RegulonDB RegulonDB 11.2: Gene Form
   

mutY gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

mutY trmB yggX TSS_3294 TSS_3294 yggXp yggXp mutYp1 mutYp1 mutYp2 mutYp2 TSS_3292 TSS_3292 TSS_3291 TSS_3291 TSS_3290 TSS_3290 yggLp3 yggLp3 yggLp2 yggLp2 TSS_3288 TSS_3288 TSS_3287 (cluster) TSS_3287 (cluster) TSS_3286 (cluster) TSS_3286 (cluster) TSS_3285 (cluster) TSS_3285 (cluster) TSS_3284 TSS_3284

Gene      
Name: mutY    Texpresso search in the literature
Synonym(s): ECK2956, EG10627, b2961, micA
Genome position(nucleotides): 3103013 --> 3104065
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 55.18
External database links:  
ASAP:
 ABE-0009720
CGSC:
 18130
ECHOBASE:
 EB0622
ECOLIHUB:
 mutY
MIM:
 604933
MIM:
 608456
MIM:
 613659
OU-MICROARRAY:
 b2961
STRING:
 511145.b2961
COLOMBOS: mutY


Product      
Name: adenine DNA glycosylase
Synonym(s): MicA, MutY
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space,cytosol
Molecular weight: 39.149
Isoelectric point: 8.463
Motif(s):
 
Type Positions Sequence Comment
36 -> 168 SEVMLQQTQVATVIPYFERFMARFPTVTDLANAPLDEVLHLWTGLGYYARARNLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGAILSLSLGKHFPILDGNVKRVLARCYAVSGWPGKKEVENKLWSLS
37 -> 37 E E → S: loss of function mutation (in cMutY1-225)
45 -> 45 V V → N: loss of function mutation (in cMutY1-225)
82 -> 82 Y Y → C: reduced adenine glycosylase activity (see also |CITS: [16245934]|)
100 -> 127 HGGKFPETFEEVAALPGVGRSTAGAILS

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.4 - DNA repair
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0030288 - outer membrane-bounded periplasmic space
molecular_function GO:0000701 - purine-specific mismatch base pair DNA N-glycosylase activity
GO:0032357 - oxidized purine DNA binding
GO:0035485 - adenine/guanine mispair binding
GO:0034039 - 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity
GO:0003677 - DNA binding
GO:0003824 - catalytic activity
GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0016798 - hydrolase activity, acting on glycosyl bonds
GO:0051536 - iron-sulfur cluster binding
GO:0051539 - 4 iron, 4 sulfur cluster binding
GO:0019104 - 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:0006298 - mismatch repair
Note(s): Note(s): ...[more].
Reference(s): [1] Cronan GE., et al., 2019
[2] Francis AW., et al., 2003
[3] Gogos A., et al., 1996
[4] Li X., et al., 2000
[5] Lu AL., et al., 1996
[6] Majumdar C., et al., 2020
[7] Manlove AH., et al., 2017
[8] Manuel RC., et al., 1996
[9] Noll DM., et al., 1999
[10] Pope MA., et al., 2002
[11] Porello SL., et al., 1998
[12] Williams SD., et al., 1999
[13] Zharkov DO., et al., 2000
External database links:  
ALPHAFOLD:
 P17802
DIP:
 DIP-10289N
ECOCYC:
 EG10627-MONOMER
ECOLIWIKI:
 b2961
INTERPRO:
 IPR004036
INTERPRO:
 IPR044298
INTERPRO:
 IPR029119
INTERPRO:
 IPR023170
INTERPRO:
 IPR015797
INTERPRO:
 IPR011257
INTERPRO:
 IPR005760
INTERPRO:
 IPR004035
INTERPRO:
 IPR003651
INTERPRO:
 IPR003265
INTERPRO:
 IPR000445
MODBASE:
 P17802
PANTHER:
 PTHR42944
PDB:
 1KQJ
PDB:
 1KG3
PDB:
 1KG4
PDB:
 1KG7
PDB:
 1WEI
PDB:
 1KG6
PDB:
 1WEG
PDB:
 1WEF
PDB:
 1MUY
PDB:
 1MUD
PDB:
 1MUN
PDB:
 1KG2
PDB:
 1KG5
PFAM:
 PF00633
PFAM:
 PF14815
PFAM:
 PF10576
PFAM:
 PF00730
PRIDE:
 P17802
PRODB:
 PRO_000023328
PROSITE:
 PS01155
PROSITE:
 PS00764
REFSEQ:
 NP_417436
SMART:
 SM00525
SMART:
 SM00478
SMR:
 P17802
UNIPROT:
 P17802


Operon      
Name: mutY-yggX-mltC-nupG         
Operon arrangement:
Transcription unit        Promoter
mutY-yggX
mutY-yggX-mltC
mutY-yggX-mltC-nupG
mutY-yggX
mutY-yggX-mltC
mutY-yggX-mltC-nupG
yggX
yggX-mltC
yggX-mltC-nupG
nupG


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_3284 3102157 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_3285 (cluster) 3102193 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_3286 (cluster) 3102200 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_3287 (cluster) 3102236 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_3288 3102247 reverse nd [RS-EPT-CBR] [14]
  promoter yggLp2 3102250 reverse nd [COMP-AINF], [RS-EPT-CBR] [14], [15]
  promoter yggLp3 3102254 reverse nd [COMP-AINF] [15]
  promoter TSS_3290 3102279 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_3291 3102291 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_3292 3102390 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_3294 3104042 forward nd [RS-EPT-CBR] [14]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] 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

 [2] Francis AW., David SS., 2003, Escherichia coli MutY and Fpg utilize a processive mechanism for target location., Biochemistry 42(3):801-10

 [3] Gogos A., Cillo J., Clarke ND., Lu AL., 1996, Specific recognition of A/G and A/7,8-dihydro-8-oxoguanine (8-oxoG) mismatches by Escherichia coli MutY: removal of the C-terminal domain preferentially affects A/8-oxoG recognition., Biochemistry 35(51):16665-71

 [4] Li X., Wright PM., Lu AL., 2000, The C-terminal domain of MutY glycosylase determines the 7,8-dihydro-8-oxo-guanine specificity and is crucial for mutation avoidance., J Biol Chem 275(12):8448-55

 [5] Lu AL., Yuen DS., Cillo J., 1996, Catalytic mechanism and DNA substrate recognition of Escherichia coli MutY protein., J Biol Chem 271(39):24138-43

 [6] Majumdar C., McKibbin PL., Krajewski AE., Manlove AH., Lee JK., David SS., 2020, Unique Hydrogen Bonding of Adenine with the Oxidatively Damaged Base 8-Oxoguanine Enables Specific Recognition and Repair by DNA Glycosylase MutY., J Am Chem Soc 142(48):20340-20350

 [7] Manlove AH., McKibbin PL., Doyle EL., Majumdar C., Hamm ML., David SS., 2017, Structure-Activity Relationships Reveal Key Features of 8-Oxoguanine: A Mismatch Detection by the MutY Glycosylase., ACS Chem Biol 12(9):2335-2344

 [8] Manuel RC., Czerwinski EW., Lloyd RS., 1996, Identification of the structural and functional domains of MutY, an Escherichia coli DNA mismatch repair enzyme., J Biol Chem 271(27):16218-26

 [9] Noll DM., Gogos A., Granek JA., Clarke ND., 1999, The C-terminal domain of the adenine-DNA glycosylase MutY confers specificity for 8-oxoguanine.adenine mispairs and may have evolved from MutT, an 8-oxo-dGTPase., Biochemistry 38(20):6374-9

 [10] Pope MA., Porello SL., David SS., 2002, Escherichia coli apurinic-apyrimidinic endonucleases enhance the turnover of the adenine glycosylase MutY with G:A substrates., J Biol Chem 277(25):22605-15

 [11] Porello SL., Leyes AE., David SS., 1998, Single-turnover and pre-steady-state kinetics of the reaction of the adenine glycosylase MutY with mismatch-containing DNA substrates., Biochemistry 37(42):14756-64

 [12] Williams SD., David SS., 1999, Formation of a Schiff base intermediate is not required for the adenine glycosylase activity of Escherichia coli MutY., Biochemistry 38(47):15417-24

 [13] Zharkov DO., Gilboa R., Yagil I., Kycia JH., Gerchman SE., Shoham G., Grollman AP., 2000, Role for lysine 142 in the excision of adenine from A:G mispairs by MutY DNA glycosylase of Escherichia coli., Biochemistry 39(48):14768-78

 [14] 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.

 [15] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

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