RegulonDB RegulonDB 11.2: Gene Form
   

sbcD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

sbcC sbcD araJ phoB PhoB CRP AraC AraC CRP anti-anti-terminator anti-terminator terminator phoBp phoBp sbcDp sbcDp sbcCp2 sbcCp2 araJp araJp

Gene      
Name: sbcD    Texpresso search in the literature
Synonym(s): ECK0392, EG11094, b0398, yajA
Genome position(nucleotides): 415750 <-- 416952
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.28
External database links:  
ASAP:
 ABE-0001383
CGSC:
 30972
ECHOBASE:
 EB1086
ECOLIHUB:
 sbcD
OU-MICROARRAY:
 b0398
STRING:
 511145.b0398
COLOMBOS: sbcD


Product      
Name: ATP-dependent structure-specific DNA nuclease - SbcD subunit
Synonym(s): SbcD, YajA, orf-45
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 44.714
Isoelectric point: 5.779
Motif(s):
 
Type Positions Sequence Comment
1 -> 225 MRILHTSDWHLGQNFYSKSREAEHQAFLDWLLETAQTHQVDAIIVAGDVFDTGSPPSYARTLYNRFVVNLQQTGCHLVVLAGNHDSVATLNESRDIMAFLNTTVVASAGHAPQILPRRDGTPGAVLCPIPFLRPRDIITSQAGLNGIEKQQHLLAAITDYYQQHYADACKLRGDQPLPIIATGHLTTVGASKSDAVRDIYIGTLDAFPAQNFPPADYIALGHIHR
8 -> 10 DWH phosphoesterase signature sequence
47 -> 51 GDVFD phosphoesterase signature sequence
68 -> 68 V V → D: disrupts homodimeric interface; disrupts endonuclease activity, but not exonuclease activity, on duplex DNA in vitro
82 -> 85 GNHD phosphoesterase signature sequence

 
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
GO:1990391 - DNA repair complex
molecular_function GO:0003677 - DNA binding
GO:0004518 - nuclease activity
GO:0004519 - endonuclease activity
GO:0004527 - exonuclease activity
GO:0004529 - exodeoxyribonuclease activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0008408 - 3'-5' exonuclease activity
GO:1990238 - double-stranded DNA endodeoxyribonuclease activity
GO:0000014 - single-stranded DNA endodeoxyribonuclease activity
biological_process GO:0006259 - DNA metabolic process
GO:0006260 - DNA replication
GO:0006281 - DNA repair
GO:0006310 - DNA recombination
GO:0006274 - DNA replication termination
GO:0090305 - nucleic acid phosphodiester bond hydrolysis
Note(s): Note(s): ...[more].
Reference(s): [1] Kurilovich E., et al., 2019
External database links:  
ALPHAFOLD:
 P0AG76
DIP:
 DIP-10828N
ECOCYC:
 EG11094-MONOMER
ECOLIWIKI:
 b0398
INTERPRO:
 IPR004593
INTERPRO:
 IPR029052
INTERPRO:
 IPR041796
INTERPRO:
 IPR026843
INTERPRO:
 IPR004843
MODBASE:
 P0AG76
PDB:
 6S6V
PDB:
 6S85
PFAM:
 PF12320
PFAM:
 PF00149
PRIDE:
 P0AG76
PRODB:
 PRO_000023911
REFSEQ:
 NP_414932
SMR:
 P0AG76
UNIPROT:
 P0AG76


Operon      
Name: sbcDC         
Operon arrangement:
Transcription unit        Promoter
sbcDC


Transcriptional Regulation      
Display Regulation             
Repressed by: PhoB


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 sbcCp2 415847 reverse nd [COMP-AINF] [2]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Kurilovich E., Shiriaeva A., Metlitskaya A., Morozova N., Ivancic-Bace I., Severinov K., Savitskaya E., 2019, Genome Maintenance Proteins Modulate Autoimmunity Mediated Primed Adaptation by the Escherichia coli Type I-E CRISPR-Cas System., Genes (Basel) 10(11)

 [2] 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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