RegulonDB RegulonDB 10.9: 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
ECOLIHUB:
 holB
OU-MICROARRAY:
 b1099
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 -> 166 EKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAP
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
MODBASE:
 P28631
PDB:
 3GLI
PDB:
 3GLH
PDB:
 3GLG
PDB:
 3GLF
PDB:
 1XXI
PDB:
 1XXH
PDB:
 1JR3
PDB:
 1A5T
PFAM:
 PF09115
PFAM:
 PF13177
PRIDE:
 P28631
PRODB:
 PRO_000022917
REFSEQ:
 NP_415617
SMR:
 P28631
UNIPROT:
 P28631


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


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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