RegulonDB RegulonDB 10.9: Gene Form
   

polB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rapA polB araD LexA terminator terminator polBp polBp hepAp2 hepAp2 TSS_118 TSS_118 rapAp rapAp TSS_117 TSS_117 TSS_116 TSS_116 rluAp1 rluAp1

Gene      
Name: polB    Texpresso search in the literature
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
ECOLIHUB:
polB
MIM:
612591
MIM:
615381
OU-MICROARRAY:
b0060
STRING:
511145.b0060
COLOMBOS: polB


Product      
Name: DNA polymerase II
Synonym(s): DinA, PolB
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 90.052
Isoelectric point: 6.854
Motif(s):
 
Type Positions Sequence
172 -> 172 G
200 -> 296 SRPQLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRLPLRLGRDNSELEWREHGFKNGVFFAQAKGRLIIDGIEALKSAFWNFSSFSLETV
257 -> 258 EH
740 -> 783 LDYQRSPLDYEHYLTRQLQPVAEGILPFIEDNFATLMTGQLGLF
401 -> 401 G

 

Classification:
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
Note(s): Note(s): ...[more].
Reference(s): [1] Al Mamun AA. 2007
[2] Bonner CA., et al., 1990
[3] Cai H., et al., 1995
[4] Campbell JL., et al., 1974
[5] Campbell JL., et al., 1972
[6] Hastings PJ., et al., 2010
[7] Hirota Y., et al., 1972
[8] Kath JE., et al., 2016
[9] Miyaki M., et al., 1977
[10] Moses RE. 1974
[11] Qiu Z., et al., 1997
[12] Rama Reddy GV., et al., 1971
[13] Shinagawa H., et al., 1991
[14] Tait RC., et al., 1974
[15] Wang F., et al., 2009
External database links:  
ECOCYC:
EG10747-MONOMER
ECOLIWIKI:
b0060
INTERPRO:
IPR017964
INTERPRO:
IPR012337
INTERPRO:
IPR006172
INTERPRO:
IPR043502
INTERPRO:
IPR006133
INTERPRO:
IPR042087
INTERPRO:
IPR023211
INTERPRO:
IPR036397
INTERPRO:
IPR006134
MODBASE:
P21189
PDB:
3MAQ
PDB:
3K5O
PDB:
3K5N
PDB:
3K5M
PDB:
3K5L
PDB:
3K59
PDB:
3K58
PDB:
3K57
PDB:
1Q8I
PFAM:
PF00136
PFAM:
PF03104
PRIDE:
P21189
PRINTS:
PR00106
PRODB:
PRO_000023566
PROSITE:
PS00116
REFSEQ:
NP_414602
SMART:
SM00486
SMR:
P21189
UNIPROT:
P21189


Operon      
Name: polB         
Operon arrangement:
Transcription unit        Promoter
polB


Transcriptional Regulation      
Display Regulation             
Repressed by: LexA


RNA cis-regulatory element    
Attenuation: Translational


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
  promoter rluAp1 60450 reverse Similarity to the consensus
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]


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.


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