RegulonDB RegulonDB 10.10: Gene Form
   

alkA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

dgcE yegD alkA Ada anti-anti-terminator anti-terminator terminator yegDp2 yegDp2 alkAp alkAp

Gene      
Name: alkA    Texpresso search in the literature
Synonym(s): ECK2062, EG11222, aidA, b2068
Genome position(nucleotides): 2146692 <-- 2147540 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 55.59
External database links:  
ASAP:
 ABE-0006848
CGSC:
 1035
ECHOBASE:
 EB1204
ECOLIHUB:
 alkA
OU-MICROARRAY:
 b2068
STRING:
 511145.b2068
COLOMBOS: alkA


Product      
Name: DNA-3-methyladenine glycosylase 2
Synonym(s): 3-methyl-adenine DNA glycosylase II, inducible, AidA, AlkA
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 31.393
Isoelectric point: 8.287
Motif(s):
 
Type Positions Sequence
3 -> 112 TLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVD
238 -> 238 D
118 -> 239 VRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDY
237 -> 237 D
124 -> 124 Q

 
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
GO:0032993 - protein-DNA complex
molecular_function GO:0003824 - catalytic activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0003905 - alkylbase DNA N-glycosylase activity
GO:0008725 - DNA-3-methyladenine glycosylase activity
GO:0043916 - DNA-7-methylguanine glycosylase activity
GO:0052821 - DNA-7-methyladenine glycosylase activity
GO:0052822 - DNA-3-methylguanine glycosylase activity
GO:0032131 - alkylated DNA binding
biological_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:0006307 - DNA dealkylation involved in DNA repair
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
Reference(s): [1] Cronan GE., et al., 2019
[2] Lindahl T. 1982
[3] Taylor EL., et al., 2015
External database links:  
DIP:
 DIP-9084N
ECOCYC:
 EG11222-MONOMER
ECOLIWIKI:
 b2068
INTERPRO:
 IPR000035
INTERPRO:
 IPR037046
INTERPRO:
 IPR003265
INTERPRO:
 IPR010316
INTERPRO:
 IPR011257
INTERPRO:
 IPR023170
MODBASE:
 P04395
PDB:
 3OGD
PDB:
 3OH6
PDB:
 3D4V
PDB:
 3CWU
PDB:
 3CWT
PDB:
 3CWS
PDB:
 3OH9
PDB:
 1DIZ
PDB:
 1MPG
PDB:
 1PVS
PDB:
 3CVS
PDB:
 3CVT
PDB:
 3CW7
PDB:
 3CWA
PFAM:
 PF06029
PFAM:
 PF00730
PRIDE:
 P04395
PRODB:
 PRO_000022077
PROSITE:
 PS00516
REFSEQ:
 NP_416572
SMART:
 SM00478
SMART:
 SM01009
SMR:
 P04395
UNIPROT:
 P04395


Operon      
Name: alkA         
Operon arrangement:
Transcription unit        Promoter
alkA
alkA


Transcriptional Regulation      
Display Regulation             
Activated by: Ada


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 yegDp2 2147644 forward nd [ICWHO] [4]


Evidence    

 [ICWHO] 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] Lindahl T., 1982, DNA repair enzymes., Annu Rev Biochem 51:61-87

 [3] Taylor EL., O'Brien PJ., 2015, Kinetic mechanism for the flipping and excision of 1,N(6)-ethenoadenine by AlkA., Biochemistry 54(3):898-908

 [4] 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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