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Escherichia coli K-12 substr. MG1655 Polypeptide: inner membrane protein YrbG



Gene: yrbG Accession Numbers: EG12802 (EcoCyc), b3196, ECK3185

Regulation Summary Diagram: ?

Summary:
YrbG is an uncharacterized member of the CaCA family of metal cation exchangers [Saier99, Saaf01]. Sequence similarity suggests it may function as a sodium ion/calcium ion exchanger. However direct measurement of cytosolic calcium levels using the Ca2+ activated photoprotein aequorin suggests that it does not play a role in regulating cytosolic Ca2+ [Naseem08].

The membrane topology of YrbG has been studied experimentally, providing support for the predicted topology with 5+5 transmembrane segments [Saaf01]; the C terminus is located in the periplasm [Daley05].

yrbG is not essential for growth [Sperandeo06].

Gene Citations: [Martorana11]

Locations: inner membrane

Map Position: [3,338,297 -> 3,339,274] (71.95 centisomes)
Length: 978 bp / 325 aa

Molecular Weight of Polypeptide: 34.741 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010502 , EchoBASE:EB2654 , EcoGene:EG12802 , EcoliWiki:b3196 , OU-Microarray:b3196 , PortEco:yrbG , Pride:P45394 , Protein Model Portal:P45394 , RefSeq:NP_417663 , RegulonDB:EG12802 , SMR:P45394 , String:511145.b3196 , UniProt:P45394

Relationship Links: InterPro:IN-FAMILY:IPR004481 , InterPro:IN-FAMILY:IPR004837 , Panther:IN-FAMILY:PTHR10846 , Pfam:IN-FAMILY:PF01699

GO Terms:

Biological Process: GO:0055085 - transmembrane transport Inferred by computational analysis [GOA01, Saaf01]
Molecular Function: GO:0022857 - transmembrane transporter activity Inferred by computational analysis [Saaf01]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Daley05]
GO:0005887 - integral component of plasma membrane Inferred from experiment [Hsieh10]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11, GOA01]

MultiFun Terms: cell structure membrane
transport Electrochemical potential driven transporters Porters (Uni-, Sym- and Antiporters)

Essentiality data for yrbG 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]
Yes [Feist07, Comment 4]

Credits:
Last-Curated ? 28-Dec-2006 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 6 -> 26
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 38 -> 58
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 68 -> 88
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 105 -> 125
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 127 -> 147
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 170 -> 190
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 199 -> 219
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 244 -> 264
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 270 -> 290
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 303 -> 323
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3196 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12802; confirmed by SwissProt match.


References

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

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Hsieh10: Hsieh JM, Besserer GM, Madej MG, Bui HQ, Kwon S, Abramson J (2010). "Bridging the gap: a GFP-based strategy for overexpression and purification of membrane proteins with intra and extracellular C-termini." Protein Sci 19(4);868-80. PMID: 20196076

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

Martorana11: Martorana AM, Sperandeo P, Polissi A, Deho G (2011). "Complex transcriptional organization regulates an Escherichia coli locus implicated in lipopolysaccharide biogenesis." Res Microbiol 162(5);470-82. PMID: 21402154

Naseem08: Naseem R, Holland IB, Jacq A, Wann KT, Campbell AK (2008). "pH and monovalent cations regulate cytosolic free Ca(2+) in E. coli." Biochim Biophys Acta 1778(6);1415-22. PMID: 18342619

Saaf01: Saaf A, Baars L, von Heijne G (2001). "The internal repeats in the Na+/Ca2+ exchanger-related Escherichia coli protein YrbG have opposite membrane topologies." J Biol Chem 276(22);18905-7. PMID: 11259419

Saier99: Saier MH, Eng BH, Fard S, Garg J, Haggerty DA, Hutchinson WJ, Jack DL, Lai EC, Liu HJ, Nusinew DP, Omar AM, Pao SS, Paulsen IT, Quan JA, Sliwinski M, Tseng TT, Wachi S, Young GB (1999). "Phylogenetic characterization of novel transport protein families revealed by genome analyses." Biochim Biophys Acta 1999;1422(1);1-56. PMID: 10082980

Sperandeo06: Sperandeo P, Pozzi C, Deho G, Polissi A (2006). "Non-essential KDO biosynthesis and new essential cell envelope biogenesis genes in the Escherichia coli yrbG-yhbG locus." Res Microbiol 157(6);547-58. PMID: 16765569

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 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 18.5 on Fri Dec 19, 2014, biocyc11.