RegulonDB RegulonDB 10.8: Gene Form
   

holB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

mltG holB ycfH tmk TSS_1420 TSS_1420 TSS_1419 TSS_1419 TSS_1418 TSS_1418

Gene      
Name: holB    Texpresso search in the literature
Synonym(s): ECK1085, EG11500, b1099
Genome position(nucleotides): 1155762 --> 1156766 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
54.03
External database links:  
ASAP:
ABE-0003716
CGSC:
31447
ECHOBASE:
EB1463
OU-MICROARRAY:
b1099
PortEco:
holB
STRING:
511145.b1099
COLOMBOS: holB


Product      
Name: DNA polymerase III subunit δ'
Synonym(s): DNA polymerase III, delta; prime subunit, HolB
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 36.937
Isoelectric point: 7.059
Motif(s):
 
Type Positions Sequence
12 -> 164 EKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYL
166 -> 166 P
208 -> 320 DNWQARETLCQALAYSVPSGDWYSLLAALNHEQAPARLHWLATLLMDALKRHHGAAQVTNVDVPGLVAELANHLSPSRLQAILGDVCHIREQLMSVTGINRELLITDLLLRIE

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.1 - DNA replication
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0009360 - DNA polymerase III complex
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
biological_process GO:0006260 - DNA replication
GO:0006261 - DNA-dependent DNA replication
GO:0090305 - nucleic acid phosphodiester bond hydrolysis
GO:0071897 - DNA biosynthetic process
Note(s): Note(s): ...[more].
Reference(s): [1] Carter JR., et al., 1993
[2] Chaperon DN. 2006
[3] Dong Z., et al., 1993
External database links:  
DIP:
DIP-9932N
ECOCYC:
EG11500-MONOMER
ECOLIWIKI:
b1099
INTERPRO:
IPR027417
INTERPRO:
IPR015199
INTERPRO:
IPR008921
INTERPRO:
IPR004622
MINT:
MINT-1239429
MODBASE:
P28631
PDB:
3GLG
PDB:
3GLH
PDB:
3GLI
PDB:
1XXI
PDB:
3GLF
PDB:
1XXH
PDB:
1JR3
PDB:
1A5T
PFAM:
PF09115
PRIDE:
P28631
PRODB:
PRO_000022917
REFSEQ:
NP_415617
SMR:
P28631
UNIPROT:
P28631


Operon      
Name: pabC-mltG-tmk-holB-ycfH         
Operon arrangement:
Transcription unit        Promoter
 


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_1418 1155058 forward nd [RS-EPT-CBR] [4]
  promoter TSS_1419 1156471 forward nd [RS-EPT-CBR] [4]
  promoter TSS_1420 1156478 forward nd [RS-EPT-CBR] [4]


Evidence    

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



Reference(s)    

 [1] Carter JR., Franden MA., Aebersold R., McHenry CS., 1993, Identification, isolation, and characterization of the structural gene encoding the delta' subunit of Escherichia coli DNA polymerase III holoenzyme., J Bacteriol 175(12):3812-22

 [2] Chaperon DN., 2006, A method for the construction of in frame substitutions in operons: deletion of the essential Escherichia coli holB gene coding for a subunit of the DNA polymerase III holoenzyme., J Microbiol Methods 65(1):127-34

 [3] Dong Z., Onrust R., Skangalis M., O'Donnell M., 1993, DNA polymerase III accessory proteins. I. holA and holB encoding delta and delta'., J Biol Chem 268(16):11758-65

 [4] 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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