RegulonDB RegulonDB 11.0: Gene Form
   

dinB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

lfhA dinB lafU rayT yafN LexA LexA yafNp yafNp dinBp2 dinBp2 dinBp dinBp

Gene      
Name: dinB    Texpresso search in the literature
Synonym(s): ECK0232, G6115, b0231, dinP
Genome position(nucleotides): 250898 --> 251953
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.17
External database links:  
ASAP:
 ABE-0000789
ECHOBASE:
 EB2935
ECOLIHUB:
 dinB
OU-MICROARRAY:
 b0231
STRING:
 511145.b0231
COLOMBOS: dinB


Product      
Name: DNA polymerase IV
Synonym(s): DinB, DinP, pol IV
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 39.516
Isoelectric point: 9.619
Motif(s):
 
Type Positions Sequence Comment
4 -> 185 IIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPARKFGVRSAMPTGMALKLCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEPLSLDEAYLDVTDSVHCHGSATLIAQEIRQTIFNELQLTASAGVAPVKFLAKIASDMNKPNGQFVITPAEVPAFLQTLPLAKIPGVG UniProt: UmuC.
7 -> 154 VDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPARKFGVRSAMPTGMALKLCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEPLSLDEAYLDVTDSVHCHGSATLIAQEIRQTIFNELQLTASAGVAPVKFLAKIASD
8 -> 8 D UniProt: Loss of function..
13 -> 13 F F → A: 35-fold increase in level of rCTP incorporation compared to wild type in vitro; no effect on incorporation of dCTP
36 -> 38 ERR UniProt: In strain: ECOR 45B1..

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.1 - DNA replication
  5 - cell processes --> 5.8 - SOS response
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003887 - DNA-directed DNA polymerase activity
GO:0016779 - nucleotidyltransferase activity
GO:0005515 - protein binding
GO:0016740 - transferase activity
GO:0046872 - metal ion binding
GO:0003684 - damaged DNA binding
GO:0000287 - magnesium ion binding
biological_process GO:0042276 - error-prone translesion synthesis
GO:0070987 - error-free translesion synthesis
GO:0006260 - DNA replication
GO:0006261 - DNA-templated DNA replication
GO:0006281 - DNA repair
GO:0006974 - cellular response to DNA damage stimulus
GO:0009432 - SOS response
GO:0000731 - DNA synthesis involved in DNA repair
Note(s): Note(s): ...[more].
Reference(s): [1] Al Mamun AA., et al., 2000
[2] Bjedov I., et al., 2003
[3] Boudsocq F., et al., 2002
[4] Brotcorne-Lannoye A., et al., 1986
[5] Bull HJ., et al., 2001
[6] Burnouf DY., et al., 2004
[7] Cafarelli TM., et al., 2014
[8] Chandani S., et al., 2009
[9] Dalrymple BP., et al., 2001
[10] Frisch RL., et al., 2010
[11] Gabbai CB., et al., 2014
[12] Galhardo RS., et al., 2009
[13] Godoy VG., et al., 2006
[14] Goswami M., et al., 2018
[15] Hastings PJ., et al., 2010
[16] Henrikus SS., et al., 2021
[17] Ikeda M., et al., 2012
[18] Jacob KD., et al., 2007
[19] Kobayashi S., et al., 2002
[20] Kottur J., et al., 2018
[21] Krasovec R., et al., 2018
[22] Layton JC., et al., 2003
[23] Lee CH., et al., 2006
[24] Lovett ST. 2006
[25] Maul RW., et al., 2007
[26] McKenzie GJ., et al., 2001
[27] Moore JM., et al., 2017
[28] Mori T., et al., 2012
[29] Nevin P., et al., 2015
[30] Nguyen A., et al., 2020
[31] Niccum BA., et al., 2018
[32] Nowosielska A., et al., 2004
[33] Perez-Capilla T., et al., 2005
[34] Ren L., et al., 1999
[35] Seo KY., et al., 2006
[36] Sharma A., et al., 2013
[37] Shen X., et al., 2002
[38] Sholder G., et al., 2015
[39] Storvik KA., et al., 2010
[40] Sutton MD., et al., 2006
[41] Tashjian TF., et al., 2017
[42] Thrall ES., et al., 2017
[43] Tippin B., et al., 2004
[44] Tompkins JD., et al., 2003
[45] Uchida K., et al., 2008
[46] Wagner J., et al., 2009
[47] Walsh JM., et al., 2011
[48] Wrzesinski M., et al., 2005
[49] Yang IY., et al., 2001
[50] Yeiser B., et al., 2002
External database links:  
ALPHAFOLD:
 Q47155
ECOCYC:
 G6115-MONOMER
ECOLIWIKI:
 b0231
INTERPRO:
 IPR017961
INTERPRO:
 IPR022880
INTERPRO:
 IPR043128
INTERPRO:
 IPR036775
INTERPRO:
 IPR001126
INTERPRO:
 IPR043502
INTERPRO:
 IPR024728
MINT:
 Q47155
MODBASE:
 Q47155
PDB:
 5YUR
PDB:
 5YUS
PDB:
 5YUT
PDB:
 5YUU
PDB:
 5YUV
PDB:
 5YUX
PDB:
 5YUY
PDB:
 5YUZ
PDB:
 5YV0
PDB:
 5YV1
PDB:
 5YV2
PDB:
 5YV3
PDB:
 5YYD
PDB:
 5YYE
PDB:
 5ZLV
PDB:
 6IG1
PDB:
 6JUP
PDB:
 6JUQ
PDB:
 5C5J
PDB:
 4R8U
PDB:
 4Q45
PDB:
 4Q44
PDB:
 4Q43
PDB:
 4IRK
PDB:
 4IRD
PDB:
 4IRC
PDB:
 4IR9
PDB:
 4IR1
PDB:
 1UNN
PDB:
 1OK7
PDB:
 5YUW
PFAM:
 PF11798
PFAM:
 PF00817
PFAM:
 PF11799
PRIDE:
 Q47155
PRODB:
 PRO_000022446
PROSITE:
 PS50173
REFSEQ:
 NP_414766
SMR:
 Q47155
SWISSMODEL:
 Q47155
UNIPROT:
 Q47155


Operon      
Name: dinB-yafNOP         
Operon arrangement:
Transcription unit        Promoter
dinB-yafNOP
dinB-yafNOP
yafNOP


Transcriptional Regulation      
Display Regulation             
Repressed by: LexA


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References


Reference(s)    

 [1] Al Mamun AA., Yadava RS., Ren L., Humayun MZ., 2000, The Escherichia coli UVM response is accompanied by an SOS-independent error-prone DNA replication activity demonstrable in vitro., Mol Microbiol 38(2):368-80

 [2] Bjedov I., Lecointre G., Tenaillon O., Vaury C., Radman M., Taddei F., Denamur E., Matic I., 2003, Polymorphism of genes encoding SOS polymerases in natural populations of Escherichia coli., DNA Repair (Amst) 2(4):417-26

 [3] Boudsocq F., Ling H., Yang W., Woodgate R., 2002, Structure-based interpretation of missense mutations in Y-family DNA polymerases and their implications for polymerase function and lesion bypass., DNA Repair (Amst) 1(5):343-58

 [4] Brotcorne-Lannoye A., Maenhaut-Michel G., 1986, Role of RecA protein in untargeted UV mutagenesis of bacteriophage lambda: evidence for the requirement for the dinB gene., Proc Natl Acad Sci U S A 83(11):3904-8

 [5] Bull HJ., Lombardo MJ., Rosenberg SM., 2001, Stationary-phase mutation in the bacterial chromosome: recombination protein and DNA polymerase IV dependence., Proc Natl Acad Sci U S A 98(15):8334-41

 [6] Burnouf DY., Olieric V., Wagner J., Fujii S., Reinbolt J., Fuchs RP., Dumas P., 2004, Structural and biochemical analysis of sliding clamp/ligand interactions suggest a competition between replicative and translesion DNA polymerases., J Mol Biol 335(5):1187-97

 [7] Cafarelli TM., Rands TJ., Godoy VG., 2014, The DinB·RecA complex of Escherichia coli mediates an efficient and high-fidelity response to ubiquitous alkylation lesions., Environ Mol Mutagen 55(2):92-102

 [8] Chandani S., Loechler EL., 2009, Y-Family DNA polymerases may use two different dNTP shapes for insertion: a hypothesis and its implications., J Mol Graph Model 27(7):759-69

 [9] Dalrymple BP., Kongsuwan K., Wijffels G., Dixon NE., Jennings PA., 2001, A universal protein-protein interaction motif in the eubacterial DNA replication and repair systems., Proc Natl Acad Sci U S A 98(20):11627-32

 [10] Frisch RL., Su Y., Thornton PC., Gibson JL., Rosenberg SM., Hastings PJ., 2010, Separate DNA Pol II- and Pol IV-dependent pathways of stress-induced mutation during double-strand-break repair in Escherichia coli are controlled by RpoS., J Bacteriol 192(18):4694-700

 [11] Gabbai CB., Yeeles JT., Marians KJ., 2014, Replisome-mediated translesion synthesis and leading strand template lesion skipping are competing bypass mechanisms., J Biol Chem 289(47):32811-23

 [12] Galhardo RS., Do R., Yamada M., Friedberg EC., Hastings PJ., Nohmi T., Rosenberg SM., 2009, DinB Upregulation Is the Sole Role of the SOS Response in Stress-Induced Mutagenesis in Escherichia coli., Genetics 182(1):55-68

 [13] Godoy VG., Jarosz DF., Walker FL., Simmons LA., Walker GC., 2006, Y-family DNA polymerases respond to DNA damage-independent inhibition of replication fork progression., EMBO J 25(4):868-79

 [14] Goswami M., Narayana Rao AVSS., 2018, Transcriptome Profiling Reveals Interplay of Multifaceted Stress Response in Escherichia coli on Exposure to Glutathione and Ciprofloxacin., mSystems 3(1)

 [15] Hastings PJ., Hersh MN., Thornton PC., Fonville NC., Slack A., Frisch RL., Ray MP., Harris RS., Leal SM., Rosenberg SM., 2010, Competition of Escherichia coli DNA polymerases I, II and III with DNA Pol IV in stressed cells., PLoS One 5(5):e10862

 [16] Henrikus SS., van Oijen AM., Robinson A., 2021, Single-molecule fluorescence microscopy reveals modulation of DNA polymerase IV-binding lifetimes by UmuD (K97A) and UmuD'., Curr Genet

 [17] Ikeda M., Shinozaki Y., Uchida K., Ohshika Y., Furukohri A., Maki H., Akiyama MT., 2012, Quick replication fork stop by overproduction of Escherichia coli DinB produces non-proliferative cells with an aberrant chromosome., Genes Genet Syst 87(4):221-31

 [18] Jacob KD., Eckert KA., 2007, Escherichia coli DNA polymerase IV contributes to spontaneous mutagenesis at coding sequences but not microsatellite alleles., Mutat Res 619(1-2):93-103

 [19] Kobayashi S., Valentine MR., Pham P., O'Donnell M., Goodman MF., 2002, Fidelity of Escherichia coli DNA polymerase IV. Preferential generation of small deletion mutations by dNTP-stabilized misalignment., J Biol Chem 277(37):34198-207

 [20] Kottur J., Nair DT., 2018, Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction., Nucleic Acids Res 46(12):5875-5885

 [21] Krasovec R., Richards H., Gifford DR., Belavkin RV., Channon A., Aston E., McBain AJ., Knight CG., 2018, Opposing effects of final population density and stress on Escherichia coli mutation rate., ISME J 12(12):2981-2987

 [22] Layton JC., Foster PL., 2003, Error-prone DNA polymerase IV is controlled by the stress-response sigma factor, RpoS, in Escherichia coli., Mol Microbiol 50(2):549-61

 [23] Lee CH., Chandani S., Loechler EL., 2006, Homology modeling of four Y-family, lesion-bypass DNA polymerases: the case that E. coli Pol IV and human Pol kappa are orthologs, and E. coli Pol V and human Pol eta are orthologs., J Mol Graph Model 25(1):87-102

 [24] Lovett ST., 2006, Replication arrest-stimulated recombination: Dependence on the RecA paralog, RadA/Sms and translesion polymerase, DinB., DNA Repair (Amst) 5(12):1421-7

 [25] Maul RW., Ponticelli SK., Duzen JM., Sutton MD., 2007, Differential binding of Escherichia coli DNA polymerases to the beta-sliding clamp., Mol Microbiol 65(3):811-27

 [26] McKenzie GJ., Rosenberg SM., 2001, Adaptive mutations, mutator DNA polymerases and genetic change strategies of pathogens., Curr Opin Microbiol 4(5):586-94

 [27] Moore JM., Correa R., Rosenberg SM., Hastings PJ., 2017, Persistent damaged bases in DNA allow mutagenic break repair in Escherichia coli., PLoS Genet 13(7):e1006733

 [28] Mori T., Nakamura T., Okazaki N., Furukohri A., Maki H., Akiyama MT., 2012, Escherichia coli DinB inhibits replication fork progression without significantly inducing the SOS response., Genes Genet Syst 87(2):75-87

 [29] Nevin P., Lu X., Zhang K., Engen JR., Beuning PJ., 2015, Noncognate DNA damage prevents the formation of the active conformation of the Y-family DNA polymerases DinB and DNA polymerase κ., FEBS J 282(14):2646-60

 [30] Nguyen A., Maisnier-Patin S., Yamayoshi I., Kofoid E., Roth JR., 2020, Selective Inbreeding: Genetic Crosses Drive Apparent Adaptive Mutation in the Cairns-Foster System of Escherichia coli., Genetics 214(2):333-354

 [31] Niccum BA., Lee H., MohammedIsmail W., Tang H., Foster PL., 2018, The Spectrum of Replication Errors in the Absence of Error Correction Assayed Across the Whole Genome of Escherichia coli., Genetics 209(4):1043-1054

 [32] Nowosielska A., Janion C., Grzesiuk E., 2004, Effect of deletion of SOS-induced polymerases, pol II, IV, and V, on spontaneous mutagenesis in Escherichia coli mutD5., Environ Mol Mutagen 43(4):226-34

 [33] Perez-Capilla T., Baquero MR., Gomez-Gomez JM., Ionel A., Martin S., Blazquez J., 2005, SOS-independent induction of dinB transcription by beta-lactam-mediated inhibition of cell wall synthesis in Escherichia coli., J Bacteriol 187(4):1515-8

 [34] Ren L., Al Mamun AA., Humayun MZ., 1999, The mutA mistranslator tRNA-induced mutator phenotype requires recA and recB genes, but not the derepression of lexA-regulated functions., Mol Microbiol 32(3):607-15

 [35] Seo KY., Nagalingam A., Miri S., Yin J., Chandani S., Kolbanovskiy A., Shastry A., Loechler EL., 2006, Mirror image stereoisomers of the major benzo[a]pyrene N2-dG adduct are bypassed by different lesion-bypass DNA polymerases in E. coli., DNA Repair (Amst) 5(4):515-22

 [36] Sharma A., Kottur J., Narayanan N., Nair DT., 2013, A strategically located serine residue is critical for the mutator activity of DNA polymerase IV from Escherichia coli., Nucleic Acids Res 41(9):5104-14

 [37] Shen X., Sayer JM., Kroth H., Ponten I., O'Donnell M., Woodgate R., Jerina DM., Goodman MF., 2002, Efficiency and accuracy of SOS-induced DNA polymerases replicating benzo[a]pyrene-7,8-diol 9,10-epoxide A and G adducts., J Biol Chem 277(7):5265-74

 [38] Sholder G., Creech A., Loechler EL., 2015, How Y-Family DNA polymerase IV is more accurate than Dpo4 at dCTP insertion opposite an N2-dG adduct of benzo[a]pyrene., DNA Repair (Amst) 35:144-53

 [39] Storvik KA., Foster PL., 2010, RpoS, the stress response sigma factor, plays a dual role in the regulation of Escherichia coli's error-prone DNA polymerase IV., J Bacteriol 192(14):3639-44

 [40] Sutton MD., Duzen JM., 2006, Specific amino acid residues in the beta sliding clamp establish a DNA polymerase usage hierarchy in Escherichia coli., DNA Repair (Amst) 5(3):312-23

 [41] Tashjian TF., Lin I., Belt V., Cafarelli TM., Godoy VG., 2017, RNA Primer Extension Hinders DNA Synthesis by Escherichia coli Mutagenic DNA Polymerase IV., Front Microbiol 8:288

 [42] Thrall ES., Kath JE., Chang S., Loparo JJ., 2017, Single-molecule imaging reveals multiple pathways for the recruitment of translesion polymerases after DNA damage., Nat Commun 8(1):2170

 [43] Tippin B., Kobayashi S., Bertram JG., Goodman MF., 2004, To slip or skip, visualizing frameshift mutation dynamics for error-prone DNA polymerases., J Biol Chem 279(44):45360-8

 [44] Tompkins JD., Nelson JL., Hazel JC., Leugers SL., Stumpf JD., Foster PL., 2003, Error-prone polymerase, DNA polymerase IV, is responsible for transient hypermutation during adaptive mutation in Escherichia coli., J Bacteriol 185(11):3469-72

 [45] Uchida K., Furukohri A., Shinozaki Y., Mori T., Ogawara D., Kanaya S., Nohmi T., Maki H., Akiyama M., 2008, Overproduction of Escherichia coli DNA polymerase DinB (Pol IV) inhibits replication fork progression and is lethal., Mol Microbiol 70(3):608-22

 [46] Wagner J., Etienne H., Fuchs RP., Cordonnier A., Burnouf D., 2009, Distinct beta-clamp interactions govern the activities of the Y family PolIV DNA polymerase., Mol Microbiol 74(5):1143-51

 [47] Walsh JM., Bouamaied I., Brown T., Wilhelmsson LM., Beuning PJ., 2011, Discrimination against the cytosine analog tC by Escherichia coli DNA polymerase IV DinB., J Mol Biol 409(2):89-100

 [48] Wrzesinski M., Nowosielska A., Nieminuszczy J., Grzesiuk E., 2005, Effect of SOS-induced Pol II, Pol IV, and Pol V DNA polymerases on UV-induced mutagenesis and MFD repair in Escherichia coli cells., Acta Biochim Pol 52(1):139-47

 [49] Yang IY., Hossain M., Miller H., Khullar S., Johnson F., Grollman A., Moriya M., 2001, Responses to the major acrolein-derived deoxyguanosine adduct in Escherichia coli., J Biol Chem 276(12):9071-6

 [50] Yeiser B., Pepper ED., Goodman MF., Finkel SE., 2002, SOS-induced DNA polymerases enhance long-term survival and evolutionary fitness., Proc Natl Acad Sci U S A 99(13):8737-41

RegulonDB