Escherichia coli K-12 substr. MG1655 Polypeptide: DLP12 prophage; periplasmic protein

Gene: ybcL Accession Numbers: G6301 (EcoCyc), b0545, ECK0536

Regulation Summary Diagram: ?

Regulation summary diagram for ybcL

YbcL from uropathogenic E. coli (strain UTI89) suppresses acute neutrophil migration which is associated with pathogenicity [Lau12]. There are 6 amino acid differences between YbcL from E. coli K-12 MG1655 and strain UTI89 - one of which (V78T) is non-conservative. Episomal expression of YbcL UTI89(T78V) in an E. coli UTI189 ybcL deleted strain results in loss of function (ie. lack of suppression of neutrophils in a transepithelial migration assay) whereas expression of YbcLMG1655(V78T) in the same background results in a gain-of-function phenotype [Lau12]. Expression of YbcLUTI89 or YbcLMG1655(V78T) in E. coli K-12 MG1655 results in suppression of neutrophil migration levels similar to those seen in E. coli UTI89 [Lau12].

YbcL from uropathogenic E. coli UTI89 is secreted from the bacterial periplasm during infection [Lau12].

YbcL has sequence and structural similarity to rat and human RKIP (Raf kinase inhibitor protein), which modulates signal transduction pathways [Serre01].

A crystal structure of the protein has been solved at 1.8 Å resolution [Serre01].

YbcL is periplasmic [Serre01].

Locations: periplasmic space

Map Position: [570,116 -> 570,667] (12.29 centisomes, 44°)
Length: 552 bp / 183 aa

Molecular Weight of Polypeptide: 19.476 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0001869 , EchoBASE:EB3393 , EcoGene:EG13628 , EcoliWiki:b0545 , ModBase:P77368 , OU-Microarray:b0545 , PortEco:ybcL , Pride:P77368 , Protein Model Portal:P77368 , RefSeq:NP_415077 , RegulonDB:G6301 , SMR:P77368 , String:511145.b0545 , UniProt:P77368

Relationship Links: InterPro:IN-FAMILY:IPR005247 , InterPro:IN-FAMILY:IPR008914 , PDB:Structure:1FUX , Pfam:IN-FAMILY:PF01161

GO Terms:

Biological Process: GO:0043086 - negative regulation of catalytic activity Inferred by computational analysis [Serre01]
Molecular Function: GO:0004857 - enzyme inhibitor activity Inferred by computational analysis [Serre01]
Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space Inferred from experiment Inferred by computational analysis [DiazMejia09, Serre01]
GO:0042597 - periplasmic space Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]

MultiFun Terms: extrachromosomal prophage genes and phage related functions
regulation type of regulation posttranscriptional inhibition / activation of enzymes

Essentiality data for ybcL knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Curated 18-Jan-2007 by Keseler I , SRI International
Last-Curated ? 14-Oct-2012 by Mackie A , Macquarie University

Sequence Features

Protein sequence of DLP12 prophage; periplasmic protein with features indicated

Feature Class Location Citations Comment
Signal-Sequence 1 -> 21
Chain 22 -> 183
UniProt: UPF0098 protein ybcL;
Disulfide-Bond-Site 46, 129

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

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

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

Lau12: Lau ME, Loughman JA, Hunstad DA (2012). "YbcL of uropathogenic Escherichia coli suppresses transepithelial neutrophil migration." Infect Immun 80(12);4123-32. PMID: 22966043

Serre01: Serre L, Pereira de Jesus K, Zelwer C, Bureaud N, Schoentgen F, Benedetti H (2001). "Crystal structures of YBHB and YBCL from Escherichia coli, two bacterial homologues to a Raf kinase inhibitor protein." J Mol Biol 2001;310(3);617-34. PMID: 11439028

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

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 Tue Oct 6, 2015, biocyc13.