisi49R → A or F: Loss of function. 1 Publication1
Mutagenesisi103D → A or N: Loss of function. 1 Publication1
Mutagenesisi104E → A: Loss of function. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001739121 – 351DNA polymerase IVAdd BLAST351

Proteomic databases

PaxDbiQ47155
PRIDEiQ47155

Expressioni

Inductioni

By SOS response. A member of the dinB-yafNOP operon (PubMed:12813093). Induced by hydroxyurea (PubMed:20005847).2 Publications

Interactioni

Subunit structurei

Monomer. Interacts with beta sliding clamp, which confers increased processivity (PubMed:14592985, PubMed:14729336,PubMed:16168375).Curated3 Publications

Binary interactionsi

Protein-protein interaction databases

BioGridi4261678, 55 interactors
IntActiQ47155, 3 interactors
MINTiQ47155
STRINGi316385.ECDH10B_0213

Structurei

Secondary structure

1351
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ47155
SMRiQ47155
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ47155

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini4 – 185UmuCAdd BLAST182

Domaini

The catalytic core consists of fingers, palm and thumb subdomains, but the fingers and thumb subdomains are much smaller than in high-fidelity polymerases; residues from five sequence motifs of the Y-family cluster around an active site cleft that can accommodate DNA and nucleotide substrates with relaxed geometric constraints, with consequently higher rates of misincorporation and low processivity. It lacks the O helices present in high-fidelity DNA polymerases in the fingers domain (By similarity).By similarity

Sequence similaritiesi

Belongs to the DNA polymerase type-Y family.Curated

Phylogenomic databases

eggNOGiENOG4105CQ3 Bacteria
COG0389 LUCA
InParanoidiQ47155
KOiK02346
PhylomeDBiQ47155

Family and domain databases

CDDicd03586 PolY_Pol_IV_kappa, 1 hit
Gene3Di3.30.1490.100, 1 hit
HAMAPiMF_01113 DNApol_IV, 1 hit
InterProiView protein in InterPro
IPR036775 DNA_pol_Y-fam_lit_finger_sf
IPR017961 DNA_pol_Y-fam_little_finger
IPR022880 DNApol_IV
IPR024728 PolY_HhH_motif
IPR001126 UmuC
PfamiView protein in Pfam
PF00817 IMS, 1 hit
PF11799 IMS_C, 1 hit
PF11798 IMS_HHH, 1 hit
SUPFAMiSSF100879 SSF100879, 1 hit
PROSITEiView protein in PROSITE
PS50173 UMUC, 1 hit

Sequencei

Sequence statusi: Complete.

Q47155-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MRKIIHVDMD CFFAAVEMRD NPALRDIPIA IGGSRERRGV ISTANYPARK
60 70 80 90 100
FGVRSAMPTG MALKLCPHLT LLPGRFDAYK EASNHIREIF SRYTSRIEPL
110 120 130 140 150
SLDEAYLDVT DSVHCHGSAT LIAQEIRQTI FNELQLTASA GVAPVKFLAK
160 170 180 190 200
IASDMNKPNG QFVITPAEVP AFLQTLPLAK IPGVGKVSAA KLEAMGLRTC
210 220 230 240 250
GDVQKCDLVM LLKRFGKFGR ILWERSQGID ERDVNSERLR KSVGVERTMA
260 270 280 290 300
EDIHHWSECE AIIERLYPEL ERRLAKVKPD LLIARQGVKL KFDDFQQTTQ
310 320 330 340 350
EHVWPRLNKA DLIATARKTW DERRGGRGVR LVGLHVTLLD PQMERQLVLG

L
Length:351
Mass (Da):39,516
Last modified:November 1, 1997 - v1
Checksum:i74DF44DCA18D405F
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti36 – 38ERR → ARG in strain: ECOR 45B1. 3
Natural varianti124Q → K in strain: ECOR 35D. 1
Natural varianti132N → S in strain: ECOR 34B1 and ECOR 37UG. 1
Natural varianti135Q → H in strain: ECOR 70B1. 1
Natural varianti170P → S in strain: ECOR 37UG. 1
Natural varianti171A → T in strain: ECOR 45B1, ECOR 46D, ECOR 49D and ECOR 50D. 1
Natural varianti176L → F in strain: ECOR 37UG. 1
Natural varianti201G → S in strain: ECOR 59B2. 1
Natural varianti210M → I in strain: ECOR 37UG, ECOR 45B1, ECOR 51B2, ECOR 52B2, ECOR 58B1 and ECOR 70B1. 1
Natural varianti210M → T in strain: ECOR 35D, ECOR 46D, ECOR 49D, ECOR 50D, ECOR 57B2, ECOR 59B2, ECOR 60B2 and ECOR 62B2. 1
Natural varianti225R → C in strain: ECOR 59B2 and ECOR 60B2. 1
Natural varianti310A → S in strain: ECOR 57B2, ECOR 59B2, ECOR 60B2 and ECOR 62B2. 1
Natural varianti321D → N in strain: ECOR 35D. 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D38582 Genomic DNA Translation: BAA07593.1
U70214 Genomic DNA Translation: AAB08651.1
U00096 Genomic DNA Translation: AAC73335.1
AP009048 Genomic DNA Translation: BAA77901.1
AF483080 Genomic DNA Translation: AAL91943.1
AF483081 Genomic DNA Translation: AAL91944.1
AF483082 Genomic DNA Translation: AAL91945.1
AF483083 Genomic DNA Translation: AAL91946.1
AF483084 Genomic DNA Translation: AAL91947.1
AF483085 Genomic DNA Translation: AAL91948.1
AF483086 Genomic DNA Translation: AAL91949.1
AF483087 Genomic DNA Translation: AAL91950.1
AF483088 Genomic DNA Translation: AAL91951.1
AF483089 Genomic DNA Translation: AAL91952.1
AF483090 Genomic DNA Translation: AAL91953.1
AF483091 Genomic DNA Translation: AAL91954.1
AF483092 Genomic DNA Translation: AAL91955.1
AF483093 Genomic DNA Translation: AAL91956.1
AF483094 Genomic DNA Translation: AAL91957.1
AF483095 Genomic DNA Translation: AAL91958.1
AF483096 Genomic DNA Translation: AAL91959.1
AF483097 Genomic DNA Translation: AAL91960.1
AF483098 Genomic DNA Translation: AAL91961.1
AF483099 Genomic DNA Translation: AAL91962.1
AF483100 Genomic DNA Translation: AAL91963.1
AF483101 Genomic DNA Translation: AAL91964.1
AF483102 Genomic DNA Translation: AAL91965.1
AF483103 Genomic DNA Translation: AAL91966.1
AF483104 Genomic DNA Translation: AAL91967.1
AF483105 Genomic DNA Translation: AAL91968.1
PIRiH64747
RefSeqiNP_414766.1, NC_000913.3
WP_001226164.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC73335; AAC73335; b0231
BAA77901; BAA77901; BAA77901
GeneIDi944922
KEGGiecj:JW0221
eco:b0231
PATRICifig|1411691.4.peg.2052

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D38582 Genomic DNA Translation: BAA07593.1
U70214 Genomic DNA Translation: AAB08651.1
U00096 Genomic DNA Translation: AAC73335.1
AP009048 Genomic DNA Translation: BAA77901.1
AF483080 Genomic DNA Translation: AAL91943.1
AF483081 Genomic DNA Translation: AAL91944.1
AF483082 Genomic DNA Translation: AAL91945.1
AF483083 Genomic DNA Translation: AAL91946.1
AF483084 Genomic DNA Translation: AAL91947.1
AF483085 Genomic DNA Translation: AAL91948.1
AF483086 Genomic DNA Translation: AAL91949.1
AF483087 Genomic DNA Translation: AAL91950.1
AF483088 Genomic DNA Translation: AAL91951.1
AF483089 Genomic DNA Translation: AAL91952.1
AF483090 Genomic DNA Translation: AAL91953.1
AF483091 Genomic DNA Translation: AAL91954.1
AF483092 Genomic DNA Translation: AAL91955.1
AF483093 Genomic DNA Translation: AAL91956.1
AF483094 Genomic DNA Translation: AAL91957.1
AF483095 Genomic DNA Translation: AAL91958.1
AF483096 Genomic DNA Translation: AAL91959.1
AF483097 Genomic DNA Translation: AAL91960.1
AF483098 Genomic DNA Translation: AAL91961.1
AF483099 Genomic DNA Translation: AAL91962.1
AF483100 Genomic DNA Translation: AAL91963.1
AF483101 Genomic DNA Translation: AAL91964.1
AF483102 Genomic DNA Translation: AAL91965.1
AF483103 Genomic DNA Translation: AAL91966.1
AF483104 Genomic DNA Translation: AAL91967.1
AF483105 Genomic DNA Translation: AAL91968.1
PIRiH64747
RefSeqiNP_414766.1, NC_000913.3
WP_001226164.1, NZ_LN832404.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1OK7X-ray1.65C336-351[»]
1UNNX-ray1.90C/D243-351[»]
4IR1X-ray2.38A/F2-351[»]
4IR9X-ray2.33A/F2-351[»]
4IRCX-ray2.67A/F2-341[»]
4IRDX-ray2.48A/F2-341[»]
4IRKX-ray2.32A/B2-341[»]
4Q43X-ray2.45A/F2-351[»]
4Q44X-ray2.71A/F2-341[»]
4Q45X-ray2.18A/F2-341[»]
4R8UX-ray2.30A2-340[»]
B2-338[»]
5C5JX-ray2.10A/F2-351[»]
5YURX-ray2.04A/F2-351[»]
5YUTX-ray2.15A/F2-351[»]
5YV1X-ray2.09A/F2-351[»]
5YV2X-ray1.90A/F2-351[»]
5YV4X-ray1.97A/F2-351[»]
5YYDX-ray2.05A/F2-351[»]
5YYEX-ray2.33A/F2-351[»]
ProteinModelPortaliQ47155
SMRiQ47155
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261678, 55 interactors
IntActiQ47155, 3 interactors
MINTiQ47155
STRINGi316385.ECDH10B_0213

Proteomic databases

PaxDbiQ47155
PRIDEiQ47155

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73335; AAC73335; b0231
BAA77901; BAA77901; BAA77901
GeneIDi944922
KEGGiecj:JW0221
eco:b0231
PATRICifig|1411691.4.peg.2052

Organism-specific databases

EchoBASEiEB2935
EcoGeneiEG13141 dinB

Phylogenomic databases

eggNOGiENOG4105CQ3 Bacteria
COG0389 LUCA
InParanoidiQ47155
KOiK02346
PhylomeDBiQ47155

Enzyme and pathway databases

BioCyciEcoCyc:G6115-MONOMER
MetaCyc:G6115-MONOMER

Miscellaneous databases

EvolutionaryTraceiQ47155
PROiPR:Q47155

Family and domain databases

CDDicd03586 PolY_Pol_IV_kappa, 1 hit
Gene3Di3.30.1490.100, 1 hit
HAMAPiMF_01113 DNApol_IV, 1 hit
InterProiView protein in InterPro
IPR036775 DNA_pol_Y-fam_lit_finger_sf
IPR017961 DNA_pol_Y-fam_little_finger
IPR022880 DNApol_IV
IPR024728 PolY_HhH_motif
IPR001126 UmuC
PfamiView protein in Pfam
PF00817 IMS, 1 hit
PF11799 IMS_C, 1 hit
PF11798 IMS_HHH, 1 hit
SUPFAMiSSF100879 SSF100879, 1 hit
PROSITEiView protein in PROSITE
PS50173 UMUC, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiDPO4_ECOLI
AccessioniPrimary (citable) accession number: Q47155
Secondary accession number(s): Q47683
, Q8RJ78, Q8RJ81, Q8RJ86, Q8RJ87, Q8RNI5, Q8RNI6, Q8RNI7, Q8RNI8, Q8RNI9, Q8RNJ0, Q8RNJ1, Q8RNJ2, Q8RNJ3, Q8RNJ4, Q8RNJ5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: November 7, 2018
This is version 148 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
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Main funding by: National Institutes of Health

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