RegulonDB RegulonDB 10.8: Gene Form
   

sbcB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

sbcB dacD yeeD TSS_2319 TSS_2319 TSS_2318 TSS_2318 sbcBp sbcBp TSS_2317 TSS_2317

Gene      
Name: sbcB    Texpresso search in the literature
Synonym(s): ECK2005, EG10926, b2011, cpeA, exoI, rmuA, xonA
Genome position(nucleotides): 2082756 --> 2084183 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
50.07
External database links:  
ASAP:
ABE-0006686
CGSC:
178
ECHOBASE:
EB0919
OU-MICROARRAY:
b2011
PortEco:
sbcB
STRING:
511145.b2011
COLOMBOS: sbcB


Product      
Name: exodeoxyribonuclease I
Synonym(s): CpeA, ExoI, RmuA, SbcB, XonA, exonuclease I, 3' --> 5' specific, deoxyribophosphodiesterase
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 54.501
Isoelectric point: 5.474
Motif(s):
 
Type Positions Sequence
225 -> 225 Q
316 -> 316 R
327 -> 327 R
311 -> 311 Q
212 -> 472 RNKHKLMALIDVPQMKPLVHVSGMFGAWRGNTSWVAPLAWHPENRNAVIMVDLAGDISPLLELDSDTLRERLYTAKTDLGDNAAVPVKLVHINKCPVLAQANTLRPEDADRLGINRQHCLDNLKILRENPQVREKVVAIFAEAEPFTPSDNVDAQLYNGFFSDADRAAMKIVLETEPRNLPALDITFVDKRIEKLLFNYRARNFPGTLDYAEQQRWLEHRRQVFTPEFLQGYADELQMLVQQYADDKEKVALLKALWQYAE

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.2 - degradation of macromolecules --> 1.2.2 - DNA
  2 - information transfer --> 2.1 - DNA related --> 2.1.5 - DNA degradation
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003676 - nucleic acid binding
GO:0003677 - DNA binding
GO:0003697 - single-stranded DNA binding
GO:0004518 - nuclease activity
GO:0004527 - exonuclease activity
GO:0004529 - exodeoxyribonuclease activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0000175 - 3'-5'-exoribonuclease activity
GO:0008852 - exodeoxyribonuclease I activity
GO:0000287 - magnesium ion binding
GO:0008310 - single-stranded DNA 3'-5' exodeoxyribonuclease activity
GO:0051575 - 5'-deoxyribose-5-phosphate lyase activity
biological_process GO:0006308 - DNA catabolic process
GO:0006281 - DNA repair
GO:0006974 - cellular response to DNA damage stimulus
GO:0006274 - DNA replication termination
GO:0000738 - DNA catabolic process, exonucleolytic
GO:0090503 - RNA phosphodiester bond hydrolysis, exonucleolytic
Note(s): Note(s): ...[more].
Evidence: [APP] Assay of partially-purified protein
[APPH] Assay of protein purified to homogeneity
[AUP] Assay of unpurified protein
[IGI] Inferred from genetic interaction
[IMP] Inferred from mutant phenotype
Reference(s): [1] Allgood ND., et al., 1991
[2] Gopalakrishna K., et al., 1976
[3] Jayashree P., et al., 1995
[4] Lehman IR., et al., 1964
[5] Phillips GJ., et al., 1988
[6] Prasher D., et al., 1983
[7] Prasher DC., et al., 1983
[8] Sandigursky M., et al., 1992
[9] Wang TC., et al., 1985
[10] Wendel BM., et al., 2014
[11] Yamaguchi H., et al., 2000
External database links:  
DIP:
DIP-10827N
ECOCYC:
EG10926-MONOMER
ECOLIWIKI:
b2011
INTERPRO:
IPR012337
INTERPRO:
IPR034747
INTERPRO:
IPR034748
INTERPRO:
IPR013520
INTERPRO:
IPR013620
INTERPRO:
IPR023607
INTERPRO:
IPR038649
INTERPRO:
IPR036397
MINT:
MINT-1241098
MODBASE:
P04995
PANTHER:
PTHR11046:SF2
PDB:
4JS5
PDB:
4JRQ
PDB:
4JRP
PDB:
4HCC
PDB:
4HCB
PDB:
3HP9
PDB:
3HL8
PDB:
3C95
PDB:
3C94
PDB:
2QXF
PDB:
1FXX
PDB:
4JS4
PFAM:
PF00929
PFAM:
PF08411
PRIDE:
P04995
PRODB:
PRO_000023909
PROSITE:
PS51784
PROSITE:
PS51785
REFSEQ:
NP_416515
SMART:
SM00479
SMR:
P04995
UNIPROT:
P04995


Operon      
Name: sbcB         
Operon arrangement:
Transcription unit        Promoter
sbcB


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_2317 2081705 reverse nd [RS-EPT-CBR] [12]
  promoter TSS_2318 2082732 forward nd [RS-EPT-CBR] [12]
  promoter TSS_2319 2083283 forward nd [RS-EPT-CBR] [12]


Evidence    

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



Reference(s)    

 [1] Allgood ND., Silhavy TJ., 1991, Escherichia coli xonA (sbcB) mutants enhance illegitimate recombination., Genetics 127(4):671-80

 [2] Gopalakrishna K., Bhattacharjee SK., 1976, Role of Rec pathways on sensitivity of Escherichia coli to near-ultraviolet and visible light., J Bacteriol 127(2):1022-3

 [3] Jayashree P., Gowrishankar J., 1995, A new phenotype for sbcB mutations in Escherichia coli: RecA-dependent increase in plasmid-borne gene expression., Mol Gen Genet 246(5):648-56

 [4] Lehman IR., Nussbaum AL., 1964, The deoxyribonucleases of Escherichia coli. V. On the specificity of exonuclease I (phosphodiesterase)., J Biol Chem 239:2628-36

 [5] Phillips GJ., Prasher DC., Kushner SR., 1988, Physical and biochemical characterization of cloned sbcB and xonA mutations from Escherichia coli K-12., J Bacteriol 170(5):2089-94

 [6] Prasher D., Kasunic DA., Kushner SR., 1983, Physical and genetic characterization of the cloned sbcB (exonuclease I) region of the Escherichia coli genome., J Bacteriol 153(2):903-8

 [7] Prasher DC., Conarro L., Kushner SR., 1983, Amplification and purification of exonuclease I from Escherichia coli K12., J Biol Chem 258(10):6340-3

 [8] Sandigursky M., Franklin WA., 1992, DNA deoxyribophosphodiesterase of Escherichia coli is associated with exonuclease I., Nucleic Acids Res 20(18):4699-703

 [9] Wang TC., Smith KC., 1985, Mechanism of sbcB-suppression of the recBC-deficiency in postreplication repair in UV-irradiated Escherichia coli K-12., Mol Gen Genet 201(2):186-91

 [10] Wendel BM., Courcelle CT., Courcelle J., 2014, Completion of DNA replication in Escherichia coli., Proc Natl Acad Sci U S A 111(46):16454-9

 [11] Yamaguchi H., Hanada K., Asami Y., Kato JI., Ikeda H., 2000, Control of genetic stability in Escherichia coli: the SbcB 3'-5' exonuclease suppresses illegitimate recombination promoted by the RecE 5'-3' exonuclease., Genes Cells 5(2):101-9

 [12] 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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