RegulonDB RegulonDB 10.8: Gene Form
   

mutM gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

Gene      
Name: mutM    Texpresso search in the literature
Synonym(s): ECK3625, EG10329, b3635, fpg
Genome position(nucleotides): 3810343 <-- 3811152 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.83
External database links:  
ASAP:
ABE-0011877
CGSC:
18133
ECHOBASE:
EB0325
OU-MICROARRAY:
b3635
PortEco:
mutM
STRING:
511145.b3635
COLOMBOS: mutM


Product      
Name: DNA-formamidopyrimidine glycosylase
Synonym(s): 8-oxoguanine DNA glycosylase, Fpg, MutM
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 30.29
Isoelectric point: 8.58
Motif(s):
 
Type Positions Sequence
110 -> 110 R
132 -> 132 E
218 -> 218 K
235 -> 269 QVYGRKGEPCRVCGTPIVATKHAQRATFYCRQCQK
1 -> 114 MPELPEVETSRRGIEPHLVGATILHAVVRNGRLRWPVSEEIYRLSDQPVLSVQRRAKYLLLELPEGWIIIHLGMSGSLRILPEELPPEKHDHVDLVMSNGKVLRYTDPRRFGAW

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.4 - DNA repair
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0140078 - class I DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0034039 - 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity
GO:0003676 - nucleic acid binding
GO:0003677 - DNA binding
GO:0003824 - catalytic activity
GO:0004519 - endonuclease activity
GO:0016787 - hydrolase activity
GO:0016829 - lyase activity
GO:0046872 - metal ion binding
GO:0016798 - hydrolase activity, acting on glycosyl bonds
GO:0003684 - damaged DNA binding
GO:0008270 - zinc ion binding
GO:0019104 - DNA N-glycosylase activity
GO:0003906 - DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0016799 - hydrolase activity, hydrolyzing N-glycosyl compounds
GO:0008534 - oxidized purine nucleobase lesion DNA N-glycosylase activity
GO:0000703 - oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity
biological_process GO:0008152 - metabolic process
GO:0006281 - DNA repair
GO:0006974 - cellular response to DNA damage stimulus
GO:0006284 - base-excision repair
GO:0006285 - base-excision repair, AP site formation
GO:0006289 - nucleotide-excision repair
GO:0090305 - nucleic acid phosphodiester bond hydrolysis
Note(s): Note(s): ...[more].
Reference(s): [1] Boiteux S., et al., 2017
[2] Cronan GE., et al., 2019
[3] Foresta M., et al., 2011
[4] Francis AW., et al., 2003
[5] Graves RJ., et al., 1992
[6] Hamm ML., et al., 2007
[7] Ishchenko AA., et al., 1999
[8] Koval VV., et al., 2004
[9] Kuznetsov NA., et al., 2012
[10] Kuznetsov NA., et al., 2009
[11] Li GM. 2010
[12] McKibbin PL., et al., 2012
[13] Popov AV., et al., 2017
[14] Rogacheva M., et al., 2006
[15] Rogacheva MV., et al., 2005
[16] Sidorenko VS., et al., 2008
[17] Silva-Junior AC., et al., 2012
[18] Song K., et al., 2006
[19] Sowlati-Hashjin S., et al., 2014
[20] Sowlati-Hashjin S., et al., 2018
[21] Zharkov DO., et al., 2003
External database links:  
DIP:
DIP-10286N
ECOCYC:
EG10329-MONOMER
ECOLIWIKI:
b3635
INTERPRO:
IPR012319
INTERPRO:
IPR035937
INTERPRO:
IPR020629
INTERPRO:
IPR015887
INTERPRO:
IPR015886
INTERPRO:
IPR010979
INTERPRO:
IPR010663
INTERPRO:
IPR000214
MODBASE:
P05523
PDB:
1K82
PFAM:
PF01149
PFAM:
PF06827
PFAM:
PF06831
PRIDE:
P05523
PRODB:
PRO_000023325
PROSITE:
PS51066
PROSITE:
PS01242
PROSITE:
PS51068
REFSEQ:
NP_418092
SMART:
SM01232
SMART:
SM00898
SMR:
P05523
UNIPROT:
P05523


Operon      
Name: yicR-rpmBG-mutM         
Operon arrangement:
Transcription unit        Promoter
mutM
rpmBG
rpmBG-mutM
yicR-rpmBG
yicR-rpmBG-mutM
mutM


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_4212 3810040 forward nd [RS-EPT-CBR] [22]
  promoter mutMp2 3811277 reverse The σ factor was determined
Read more >
[AIPP] [23]


Reference(s)    

 [1] Boiteux S., Coste F., Castaing B., 2017, Repair of 8-oxo-7,8-dihydroguanine in prokaryotic and eukaryotic cells: Properties and biological roles of the Fpg and OGG1 DNA N-glycosylases., Free Radic Biol Med 107:179-201

 [2] Cronan GE., Kouzminova EA., Kuzminov A., 2019, Near-continuously synthesized leading strands in Escherichia coli are broken by ribonucleotide excision., Proc Natl Acad Sci U S A 116(4):1251-1260

 [3] Foresta M., Frosina G., Sacca SC., Cartiglia C., Longobardi M., Izzotti A., 2011, Increased resistance to oxidative DNA damage of trabecular meshwork cells by E. coli FPG gene transfection., Free Radic Res 45(7):751-8

 [4] Francis AW., Helquist SA., Kool ET., David SS., 2003, Probing the requirements for recognition and catalysis in Fpg and MutY with nonpolar adenine isosteres., J Am Chem Soc 125(52):16235-42

 [5] Graves RJ., Felzenszwalb I., Laval J., O'Connor TR., 1992, Excision of 5'-terminal deoxyribose phosphate from damaged DNA is catalyzed by the Fpg protein of Escherichia coli., J Biol Chem 267(20):14429-35

 [6] Hamm ML., Gill TJ., Nicolson SC., Summers MR., 2007, Substrate specificity of Fpg (MutM) and hOGG1, two repair glycosylases., J Am Chem Soc 129(25):7724-5

 [7] Ishchenko AA., Koval VV., Fedorova OS., Douglas KT., Nevinsky GA., 1999, Structural requirements of double and single stranded DNA substrates and inhibitors, including a photoaffinity label, of Fpg protein from Escherichia coli., J Biomol Struct Dyn 17(2):301-10

 [8] Koval VV., Kuznetsov NA., Zharkov DO., Ishchenko AA., Douglas KT., Nevinsky GA., Fedorova OS., 2004, Pre-steady-state kinetics shows differences in processing of various DNA lesions by Escherichia coli formamidopyrimidine-DNA glycosylase., Nucleic Acids Res 32(3):926-35

 [9] Kuznetsov NA., Vorobjev YN., Krasnoperov LN., Fedorova OS., 2012, Thermodynamics of the multi-stage DNA lesion recognition and repair by formamidopyrimidine-DNA glycosylase using pyrrolocytosine fluorescence--stopped-flow pre-steady-state kinetics., Nucleic Acids Res 40(15):7384-92

 [10] Kuznetsov NA., Zharkov DO., Koval VV., Buckle M., Fedorova OS., 2009, Reversible chemical step and rate-limiting enzyme regeneration in the reaction catalyzed by formamidopyrimidine-DNA glycosylase., Biochemistry 48(48):11335-43

 [11] Li GM., 2010, Novel molecular insights into the mechanism of GO removal by MutM., Cell Res 20(2):116-8

 [12] McKibbin PL., Kobori A., Taniguchi Y., Kool ET., David SS., 2012, Surprising repair activities of nonpolar analogs of 8-oxoG expose features of recognition and catalysis by base excision repair glycosylases., J Am Chem Soc 134(3):1653-61

 [13] Popov AV., Endutkin AV., Vorobjev YN., Zharkov DO., 2017, Molecular dynamics simulation of the opposite-base preference and interactions in the active site of formamidopyrimidine-DNA glycosylase., BMC Struct Biol 17(1):5

 [14] Rogacheva M., Ishchenko A., Saparbaev M., Kuznetsova S., Ogryzko V., 2006, High resolution characterization of formamidopyrimidine-DNA glycosylase interaction with its substrate by chemical cross-linking and mass spectrometry using substrate analogs., J Biol Chem 281(43):32353-65

 [15] Rogacheva MV., Saparbaev MK., Afanasov IM., Kuznetsova SA., 2005, Two sequential phosphates 3' adjacent to the 8-oxoguanosine are crucial for lesion excision by E. coli Fpg protein and human 8-oxoguanine-DNA glycosylase., Biochimie 87(12):1079-88

 [16] Sidorenko VS., Mechetin GV., Nevinsky GA., Zharkov DO., 2008, Ionic strength and magnesium affect the specificity of Escherichia coli and human 8-oxoguanine-DNA glycosylases., FEBS J 275(15):3747-60

 [17] Silva-Junior AC., Asad LM., Felzenszwalb I., Asad NR., 2012, The role of Fpg protein in UVC-induced DNA lesions., Redox Rep 17(3):95-100

 [18] Song K., Hornak V., de Los Santos C., Grollman AP., Simmerling C., 2006, Computational analysis of the mode of binding of 8-oxoguanine to formamidopyrimidine-DNA glycosylase., Biochemistry 45(36):10886-94

 [19] Sowlati-Hashjin S., Wetmore SD., 2014, Computational investigation of glycosylase and β-lyase activity facilitated by proline: applications to FPG and comparisons to hOgg1., J Phys Chem B 118(50):14566-77

 [20] Sowlati-Hashjin S., Wetmore SD., 2018, Structural Insight into the Discrimination between 8-Oxoguanine Glycosidic Conformers by DNA Repair Enzymes: A Molecular Dynamics Study of Human Oxoguanine Glycosylase 1 and Formamidopyrimidine-DNA Glycosylase., Biochemistry 57(7):1144-1154

 [21] Zharkov DO., Ishchenko AA., Douglas KT., Nevinsky GA., 2003, Recognition of damaged DNA by Escherichia coli Fpg protein: insights from structural and kinetic data., Mutat Res 531(1-2):141-56

 [22] 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.

 [23] Zhao K., Liu M., Burgess RR., 2005, The global transcriptional response of Escherichia coli to induced sigma 32 protein involves sigma 32 regulon activation followed by inactivation and degradation of sigma 32 in vivo., J Biol Chem 280(18):17758-68


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