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Protein

DNA polymerase IV

Gene

dinB

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

Functioni

Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. Overexpression of polIV 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. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII.5 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-HAMAP

GO - Biological processi

  • cellular response to DNA damage stimulus Source: EcoliWiki
  • DNA-dependent DNA replication Source: UniProtKB-HAMAP
  • DNA synthesis involved in DNA repair Source: EcoliWiki
  • SOS response Source: EcoCyc
  • translesion synthesis Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

DNA-directed DNA polymerase, Mutator protein, Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA damage, DNA repair, DNA replication

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:G6115-MONOMER.
ECOL316407:JW0221-MONOMER.
MetaCyc:G6115-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase IV (EC:2.7.7.7)
Short name:
Pol 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

  • cytoplasm Source: EcoliWiki
Complete GO annotation...

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.Curated

Binary interactionsi

WithEntry#Exp.IntActNotes
dnaNP0A9882EBI-1037359,EBI-542385
nusAP0AFF63EBI-1037359,EBI-551571

Protein-protein interaction databases

BioGridi4261678. 35 interactors.
IntActiQ47155. 3 interactors.
STRINGi511145.b0231.

Structurei

Secondary structure

1351
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 11Combined sources8
Helixi12 – 20Combined sources9
Helixi22 – 24Combined sources3
Beta strandi25 – 27Combined sources3
Beta strandi29 – 32Combined sources4
Turni35 – 38Combined sources4
Beta strandi40 – 44Combined sources5
Helixi46 – 50Combined sources5
Helixi59 – 65Combined sources7
Beta strandi70 – 72Combined sources3
Helixi76 – 91Combined sources16
Beta strandi97 – 101Combined sources5
Beta strandi104 – 108Combined sources5
Helixi114 – 117Combined sources4
Helixi119 – 134Combined sources16
Beta strandi138 – 145Combined sources8
Helixi146 – 153Combined sources8
Turni154 – 156Combined sources3
Beta strandi161 – 163Combined sources3
Turni166 – 168Combined sources3
Helixi169 – 174Combined sources6
Helixi178 – 180Combined sources3
Helixi186 – 193Combined sources8
Turni194 – 196Combined sources3
Helixi200 – 204Combined sources5
Helixi208 – 215Combined sources8
Helixi217 – 225Combined sources9
Turni226 – 228Combined sources3
Beta strandi243 – 253Combined sources11
Helixi256 – 277Combined sources22
Beta strandi284 – 292Combined sources9
Beta strandi297 – 303Combined sources7
Helixi309 – 323Combined sources15
Beta strandi329 – 337Combined sources9

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[»]
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
Contains 1 umuC domain.Curated

Phylogenomic databases

eggNOGiENOG4105CQ3. Bacteria.
COG0389. LUCA.
InParanoidiQ47155.
KOiK02346.
OMAiHTLPWAT.
PhylomeDBiQ47155.

Family and domain databases

Gene3Di3.30.1490.100. 1 hit.
HAMAPiMF_01113. DNApol_IV. 1 hit.
InterProiIPR017961. DNA_pol_Y-fam_little_finger.
IPR022880. DNApol_IV.
IPR024728. PolY_HhH_motif.
IPR001126. UmuC.
[Graphical view]
PfamiPF00817. IMS. 1 hit.
PF11799. IMS_C. 1 hit.
PF11798. IMS_HHH. 1 hit.
[Graphical view]
SUPFAMiSSF100879. SSF100879. 1 hit.
PROSITEiPS50173. UMUC. 1 hit.
[Graphical view]

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.
PATRICi32115577. VBIEscCol129921_0233.

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[»]
ProteinModelPortaliQ47155.
SMRiQ47155.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261678. 35 interactors.
IntActiQ47155. 3 interactors.
STRINGi511145.b0231.

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.
PATRICi32115577. VBIEscCol129921_0233.

Organism-specific databases

EchoBASEiEB2935.
EcoGeneiEG13141. dinB.

Phylogenomic databases

eggNOGiENOG4105CQ3. Bacteria.
COG0389. LUCA.
InParanoidiQ47155.
KOiK02346.
OMAiHTLPWAT.
PhylomeDBiQ47155.

Enzyme and pathway databases

BioCyciEcoCyc:G6115-MONOMER.
ECOL316407:JW0221-MONOMER.
MetaCyc:G6115-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ47155.
PROiQ47155.

Family and domain databases

Gene3Di3.30.1490.100. 1 hit.
HAMAPiMF_01113. DNApol_IV. 1 hit.
InterProiIPR017961. DNA_pol_Y-fam_little_finger.
IPR022880. DNApol_IV.
IPR024728. PolY_HhH_motif.
IPR001126. UmuC.
[Graphical view]
PfamiPF00817. IMS. 1 hit.
PF11799. IMS_C. 1 hit.
PF11798. IMS_HHH. 1 hit.
[Graphical view]
SUPFAMiSSF100879. SSF100879. 1 hit.
PROSITEiPS50173. UMUC. 1 hit.
[Graphical view]
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 historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: November 2, 2016
This is version 137 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.