RegulonDB

Gene
Name:	polB
Synonym(s):	ECK0061, EG10747, b0060, dinA
Genome position(nucleotides):	63429 <-- 65780 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	55.36
External database links:

ASAP:	ABE-0000202
CGSC:	374
ECHOBASE:	EB0740
MIM:	612591
MIM:	615381
OU-MICROARRAY:	b0060
PortEco:	polB
STRING:	511145.b0060
COLOMBOS:	polB

Gene

Name:

polB

Synonym(s):

ECK0061, EG10747, b0060, dinA

Genome position(nucleotides):

63429 <-- 65780 Genome Browser

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

55.36

External database links:

ASAP:

CGSC:

ECHOBASE:

MIM:

MIM:

OU-MICROARRAY:

PortEco:

STRING:

COLOMBOS:

Type

Positions

Sequence

172 -> 172

200 -> 296

SRPQLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRLPLRLGRDNSELEWREHGFKNGVFFAQAKGRLIIDGIEALKSAFWNFSSFSLETV

257 -> 258

740 -> 783

LDYQRSPLDYEHYLTRQLQPVAEGILPFIEDNFATLMTGQLGLF

401 -> 401

Type

Positions

Sequence

172 -> 172

200 -> 296

SRPQLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRLPLRLGRDNSELEWREHGFKNGVFFAQAKGRLIIDGIEALKSAFWNFSSFSLETV

257 -> 258

740 -> 783

LDYQRSPLDYEHYLTRQLQPVAEGILPFIEDNFATLMTGQLGLF

401 -> 401

2 -> 783

AQAGFILTRHWRDTPQGTEVSFWLATDNGPLQVTLAPQESVAFIPADQVPRAQHILQGEQGFRLTPLALKDFHRQPVYGLYCRAHRQLMNYEKRLREGGVTVYEADVRPPERYLMERFITSPVWVEGDMHNGTIVNARLKPHPDYRPPLKWVSIDIETTRHGELYCIGLEGCGQRIVYMLGPENGDASSLDFELEYVASRPQLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRLPLRLGRDNSELEWREHGFKNGVFFAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQELLGEGKSIDNPWDRMDEIDRRFAEDKPALATYNLKDCELVTQIFHKTEIMPFLLERATVNGLPVDRHGGSVAAFGHLYFPRMHRAGYVAPNLGEVPPHASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGMAQPDPEHSTEGFLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNKPLSQALKIIMNAFYGVLGTTACRFFDPRLASSITMRGHQIMRQTKALIEAQGYDVIYGDTDSTFVWLKGAHSEEEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYETHFCRFLMPTIRGADTGSKKRYAGLIQEGDKQRMVFKGLETVRTDWTPLAQQFQQELYLRIFRNEPYQEYVRETIDKLMAGELDARLVYRKRLRRPLSEYQRNVPPHVRAARLADEENQKRGRPLQYQNRGTIKYVWTTNGPEPLDYQRSPLDYEHYLTRQLQPVAEGILPFIEDNFATLMTGQLGLF

74 -> 164

HRQPVYGLYCRAHRQLMNYEKRLREGGVTVYEADVRPPERYLMERFITSPVWVEGDMHNGTIVNARLKPHPDYRPPLKWVSIDIETTRHGE

380 -> 738

RMHRAGYVAPNLGEVPPHASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGMAQPDPEHSTEGFLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNKPLSQALKIIMNAFYGVLGTTACRFFDPRLASSITMRGHQIMRQTKALIEAQGYDVIYGDTDSTFVWLKGAHSEEEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYETHFCRFLMPTIRGADTGSKKRYAGLIQEGDKQRMVFKGLETVRTDWTPLAQQFQQELYLRIFRNEPYQEYVRETIDKLMAGELDARLVYRKRLRRPLSEYQRNVPPHVRAARLADEENQKRGRPLQYQNRGTIKYVWTTNGPE

272 -> 272

735 -> 735

Multifun Terms (GenProtEC)

2 - information transfer --> 2.1 - DNA related --> 2.1.1 - DNA replication

2 - information transfer --> 2.1 - DNA related --> 2.1.4 - DNA repair

5 - cell processes --> 5.6 - protection --> 5.6.1 - radiation

5 - cell processes --> 5.8 - SOS response

Gene Ontology Terms (GO)

cellular_component

GO:0005829 - cytosol

molecular_function

GO:0003676 - nucleic acid binding
GO:0003677 - DNA binding
GO:0003887 - DNA-directed DNA polymerase activity
GO:0016779 - nucleotidyltransferase activity
GO:0008296 - 3'-5'-exodeoxyribonuclease activity
GO:0016740 - transferase activity
GO:0000166 - nucleotide binding

biological_process

GO:0006261 - DNA-dependent DNA replication
GO:0006281 - DNA repair
GO:0006974 - cellular response to DNA damage stimulus
GO:0009432 - SOS response
GO:0045004 - DNA replication proofreading
GO:0090305 - nucleic acid phosphodiester bond hydrolysis
GO:0071897 - DNA biosynthetic process

Transcriptional Regulation
	Display Regulation
Repressed by:	LexA

Transcriptional Regulation

Display Regulation

Repressed by:

LexA

RNA cis-regulatory element

Attenuation:	Translational

RNA cis-regulatory element

Attenuation:

Translational

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	rluAp1	60450	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: -3.53. P-value: 8.697e-5 Read more >	[ICWHO]	[16]
promoter	TSS_116	62712	reverse	nd	[RS-EPT-CBR]	[17]
promoter	TSS_117	62992	reverse	nd	[RS-EPT-CBR]	[17]
promoter	TSS_118	63450	reverse	nd	[RS-EPT-CBR]	[17]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

rluAp1

60450

reverse

Similarity to the consensus
Read more >

[ICWHO]

[16]

promoter

TSS_116

62712

reverse

[RS-EPT-CBR]

[17]

promoter

TSS_117

62992

reverse

[RS-EPT-CBR]

[17]

promoter

TSS_118

63450

reverse

[RS-EPT-CBR]

[17]

Evidence
[ICWHO] Inferred computationally without human oversight
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Evidence

[ICWHO] Inferred computationally without human oversight

[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] Al Mamun AA., 2007, Elevated expression of DNA polymerase II increases spontaneous mutagenesis in Escherichia coli., Mutat Res 625(1-2):29-39
[2] Bonner CA., Hays S., McEntee K., Goodman MF., 1990, DNA polymerase II is encoded by the DNA damage-inducible dinA gene of Escherichia coli., Proc Natl Acad Sci U S A 87(19):7663-7
[3] Cai H., Yu H., McEntee K., Goodman MF., 1995, Purification and properties of DNA polymerase II from Escherichia coli., Methods Enzymol 262:13-21
[4] Campbell JL., Shizuya H., Richardson CC., 1974, Mapping of a mutation, polB100, affecting deoxyribonucleic acid polymerase II in Escherichia coli K-12., J Bacteriol 119(2):494-9
[5] Campbell JL., Soll L., Richardson CC., 1972, Isolation and partial characterization of a mutant of Escherichia coli deficient in DNA polymerase II., Proc Natl Acad Sci U S A 69(8):2090-4
[6] 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
[7] Hirota Y., Gefter M., Mindich L., 1972, A mutant of Escherichia coli defective in DNA polymerase II activity., Proc Natl Acad Sci U S A 69(11):3238-42
[8] Kath JE., Chang S., Scotland MK., Wilbertz JH., Jergic S., Dixon NE., Sutton MD., Loparo JJ., 2016, Exchange between Escherichia coli polymerases II and III on a processivity clamp., Nucleic Acids Res 44(4):1681-90
[9] Miyaki M., Sai GE., Katagiri S., Akamatsu N., Ono T., 1977, Enhancement of DNA polymerase II activity in E. coli after treatment with N-methyl-N'-nitro-N-nitrosoguanidine., Biochem Biophys Res Commun 76(1):136-41
[10] Moses RE., 1974, The isolation and properties of DNA polymerase II from Escherichia coli., Methods Enzymol 29(0):13-22
[11] Qiu Z., Goodman MF., 1997, The Escherichia coli polB locus is identical to dinA, the structural gene for DNA polymerase II. Characterization of Pol II purified from a polB mutant., J Biol Chem 272(13):8611-7
[12] Rama Reddy GV., Goulian M., Hendler SS., 1971, Inhibition of E. coli DNA polymerase II by ara-CTP., Nat New Biol 234(52):286-8
[13] Shinagawa H., Iwasaki H., Ishino Y., Nakata A., 1991, SOS-inducible DNA polymerase II of E coli is homologous to replicative DNA polymerase of eukaryotes., Biochimie 73(4):433-5
[14] Tait RC., Harris AL., Smith DW., 1974, DNA repair in Escherichia coli mutants deficient in DNA polymerases I, II and-or 3., Proc Natl Acad Sci U S A 71(3):675-9
[15] Wang F., Yang W., 2009, Structural insight into translesion synthesis by DNA Pol II., Cell 139(7):1279-89
[16] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78
[17] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

Reference(s)

[1] Al Mamun AA., 2007, Elevated expression of DNA polymerase II increases spontaneous mutagenesis in Escherichia coli., Mutat Res 625(1-2):29-39

[2] Bonner CA., Hays S., McEntee K., Goodman MF., 1990, DNA polymerase II is encoded by the DNA damage-inducible dinA gene of Escherichia coli., Proc Natl Acad Sci U S A 87(19):7663-7

[3] Cai H., Yu H., McEntee K., Goodman MF., 1995, Purification and properties of DNA polymerase II from Escherichia coli., Methods Enzymol 262:13-21

[4] Campbell JL., Shizuya H., Richardson CC., 1974, Mapping of a mutation, polB100, affecting deoxyribonucleic acid polymerase II in Escherichia coli K-12., J Bacteriol 119(2):494-9

[5] Campbell JL., Soll L., Richardson CC., 1972, Isolation and partial characterization of a mutant of Escherichia coli deficient in DNA polymerase II., Proc Natl Acad Sci U S A 69(8):2090-4

[6] 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

[7] Hirota Y., Gefter M., Mindich L., 1972, A mutant of Escherichia coli defective in DNA polymerase II activity., Proc Natl Acad Sci U S A 69(11):3238-42

[8] Kath JE., Chang S., Scotland MK., Wilbertz JH., Jergic S., Dixon NE., Sutton MD., Loparo JJ., 2016, Exchange between Escherichia coli polymerases II and III on a processivity clamp., Nucleic Acids Res 44(4):1681-90

[9] Miyaki M., Sai GE., Katagiri S., Akamatsu N., Ono T., 1977, Enhancement of DNA polymerase II activity in E. coli after treatment with N-methyl-N'-nitro-N-nitrosoguanidine., Biochem Biophys Res Commun 76(1):136-41

[10] Moses RE., 1974, The isolation and properties of DNA polymerase II from Escherichia coli., Methods Enzymol 29(0):13-22

[11] Qiu Z., Goodman MF., 1997, The Escherichia coli polB locus is identical to dinA, the structural gene for DNA polymerase II. Characterization of Pol II purified from a polB mutant., J Biol Chem 272(13):8611-7

[12] Rama Reddy GV., Goulian M., Hendler SS., 1971, Inhibition of E. coli DNA polymerase II by ara-CTP., Nat New Biol 234(52):286-8

[13] Shinagawa H., Iwasaki H., Ishino Y., Nakata A., 1991, SOS-inducible DNA polymerase II of E coli is homologous to replicative DNA polymerase of eukaryotes., Biochimie 73(4):433-5

[14] Tait RC., Harris AL., Smith DW., 1974, DNA repair in Escherichia coli mutants deficient in DNA polymerases I, II and-or 3., Proc Natl Acad Sci U S A 71(3):675-9

[15] Wang F., Yang W., 2009, Structural insight into translesion synthesis by DNA Pol II., Cell 139(7):1279-89

[16] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

[17] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.