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Escherichia coli K-12 substr. MG1655 Polypeptide: predicted CDP-diglyceride synthase



Gene: ynbB Accession Numbers: G6728 (EcoCyc), b1409, ECK1402

Regulation Summary Diagram: ?

Summary:
YnbB is an inner membrane protein with eight predicted transmembrane domains. The C terminus is located in the periplasm [Daley05].

A ynbB deletion mutant is more sensitive to ampicillin than wild type [Skunca13].

Citations: [ParadisBleau14]

Locations: inner membrane

Map Position: [1,476,250 -> 1,477,146] (31.82 centisomes)
Length: 897 bp / 298 aa

Molecular Weight of Polypeptide: 33.054 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004706 , DIP:DIP-12743N , EchoBASE:EB3512 , EcoGene:EG13749 , EcoliWiki:b1409 , OU-Microarray:b1409 , PortEco:ynbB , Protein Model Portal:P76091 , RefSeq:NP_415927 , RegulonDB:G6728 , String:511145.b1409 , UniProt:P76091

Relationship Links: InterPro:IN-FAMILY:IPR000374 , Pfam:IN-FAMILY:PF01148 , Prosite:IN-FAMILY:PS01315

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009273 - peptidoglycan-based cell wall biogenesis Inferred from experiment [Skunca13]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11, GOA01a]
Molecular Function: GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016772 - transferase activity, transferring phosphorus-containing groups Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Zhang07, Daley05]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11, GOA01a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11]

Gene Class: ORFs Conserved-ORFs

Essentiality data for ynbB 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]

Credits:
Last-Curated ? 14-Jan-2013 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 5 -> 25
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 52 -> 72
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 105 -> 125
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 138 -> 158
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 163 -> 183
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Sequence-Conflict 187
[Aiba96, UniProt10a]
Alternate sequence: W → M; UniProt: (in Ref. 3);
Sequence-Conflict 190
[Aiba96, UniProt10a]
Alternate sequence: S → I; UniProt: (in Ref. 3);
Transmembrane-Region 208 -> 228
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 236 -> 256
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 273 -> 293
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

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


References

Aiba96: Aiba H, Baba T, Hayashi K, Inada T, Isono K, Itoh T, Kasai H, Kashimoto K, Kimura S, Kitakawa M, Kitagawa M, Makino K, Miki T, Mizobuchi K, Mori H, Mori T, Motomura K, Nakade S, Nakamura Y, Nashimoto H, Nishio Y, Oshima T, Saito N, Sampei G, Horiuchi T (1996). "A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map." DNA Res 3(6);363-77. PMID: 9097039

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

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

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

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

ParadisBleau14: Paradis-Bleau C, Kritikos G, Orlova K, Typas A, Bernhardt TG (2014). "A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism." PLoS Genet 10(1);e1004056. PMID: 24391520

Skunca13: Skunca N, Bošnjak M, Kriško A, Panov P, Džeroski S, Smuc T, Supek F (2013). "Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships." PLoS Comput Biol 9(1);e1002852. PMID: 23308060

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 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."

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111

Other References Related to Gene Regulation

Salscheider14: Salscheider SL, Jahn A, Schnetz K (2014). "Transcriptional regulation by BglJ-RcsB, a pleiotropic heteromeric activator in Escherichia coli." Nucleic Acids Res 42(5);2999-3008. PMID: 24335284


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 18.5 on Wed Nov 26, 2014, biocyc14.