RegulonDB RegulonDB 11.1: Gene Form
   

dnaN gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

gyrB dnaA dnaN recF Fis Fis dnaNp1 dnaNp1 dnaNp dnaNp TSS_4269 TSS_4269 dnaNp6 dnaNp6 dnaNp2 dnaNp2 dnaNp3 dnaNp3 TSS_4268 TSS_4268 TSS_4267 TSS_4267 dnaNp5 dnaNp5 dnaNp4 dnaNp4 recFp2 recFp2 recFp1 recFp1 TSS_4265 (cluster) TSS_4265 (cluster) gyrBp2 gyrBp2 gyrBp gyrBp TSS_4264 TSS_4264 TSS_4263 TSS_4263 TSS_4262 TSS_4262 TSS_4261 TSS_4261 TSS_4260 (cluster) TSS_4260 (cluster) TSS_4259 TSS_4259

Gene      
Name: dnaN    Texpresso search in the literature
Synonym(s): ECK3693, EG10242, b3701
Genome position(nucleotides): 3881221 <-- 3882321
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.22
External database links:  
ASAP:
 ABE-0012098
CGSC:
 842
ECHOBASE:
 EB0238
ECOLIHUB:
 dnaN
OU-MICROARRAY:
 b3701
STRING:
 511145.b3701
COLOMBOS: dnaN


Product      
Name: β sliding clamp
Synonym(s): DNA polymerase III subunit beta;, DnaN
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 40.587
Isoelectric point: 5.041
Motif(s):
 
Type Positions Sequence Comment
1 -> 120 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLD UniProt: 1; Sequence Annotation Type: region of interest.
24 -> 24 R UniProt: Mild defect in DNA replication, impaired loading of clamp on DNA, polymerase speed is wild-type. More severe replication defect and very poor clamp loading; when associated with A-149..
66 -> 66 G UniProt: In dnaN159; a temperature- and UV-sensitive mutation, displays altered DNA polymerase usage, chronically induced SOS response; when associated with A-174..
129 -> 243 TLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPD UniProt: 2; Sequence Annotation Type: region of interest.
133 -> 133 A UniProt: Reduction of synthesis of beta*, probably due to mutation of its promoter..

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.1 - DNA replication
Gene Ontology Terms (GO)  
cellular_component GO:1990085 - Hda-beta clamp complex
GO:1990078 - replication inhibiting complex
GO:0044775 - DNA polymerase III, beta sliding clamp processivity factor complex
GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0009360 - DNA polymerase III complex
GO:0030894 - replisome
molecular_function GO:0003677 - DNA binding
GO:0003887 - DNA-directed DNA polymerase activity
GO:0016779 - nucleotidyltransferase activity
GO:0005515 - protein binding
GO:0008408 - 3'-5' exonuclease activity
GO:0016740 - transferase activity
GO:0042802 - identical protein binding
GO:0042803 - protein homodimerization activity
biological_process GO:0042276 - error-prone translesion synthesis
GO:0006260 - DNA replication
GO:0006261 - DNA-templated DNA replication
GO:0006974 - cellular response to DNA damage stimulus
GO:0030174 - regulation of DNA-templated DNA replication initiation
GO:0032297 - negative regulation of DNA-templated DNA replication initiation
GO:0090305 - nucleic acid phosphodiester bond hydrolysis
GO:0006271 - DNA strand elongation involved in DNA replication
GO:0044787 - bacterial-type DNA replication
Reference(s): [1] Burgers PM., et al., 1981
[2] Quinones A., et al., 1988
External database links:  
ALPHAFOLD:
 P0A988
DIP:
 DIP-36038N
ECOCYC:
 EG10242-MONOMER
ECOLIWIKI:
 b3701
INTERPRO:
 IPR022637
INTERPRO:
 IPR001001
INTERPRO:
 IPR022634
INTERPRO:
 IPR022635
MINT:
 P0A988
MODBASE:
 P0A988
PANTHER:
 PTHR30478
PDB:
 3F1V
PDB:
 3PWE
PDB:
 3Q4J
PDB:
 3Q4K
PDB:
 3Q4L
PDB:
 3QSB
PDB:
 4K3K
PDB:
 4K3L
PDB:
 4K3M
PDB:
 4K3O
PDB:
 4K3P
PDB:
 4K3Q
PDB:
 4K3R
PDB:
 4K3S
PDB:
 4MJP
PDB:
 4MJQ
PDB:
 4MJR
PDB:
 4N94
PDB:
 4N95
PDB:
 4N96
PDB:
 4N97
PDB:
 4N98
PDB:
 4N99
PDB:
 4N9A
PDB:
 5FKU
PDB:
 5FKV
PDB:
 5FKW
PDB:
 5M1S
PDB:
 6E8E
PDB:
 6FVL
PDB:
 3D1G
PDB:
 3D1F
PDB:
 3D1E
PDB:
 3BEP
PDB:
 2XUR
PDB:
 2POL
PDB:
 1WAI
PDB:
 1UNN
PDB:
 1OK7
PDB:
 1MMI
PDB:
 1JQJ
PDB:
 1JQL
PFAM:
 PF00712
PFAM:
 PF02767
PFAM:
 PF02768
PRIDE:
 P0A988
PRODB:
 PRO_000022466
REFSEQ:
 NP_418156
SMART:
 SM00480
SMR:
 P0A988
UNIPROT:
 P0A988


Operon      
Name: dnaAN-recF         
Operon arrangement:
Transcription unit        Promoter
recF
recF
dnaN-recF
dnaN-recF
dnaN-recF
dnaN-recF
dnaN-recF
dnaN-recF
dnaN-recF
dnaAN-recF
dnaAN-recF


Transcriptional Regulation      
Display Regulation             
Activated by: ArgP, DnaA
Repressed by: DnaA, Fis


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 TSS_4259 3878251 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_4260 (cluster) 3878769 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_4261 3878772 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_4262 3879127 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_4263 3879564 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_4264 3880140 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_4265 (cluster) 3880152 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_4267 3882351 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_4268 3882359 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_4269 3882731 reverse nd [RS-EPT-CBR] [3]


Evidence    

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


Reference(s)    

 [1] Burgers PM., Kornberg A., Sakakibara Y., 1981, The dnaN gene codes for the beta subunit of DNA polymerase III holoenzyme of escherichia coli., Proc Natl Acad Sci U S A 78(9):5391-5

 [2] Quinones A., Messer W., 1988, Discoordinate gene expression in the dnaA-dnaN operon of Escherichia coli., Mol Gen Genet 213(1):118-24

 [3] 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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