Escherichia coli K-12 substr. MG1655 Protein: DLP12 prophage; DNA base-flipping protein

Gene: ybcN Accession Numbers: G6303 (EcoCyc), b0547, ECK0538

Regulation Summary Diagram: ?

Regulation summary diagram for ybcN

Subunit composition of DLP12 prophage; DNA base-flipping protein = [YbcN]2
         DLP12 prophage; DNA base-flipping protein = YbcN

YbcN is encoded by the cryptic lambdoid prophage DLP12 and is a distantly related member of the Orf phage protein family. The protein binds to single-stranded DNA [Curtis14] as well as to double-stranded DNA containing base mismatches and bubbles [Chen08, Curtis14]. YbcN interacts with the C terminus of ssDNA-binding protein [Curtis14].

YbcN binds to double-stranded DNA with a G:T mismatch and flips the mismatched base out of the DNA duplex into an extrahelical conformation. It may thus be involved in DNA mismatch repair [Chen08].

ybcN mutants are weak suppressors of the growth defect of a ΔyciM mutant [Mahalakshmi14].

Map Position: [571,689 -> 572,144] (12.32 centisomes, 44°)
Length: 456 bp / 151 aa

Molecular Weight of Polypeptide: 17.433 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0001874 , EchoBASE:EB3395 , EcoGene:EG13630 , EcoliWiki:b0547 , OU-Microarray:b0547 , PortEco:ybcN , Protein Model Portal:Q47269 , RefSeq:NP_415079 , RegulonDB:G6303 , String:511145.b0547 , UniProt:Q47269

Relationship Links: InterPro:IN-FAMILY:IPR008711

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006298 - mismatch repair Inferred from experiment [Chen08]
Molecular Function: GO:0000405 - bubble DNA binding Inferred from experiment [Chen08]
GO:0003697 - single-stranded DNA binding Inferred from experiment [Curtis14]
GO:0005515 - protein binding Inferred from experiment [Curtis14]
Cellular Component: GO:0019038 - provirus

MultiFun Terms: extrachromosomal prophage genes and phage related functions
information transfer DNA related DNA repair

Essentiality data for ybcN knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Created 28-Aug-2014 by Keseler I , SRI International
Last-Curated ? 28-Aug-2014 by Keseler I , SRI International

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Chen08: Chen CS, Korobkova E, Chen H, Zhu J, Jian X, Tao SC, He C, Zhu H (2008). "A proteome chip approach reveals new DNA damage recognition activities in Escherichia coli." Nat Methods 5(1);69-74. PMID: 18084297

Curtis14: Curtis FA, Malay AD, Trotter AJ, Wilson LA, Barradell-Black MM, Bowers LY, Reed P, Hillyar CR, Yeo RP, Sanderson JM, Heddle JG, Sharples GJ (2014). "Phage ORF family recombinases: conservation of activities and involvement of the central channel in DNA binding." PLoS One 9(8);e102454. PMID: 25083707

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Mahalakshmi14: Mahalakshmi S, Sunayana MR, SaiSree L, Reddy M (2014). "yciM is an essential gene required for regulation of lipopolysaccharide synthesis in Escherichia coli." Mol Microbiol 91(1);145-57. PMID: 24266962

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Mon Apr 27, 2015, biocyc13.