RegulonDB RegulonDB 10.9: Gene Form
   

sodB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ydhP mepH sodB CRP NsrR IHF FnrS terminator anti-terminator TSS_1943 TSS_1943 TSS_1942 (cluster) TSS_1942 (cluster) TSS_1941 TSS_1941 TSS_1940 TSS_1940 TSS_1939 TSS_1939 TSS_1938 (cluster) TSS_1938 (cluster) TSS_1937 TSS_1937 sodBp sodBp

Gene      
Name: sodB    Texpresso search in the literature
Synonym(s): ECK1652, EG10954, b1656
Genome position(nucleotides): 1735378 --> 1735959 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
50.17
External database links:  
ASAP:
ABE-0005537
CGSC:
15256
ECHOBASE:
EB0947
ECOLIHUB:
sodB
OU-MICROARRAY:
b1656
STRING:
511145.b1656
COLOMBOS: sodB


Product      
Name: superoxide dismutase (Fe)
Synonym(s): SodB
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 21.266
Isoelectric point: 5.855
Motif(s):
 
Type Positions Sequence
89 -> 189 PTGKVAEAIAASFGSFADFKAQFTDAAIKNFGSGWTWLVKNSDGKLAIVSTSNAGTPLTTDATPLLTVDVWEHAYYIDYRNARPGYLEHFWALVNWEFVAK
2 -> 82 SFELPALPYAKDALAPHISAETIEYHYGKHHQTYVTNLNNLIKGTAFEGKSLEEIIRSSEGGVFNNAAQVWNHTFYWNCLA

 

Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.6 - protection --> 5.6.2 - detoxification
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
molecular_function GO:0046872 - metal ion binding
GO:0016491 - oxidoreductase activity
GO:0004784 - superoxide dismutase activity
GO:0005506 - iron ion binding
biological_process GO:0006801 - superoxide metabolic process
GO:0019430 - removal of superoxide radicals
GO:0055114 - oxidation-reduction process
GO:0000303 - response to superoxide
Note(s): Note(s): ...[more].
Reference(s): [1] Benov L., et al., 2001
[2] Benov L., et al., 1995
[3] Benov L., et al., 1997
[4] Benov L., et al., 1999
[5] Borders CL., et al., 1989
[6] Bruno-Barcena JM., et al., 2010
[7] Burger RM., et al., 2009
[8] Ge B., et al., 2003
[9] Geslin C., et al., 2001
[10] Han WG., et al., 2002
[11] Imlay JA., et al., 1987
[12] Jackson TA., et al., 2004
[13] Jackson TA., et al., 2003
[14] Knowles RL., et al., 1994
[15] Kunert KJ., et al., 1990
[16] McManus DC., et al., 1995
[17] Nettleton CJ., et al., 1984
[18] Ojima Y., et al., 2008
[19] Perez JM., et al., 2007
[20] Prieto-Alamo MJ., et al., 1993
[21] Renault JP., et al., 2000
[22] Schinina ME., et al., 1987
[23] Sevcenco AM., et al., 2011
[24] Smyk-Randall E., et al., 1993
[25] Soulere L., et al., 2001
[26] Stallings WC., et al., 1991
[27] Steinman HM. 1992
[28] Steinman HM., et al., 1973
[29] Takechi S., et al., 2009
[30] Takeda O., et al., 2007
[31] Tian Y., et al., 2004
[32] Wang X., et al., 2009
[33] Yao XH., et al., 2006
[34] Yikilmaz E., et al., 2002
External database links:  
ECOCYC:
SUPEROX-DISMUTFE-MONOMER
ECOLIWIKI:
b1656
INTERPRO:
IPR036324
INTERPRO:
IPR036314
INTERPRO:
IPR019833
INTERPRO:
IPR019832
INTERPRO:
IPR001189
INTERPRO:
IPR019831
PDB:
1ZA5
PDB:
2BKB
PDB:
1ISC
PDB:
1ISB
PDB:
2NYB
PDB:
1ISA
PFAM:
PF02777
PFAM:
PF00081
PRIDE:
P0AGD3
PRINTS:
PR01703
PRODB:
PRO_000023965
PROSITE:
PS00088
REFSEQ:
NP_416173
SMR:
P0AGD3
SWISSMODEL:
P0AGD3
UNIPROT:
P0AGD3


Operon      
Name: sodB         
Operon arrangement:
Transcription unit        Promoter
sodB


Transcriptional Regulation      
Display Regulation             
Repressed by: CRP, NsrR, IHF


RNA cis-regulatory element    
Attenuation: Transcriptional


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_1937 1735325 forward nd [RS-EPT-CBR] [35]
  promoter TSS_1938 (cluster) 1735338 forward For this promoter, there
Read more >
[RS-EPT-CBR] [35]
  promoter TSS_1939 1735345 forward nd [RS-EPT-CBR] [35]
  promoter TSS_1940 1735349 forward nd [RS-EPT-CBR] [35]
  promoter TSS_1941 1735351 forward nd [RS-EPT-CBR] [35]
  promoter TSS_1942 (cluster) 1735355 forward For this promoter, there
Read more >
[RS-EPT-CBR] [35]
  promoter TSS_1943 1735359 forward nd [RS-EPT-CBR] [35]


Evidence    

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



Reference(s)    

 [1] Benov L., Al-Ibraheem J., 2001, Glycerol metabolism in superoxide dismutase-deficient Escherichia coli., Free Radic Res 35(6):867-72

 [2] Benov L., Fridovich I., 1995, A superoxide dismutase mimic protects sodA sodB Escherichia coli against aerobic heating and stationary-phase death., Arch Biochem Biophys 322(1):291-4

 [3] Benov L., Fridovich I., 1997, Superoxide imposes leakage of sulfite from Escherichia coli., Arch Biochem Biophys 347(2):271-4

 [4] Benov L., Fridovich I., 1999, Why superoxide imposes an aromatic amino acid auxotrophy on Escherichia coli. The transketolase connection., J Biol Chem 274(7):4202-6

 [5] Borders CL., Horton PJ., Beyer WF., 1989, Chemical modification of iron- and manganese-containing superoxide dismutases from Escherichia coli., Arch Biochem Biophys 268(1):74-80

 [6] Bruno-Barcena JM., Azcarate-Peril MA., Hassan HM., 2010, Role of antioxidant enzymes in bacterial resistance to organic acids., Appl Environ Microbiol 76(9):2747-53

 [7] Burger RM., Drlica K., 2009, Superoxide protects Escherichia coli from bleomycin mediated lethality., J Inorg Biochem 103(9):1273-7

 [8] Ge B., Scheller FW., Lisdat F., 2003, Electrochemistry of immobilized CuZnSOD and FeSOD and their interaction with superoxide radicals., Biosens Bioelectron 18(2-3):295-302

 [9] Geslin C., Llanos J., Prieur D., Jeanthon C., 2001, The manganese and iron superoxide dismutases protect Escherichia coli from heavy metal toxicity., Res Microbiol 152(10):901-5

 [10] Han WG., Lovell T., Noodleman L., 2002, Coupled redox potentials in manganese and iron superoxide dismutases from reaction kinetics and density functional/electrostatics calculations., Inorg Chem 41(2):205-18

 [11] Imlay JA., Linn S., 1987, Mutagenesis and stress responses induced in Escherichia coli by hydrogen peroxide., J Bacteriol 169(7):2967-76

 [12] Jackson TA., Brunold TC., 2004, Combined spectroscopic/computational studies on Fe- and Mn-dependent superoxide dismutases: insights into second-sphere tuning of active site properties., Acc Chem Res 37(7):461-70

 [13] Jackson TA., Yikilmaz E., Miller AF., Brunold TC., 2003, Spectroscopic and computational study of a non-heme iron [Fe-NO]7 system: exploring the geometric and electronic structures of the nitrosyl adduct of iron superoxide dismutase., J Am Chem Soc 125(27):8348-63

 [14] Knowles RL., Eisenstark A., 1994, Near-ultraviolet mutagenesis in superoxide dismutase-deficient strains of Escherichia coli., Environ Health Perspect 102(1):88-94

 [15] Kunert KJ., Cresswell CF., Schmidt A., Mullineaux PM., Foyer CH., 1990, Variations in the activity of glutathione reductase and the cellular glutathione content in relation to sensitivity to methylviologen in Escherichia coli., Arch Biochem Biophys 282(2):233-8

 [16] McManus DC., Josephy PD., 1995, Superoxide dismutase protects Escherichia coli against killing by human serum., Arch Biochem Biophys 317(1):57-61

 [17] Nettleton CJ., Bull C., Baldwin TO., Fee JA., 1984, Isolation of the Escherichia coli iron superoxide dismutase gene: evidence that intracellular superoxide concentration does not regulate oxygen-dependent synthesis of the manganese superoxide dismutase., Proc Natl Acad Sci U S A 81(15):4970-3

 [18] Ojima Y., Nishioka M., Taya M., 2008, Metabolic alternations in SOD-deficient Escherichia coli cells when cultivated under oxidative stress from photoexcited titanium dioxide., Biotechnol Lett 30(6):1107-13

 [19] Perez JM., Calderon IL., Arenas FA., Fuentes DE., Pradenas GA., Fuentes EL., Sandoval JM., Castro ME., Elias AO., Vasquez CC., 2007, Bacterial toxicity of potassium tellurite: unveiling an ancient enigma., PLoS One 2(2):e211

 [20] Prieto-Alamo MJ., Abril N., Pueyo C., 1993, Mutagenesis in Escherichia coli K-12 mutants defective in superoxide dismutase or catalase., Carcinogenesis 14(2):237-44

 [21] Renault JP., Verchere-Beaur C., Morgenstern-Badarau I., Yamakura F., Gerloch M., 2000, EPR and ligand field studies of iron superoxide dismutases and iron-substituted manganese superoxide dismutases: relationships between electronic structure of the active site and activity., Inorg Chem 39(12):2666-75

 [22] Schinina ME., Maffey L., Barra D., Bossa F., Puget K., Michelson AM., 1987, The primary structure of iron superoxide dismutase from Escherichia coli., FEBS Lett 221(1):87-90

 [23] Sevcenco AM., Pinkse MW., Wolterbeek HT., Verhaert PD., Hagen WR., Hagedoorn PL., 2011, Exploring the microbial metalloproteome using MIRAGE., Metallomics 3(12):1324-30

 [24] Smyk-Randall E., Brown OR., Wilke A., Eisenstark A., Flint DH., 1993, Near ultraviolet light inactivation of dihydroxyacid dehydratase in Escherichia coli., Free Radic Biol Med 14(6):609-13

 [25] Soulere L., Claparols C., Perie J., Hoffmann P., 2001, Peroxynitrite-induced nitration of tyrosine-34 does not inhibit Escherichia coli iron superoxide dismutase., Biochem J 360(Pt 3):563-7

 [26] Stallings WC., Metzger AL., Pattridge KA., Fee JA., Ludwig ML., 1991, Structure-function relationships in iron and manganese superoxide dismutases., Free Radic Res Commun 12-13 Pt 1:259-68

 [27] Steinman HM., 1992, Construction of an Escherichia coli K-12 strain deleted for manganese and iron superoxide dismutase genes and its use in cloning the iron superoxide dismutase gene of Legionella pneumophila., Mol Gen Genet 232(3):427-30

 [28] Steinman HM., Hill RL., 1973, Sequence homologies among bacterial and mitochondrial superoxide dismutases., Proc Natl Acad Sci U S A 70(12):3725-9

 [29] Takechi S., Nakahara K., Adachi M., Yamaguchi T., 2009, Oxidative stress induced by a dihydropyrazine derivative., Biol Pharm Bull 32(2):186-9

 [30] Takeda O., Takechi S., Ito S., Omori H., Katoh T., Yamaguchi T., 2007, Effects of phenyl derivatives of dihydropyrazines with ability to generate radical species on Escherichia coli., Biol Pharm Bull 30(9):1663-7

 [31] Tian Y., Mao L., Okajima T., Ohsaka T., 2004, Electrochemistry and electrocatalytic activities of superoxide dismutases at gold electrodes modified with a self-assembled monolayer., Anal Chem 76(14):4162-8

 [32] Wang X., Zhao X., 2009, Contribution of oxidative damage to antimicrobial lethality., Antimicrob Agents Chemother 53(4):1395-402

 [33] Yao XH., Min H., Lv ZM., 2006, Response of superoxide dismutase, catalase, and ATPase activity in bacteria exposed to acetamiprid., Biomed Environ Sci 19(4):309-14

 [34] Yikilmaz E., Xie J., Brunold TC., Miller AF., 2002, Hydrogen-bond-mediated tuning of the redox potential of the non-heme Fe site of superoxide dismutase., J Am Chem Soc 124(14):3482-3

 [35] 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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