Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Polypeptide: YajR MFS transporter



Gene: yajR Accession Numbers: G6241 (EcoCyc), b0427, ECK0421

Regulation Summary Diagram: ?

Summary:
The YajR protein is an uncharacterised member of the major facilitator superfamily (MFS) of transporters [Pao98]. The crystal structure of YajR in an outward facing conformation has been resolved. The 12 transmembrane regions form an N-terminal domain (residues 3-184) and a C terminal domain (215 - 386) connected by a 30 residue helical linker. YajR also contains a small 65 amino acid (residues 389 - 454) cytoplasmic domain which contains a ferredoxin-like fold. The N and C termini are located in the cytoplasm and the structure contains a central cavity which is open to the periplasm and closed to the cytoplasm [Jiang13]. The signature motif A, which is conserved in MFS transporters, is located in the loop connecting TM 2 and 3 [Jiang13].

Locations: inner membrane

Map Position: [444,526 <- 445,890] (9.58 centisomes)
Length: 1365 bp / 454 aa

Molecular Weight of Polypeptide: 48.81 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0001481 , EchoBASE:EB3380 , EcoGene:EG13614 , EcoliWiki:b0427 , ModBase:P77726 , OU-Microarray:b0427 , PortEco:yajR , Pride:P77726 , Protein Model Portal:P77726 , RefSeq:NP_414961 , RegulonDB:G6241 , SMR:P77726 , String:511145.b0427 , UniProt:P77726

Relationship Links: InterPro:IN-FAMILY:IPR011701 , InterPro:IN-FAMILY:IPR016196 , InterPro:IN-FAMILY:IPR020846 , PDB:Structure:3WDO , Pfam:IN-FAMILY:PF07690 , Prosite:IN-FAMILY:PS50850

In Paralogous Gene Group: 17 (37 members)

GO Terms:

Biological Process: GO:0006810 - transport Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Jiang13]
GO:0055085 - transmembrane transport Inferred from experiment Inferred by computational analysis [GOA01, Jiang13]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09, Daley05]
GO:0005887 - integral component of plasma membrane Inferred from experiment [Jiang13]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a, GOA01]

MultiFun Terms: cell processes protection drug resistance/sensitivity
cell structure membrane
transport Electrochemical potential driven transporters Porters (Uni-, Sym- and Antiporters)

Essentiality data for yajR 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]

Credits:
Last-Curated ? 02-Oct-2013 by Mackie A , Macquarie University


Sequence Features

Feature Class Location Common Name Citations Comment
Transmembrane-Region 9 -> 37 TM 1
[Jiang13]
 
Transmembrane-Region 15 -> 35  
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 47 -> 74 TM 2
[Jiang13]
 
Transmembrane-Region 48 -> 68  
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Conserved-Region 69 -> 79 signature motif A
[Jiang13]
 
Transmembrane-Region 78 -> 97 TM 3
[Jiang13]
 
Transmembrane-Region 85 -> 105  
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 101 -> 126 TM 4
[Jiang13]
 
Transmembrane-Region 130 -> 160 TM 5
[Jiang13]
 
Transmembrane-Region 138 -> 158  
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 165 -> 183 TM 6
[Jiang13]
 
Transmembrane-Region 166 -> 186  
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 212 -> 243 TM 7
[Jiang13]
 
Transmembrane-Region 217 -> 237  
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 246 -> 273 TM 8
[Jiang13]
 
Transmembrane-Region 253 -> 273  
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 280 -> 298 TM 9
[Jiang13]
 
Transmembrane-Region 280 -> 300  
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 303 -> 329 TM 10
[Jiang13]
 
Transmembrane-Region 307 -> 327  
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 336 -> 364 TM 11
[Jiang13]
 
Transmembrane-Region 341 -> 361  
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 364 -> 384  
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 367 -> 386 TM 12
[Jiang13]
 
Protein-Segment 389 -> 454 YAM domain
[Jiang13]
cytoplasmic domain containing a ferredoxin-like fold


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

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."

Jiang13: Jiang D, Zhao Y, Wang X, Fan J, Heng J, Liu X, Feng W, Kang X, Huang B, Liu J, Zhang XC (2013). "Structure of the YajR transporter suggests a transport mechanism based on the conserved motif A." Proc Natl Acad Sci U S A 110(36);14664-9. PMID: 23950222

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

Pao98: Pao SS, Paulsen IT, Saier MH (1998). "Major facilitator superfamily." Microbiol Mol Biol Rev 1998;62(1);1-34. PMID: 9529885

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

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 the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

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

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305


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, biocyc14.