Transporter Protein
YgcS


    Transport Function
Transporter Name: YgcS
Transporter Type: Secondary Transporter
Transporter Family: MFS (TC#: 2.A.1)
The Major Facilitator Superfamily (MFS)
Transporter Subfamily: 
Substrate/Function: AraE family
TC#: 2.A.1.1.X
^ Return to the top ^

    Genome Locus
PID:   16130678     Blast
Source:   Escherichia coli K12-MG1655
Chromosome:   -
Location:   2894555..2895964
Gene:   b2771
Length:  469
Strand:  -
Code:   G (Carbohydrate transport and metabolism)
COG:   COG0477
Product:  putative benzoate transport protein (MFS family)
^ Return to the top ^

    Transmembrane Segment
TMSs: 
TMHMM Server 
Total:     12
TMS 1:  47-69
TMS 2:  79-101
TMS 3:  110-129
TMS 4:  134-156
TMS 5:  168-187
TMS 6:  197-219
TMS 7:  275-297
TMS 8:  307-329
TMS 9:  336-355
TMS 10:  360-382
TMS 11:  394-416
TMS 12:  421-443
Topology:   >YgcS
MTGRCLFGFSGEKPFLLPDNEGVKMNTSPVRMDDLPLNRFHCRIAALTFGAHLTDGYVLGVIGYAIIQLT
PAMQLTPFMAGMIGGSALLGLFLGSLVLGWISDHIGRQKIFTFSFLLITLASFLQFFATTPEHLIGLRIL
IGIGLGGDYSVGHTLLAEFSPRRHRGILLGAFSVVWTVGYVLASIAGHHFISENPEAWRWLLASAALPAL
LITLLRWGTPESPRWLLRQGRFAEAHAIVHRYFGPHVLLGDEVVTATHKHIKTLFSSRYWRRTAFNSVFF
VCLVIPWFVIYTWLPTIAQTIGLEDALTASLMLNALLIVGALLGLVLTHLLAHRKFLLGSFLLLAATLVV
MACLPSGSSLTLLLFVLFSTTISAVSNLVGILPAESFPTDIRSLGVGFATAMSRLGAAVSTGLLPWVLAQ
WGMQVTLLLLATVLLVGFVVTWLWAPETKALPLVAAGNVGGANEHSVSV
^ Return to the top ^

    Sequence
Protein Sequence: >YgcS 16130678 putative benzoate transport protein (MFS family) [Escherichia coli K12-MG1655]
MTGRCLFGFSGEKPFLLPDNEGVKMNTSPVRMDDLPLNRFHCRIAALTFGAHLTDGYVLGVIGYAIIQLT
PAMQLTPFMAGMIGGSALLGLFLGSLVLGWISDHIGRQKIFTFSFLLITLASFLQFFATTPEHLIGLRIL
IGIGLGGDYSVGHTLLAEFSPRRHRGILLGAFSVVWTVGYVLASIAGHHFISENPEAWRWLLASAALPAL
LITLLRWGTPESPRWLLRQGRFAEAHAIVHRYFGPHVLLGDEVVTATHKHIKTLFSSRYWRRTAFNSVFF
VCLVIPWFVIYTWLPTIAQTIGLEDALTASLMLNALLIVGALLGLVLTHLLAHRKFLLGSFLLLAATLVV
MACLPSGSSLTLLLFVLFSTTISAVSNLVGILPAESFPTDIRSLGVGFATAMSRLGAAVSTGLLPWVLAQ
WGMQVTLLLLATVLLVGFVVTWLWAPETKALPLVAAGNVGGANEHSVSV
DNA Sequence: >YgcS 16130678 putative benzoate transport protein (MFS family) [Escherichia coli K12-MG1655]
ATGACGGGGCGTTGCCTTTTCGGCTTCTCAGGCGAGAAGCCGTTCTTATTACCGGACAATGAAGGGGTAA
AGATGAACACTTCACCGGTGCGAATGGATGATTTACCGCTTAACCGTTTTCACTGCCGCATTGCTGCGCT
CACTTTCGGCGCACACCTGACCGACGGTTATGTTCTCGGCGTCATTGGTTACGCCATTATTCAGCTTACG
CCCGCCATGCAACTGACGCCGTTTATGGCGGGAATGATCGGCGGCTCGGCGCTCCTTGGTTTGTTCCTTG
GCAGCCTGGTTCTTGGGTGGATCTCCGACCATATTGGTCGGCAAAAAATCTTCACCTTCAGCTTTTTGCT
GATTACGCTTGCTTCGTTTTTACAATTTTTTGCCACCACGCCAGAGCATCTTATTGGACTGCGCATTTTG
ATTGGCATTGGTCTGGGAGGCGATTATTCAGTAGGTCACACCTTGCTGGCTGAATTTTCCCCGCGCCGCC
ATCGCGGTATTTTGCTGGGCGCATTCAGCGTGGTGTGGACCGTAGGCTATGTGCTGGCAAGTATTGCCGG
ACATCACTTTATTTCCGAAAACCCGGAGGCCTGGCGCTGGCTACTGGCATCGGCAGCTCTGCCCGCGTTG
TTGATTACGTTATTACGCTGGGGAACGCCAGAATCACCACGCTGGCTACTGCGCCAGGGGCGTTTTGCAG
AAGCTCACGCTATCGTGCATCGCTATTTTGGTCCCCATGTTTTACTGGGCGATGAAGTGGTAACGGCGAC
CCATAAACACATCAAAACCTTGTTCTCTTCGCGTTACTGGCGGCGCACGGCGTTTAACAGCGTCTTCTTT
GTCTGCCTCGTAATCCCATGGTTTGTGATTTATACCTGGCTGCCAACTATCGCCCAGACTATTGGTCTGG
AAGATGCGCTGACTGCCAGCCTGATGCTTAATGCGTTGTTAATTGTGGGCGCGCTGCTGGGATTAGTTCT
GACGCACCTGCTGGCACATCGCAAATTTTTGCTGGGAAGTTTTTTGCTGCTGGCGGCAACGCTGGTAGTC
ATGGCCTGTTTGCCTTCCGGCAGTTCATTAACGCTGCTGCTTTTTGTTCTCTTCAGCACCACCATTTCGG
CAGTCAGTAATCTGGTGGGCATTTTGCCTGCGGAAAGTTTTCCTACTGACATTCGCTCGCTGGGCGTCGG
TTTTGCCACTGCCATGAGTCGACTTGGCGCGGCGGTAAGTACTGGCCTGCTGCCGTGGGTGCTGGCGCAG
TGGGGAATGCAAGTCACCTTATTGCTCCTGGCGACAGTGTTGTTGGTTGGTTTTGTTGTGACCTGGCTAT
GGGCACCAGAAACTAAAGCCCTCCCGCTGGTGGCGGCGGGAAATGTAGGAGGTGCGAATGAACATTCTGT
TAGCGTTTAA
^ Return to the top ^

    Publications
Publications on this gene:
1.  Curr Drug Targets 2006 Jul ; 7(7):793-811.
Microbial drug efflux proteins of the major facilitator superfamily.

Saidijam M ,Benedetti G ,Ren Q ,Xu Z ,Hoyle CJ ,Palmer SL ,Ward A ,Bettaney KE ,Szakonyi G ,Meuller J ,Morrison S ,Pos MK ,Butaye P ,Walravens K ,Langton K ,Herbert RB ,Skurray RA ,Paulsen IT ,O'reilly J ,Rutherford NG ,Brown MH ,Bill RM ,Henderson PJ ,

Astbury Centre for Structural Molecular Biology, School of Biochemistry and Microbiology, University of Leeds, Leeds LS2 9JT, UK.

Drug efflux proteins are widespread amongst microorganisms, including pathogens. They can contribute to both natural insensitivity to antibiotics and to emerging antibiotic resistance and so are potential targets for the development of new antibacterial drugs. The design of such drugs would be greatly facilitated by knowledge of the structures of these transport proteins, which are poorly understood, because of the difficulties of obtaining crystals of quality. We describe a structural genomics approach for the amplified expression, purification and characterisation of prokaryotic drug efflux proteins of the 'Major Facilitator Superfamily' (MFS) of transport proteins from Helicobacter pylori, Staphylococcus aureus, Escherichia coli, Enterococcus faecalis, Bacillus subtilis, Brucella melitensis, Campylobacter jejuni, Neisseria meningitides and Streptomyces coelicolor. The H. pylori putative drug resistance protein, HP1092, and the S. aureus QacA proteins are used as detailed examples. This strategy is an important step towards reproducible production of transport proteins for the screening of drug binding and for optimisation of crystallisation conditions to enable subsequent structure determination.

Publication Type: Research Support, Non-U.S. Gov't; Review;

2.  Nucleic Acids Res 2006 ; 1(34):1-9.
Escherichia coli K-12: a cooperatively developed annotation snapshot--2005.

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 3rd,Rudd KE ,Serres MH ,Thomas GH ,Thomson NR ,Wishart D ,Wanner BL ,

Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA. mriley@mbl.edu

The goal of this group project has been to coordinate and bring up-to-date information on all genes of Escherichia coli K-12. Annotation of the genome of an organism entails identification of genes, the boundaries of genes in terms of precise start and end sites, and description of the gene products. Known and predicted functions were assigned to each gene product on the basis of experimental evidence or sequence analysis. Since both kinds of evidence are constantly expanding, no annotation is complete at any moment in time. This is a snapshot analysis based on the most recent genome sequences of two E.coli K-12 bacteria. An accurate and up-to-date description of E.coli K-12 genes is of particular importance to the scientific community because experimentally determined properties of its gene products provide fundamental information for annotation of innumerable genes of other organisms. Availability of the complete genome sequence of two K-12 strains allows comparison of their genotypes and mutant status of alleles.

Publication Type: Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.;

3.  Nucleic Acids Res 2006 Jan 1; Database issue(34):D181-6.
TCDB: the Transporter Classification Database for membrane transport protein analyses and information.

Saier MH Jr,Tran CV ,Barabote RD ,

Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA. msaier@ucsd.edu

The Transporter Classification Database (TCDB) is a web accessible, curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from a variety of living organisms. TCDB is a curated repository for factual information compiled from >10,000 references, encompassing approximately 3000 representative transporters and putative transporters, classified into >400 families. The transporter classification (TC) system is an International Union of Biochemistry and Molecular Biology approved system of nomenclature for transport protein classification. TCDB is freely accessible at http://www.tcdb.org. The web interface provides several different methods for accessing the data, including step-by-step access to hierarchical classification, direct search by sequence or TC number and full-text searching. The functional ontology that underlies the database structure facilitates powerful query searches that yield valuable data in a quick and easy way. The TCDB website also offers several tools specifically designed for analyzing the unique characteristics of transport proteins. TCDB not only provides curated information and a tool for classifying newly identified membrane proteins, but also serves as a genome transporter-annotation tool.

Publication Type: Research Support, N.I.H., Extramural;

4.  J Mol Biol 2005 Sep 23; 3(352):489-94.
Experimentally constrained topology models for 51,208 bacterial inner membrane proteins.

Granseth E ,Daley DO ,Rapp M ,Melén K ,von Heijne G ,

Stockholm Bioinformatics Center, AlbaNova, SE-106 91 Stockholm, Sweden.

We have used 502 Escherichia coli inner membrane proteins with experimentally determined C-terminal locations (cytoplasmic or periplasmic) from a recently published data set, together with an additional 106 bacterial membrane proteins with known topology, as queries in BLAST searches against a data base of 658,210 bacterial open reading frames from GenBank. We find 51,208 homologs to the query sequences for which we can assign the location of the C terminus or an internal residue to the same side of the membrane as the query's C terminus. These assignments are then used as constraints for topology prediction. The 51,208 much improved topology models derived in this way cover approximately 30% of all predicted bacterial inner membrane proteins in 225 fully sequenced bacterial genomes.

Publication Type: Research Support, Non-U.S. Gov't;

5.  Science 2005 May 27; 5726(308):1321-3.
Global topology analysis of the Escherichia coli inner membrane proteome.

Daley DO ,Rapp M ,Granseth E ,Melén K ,Drew D ,von Heijne G ,

Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.

The protein complement of cellular membranes is notoriously resistant to standard proteomic analysis and structural studies. As a result, membrane proteomes remain ill-defined. Here, we report a global topology analysis of the Escherichia coli inner membrane proteome. Using C-terminal tagging with the alkaline phosphatase and green fluorescent protein, we established the periplasmic or cytoplasmic locations of the C termini for 601 inner membrane proteins. By constraining a topology prediction algorithm with this data, we derived high-quality topology models for the 601 proteins, providing a firm foundation for future functional studies of this and other membrane proteomes. We also estimated the overexpression potential for 397 green fluorescent protein fusions; the results suggest that a large fraction of all inner membrane proteins can be produced in sufficient quantities for biochemical and structural work.

Publication Type: Research Support, Non-U.S. Gov't;

6.  J Mol Microbiol Biotechnol 1999 Nov ; 2(1):257-79.
The major facilitator superfamily.

Saier MH Jr,Beatty JT ,Goffeau A ,Harley KT ,Heijne WH ,Huang SC ,Jack DL ,Jähn PS ,Lew K ,Liu J ,Pao SS ,Paulsen IT ,Tseng TT ,Virk PS ,

Department of Biology, University of California at San Diego, La Jolla 92093-0116, USA. saier@ucsd.edu

In 1998 we updated earlier descriptions of the largest family of secondary transport carriers found in living organisms, the major facilitator superfamily (MFS). Seventeen families of transport proteins were shown to comprise this superfamily. We here report expansion of the MFS to include 29 established families as well as five probable families. Structural, functional, and mechanistic features of the constituent permeases are described, and each newly identified family is shown to exhibit specificity for a single class of substrates. Phylogenetic analyses define the evolutionary relationships of the members of each family to each other, and multiple alignments allow definition of family-specific signature sequences as well as all well-conserved sequence motifs. The work described serves to update previous publications and allows extrapolation of structural, functional and mechanistic information obtained with any one member of the superfamily to other members with limitations determined by the degrees of sequence divergence.

Publication Type: Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, P.H.S.; Review;

7.  Microbiol Mol Biol Rev 1998 Mar ; 1(62):1-34.
Major facilitator superfamily.

Pao SS ,Paulsen IT ,Saier MH Jr,

Department of Biology, University of California at San Diego, La Jolla 92093-0116, USA.

The major facilitator superfamily (MFS) is one of the two largest families of membrane transporters found on Earth. It is present ubiquitously in bacteria, archaea, and eukarya and includes members that can function by solute uniport, solute/cation symport, solute/cation antiport and/or solute/solute antiport with inwardly and/or outwardly directed polarity. All homologous MFS protein sequences in the public databases as of January 1997 were identified on the basis of sequence similarity and shown to be homologous. Phylogenetic analyses revealed the occurrence of 17 distinct families within the MFS, each of which generally transports a single class of compounds. Compounds transported by MFS permeases include simple sugars, oligosaccharides, inositols, drugs, amino acids, nucleosides, organophosphate esters, Krebs cycle metabolites, and a large variety of organic and inorganic anions and cations. Protein members of some MFS families are found exclusively in bacteria or in eukaryotes, but others are found in bacteria, archaea, and eukaryotes. All permeases of the MFS possess either 12 or 14 putative or established transmembrane alpha-helical spanners, and evidence is presented substantiating the proposal that an internal tandem gene duplication event gave rise to a primordial MFS protein prior to divergence of the family members. All 17 families are shown to exhibit the common feature of a well-conserved motif present between transmembrane spanners 2 and 3. The analyses reported serve to characterize one of the largest and most diverse families of transport proteins found in living organisms.

Publication Type: Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, P.H.S.; Review;

9.  Trends Biochem Sci 1993 Jan ; 1(18):13-20.
A major superfamily of transmembrane facilitators that catalyse uniport, symport and antiport.

Marger MD ,Saier MH Jr,

Department of Biology, University of California, San Diego, La Jolla 92093-0116.

Many transport proteins of bacteria and eukaryotes are thought to possess a common structural motif of 12 transmembrane-spanning alpha-helical segments. In this report we use statistical methods to establish that five families or clusters of these facilitators comprise a single superfamily. The five clusters include: (1) drug-resistance proteins, (2) sugar facilitators, (3) facilitators for Krebs cycle intermediates, (4) phosphate ester-phosphate antiporters and (5) a distinct group of oligosaccharide-H+ symporters. Over 50 transporters of bacteria, lower eukaryotes, plants and animals, and one putative bacterial transcriptional regulatory protein are members of this superfamily, which we term the 'major facilitator superfamily' (MFS).

Publication Type: Research Support, U.S. Gov't, P.H.S.; Review;
Comment In: Trends Biochem Sci. 1993 Jul;18(7):248-9


^ Return to the top ^

    External Links

Ecocyc    TIGR CMRTHE SEEDThe SEED  
^ Return to the top ^

    NBCI Gene Page
^ Return to the top ^