RegulonDB

Gene
Name:	mdfA
Synonym(s):	ECK0832, G6440, b0842, cmlA, cmr
Genome position(nucleotides):	883673 --> 884905
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	52.39
External database links:

ASAP:	ABE-0002871
ECHOBASE:	EB3460
ECOLIHUB:	cmr
OU-MICROARRAY:	b0842
STRING:	511145.b0842
COLOMBOS:	mdfA

Gene

Name:

mdfA

Synonym(s):

ECK0832, G6440, b0842, cmlA, cmr

Genome position(nucleotides):

883673 --> 884905

Strand:

forward

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

52.39

External database links:

ASAP:

ECHOBASE:

ECOLIHUB:

OU-MICROARRAY:

STRING:

COLOMBOS:

Type

Positions

Sequence

Comment

15 -> 32

ALLFPLCLVLYEFSTYIG

UniProt: Helical.

26 -> 39

EFSTYIGNDMIQPG

conserved in MdfA orthologs

27 -> 361

FSTYIGNDMIQPGMLAVVEQYQAGIDWVPTSMTAYLAGGMFLQWLLGPLSDRIGRRPVMLAGVVWFIVTCLAILLAQNIEQFTLLRFLQGISLCFIGAVGYAAIQESFEEAVCIKITALMANVALIAPLLGPLVGAAWIHVLPWEGMFVLFAALAAISFFGLQRAMPETATRIGEKLSLKELGRDYKLVLKNGRFVAGALALGFVSLPLLAWIAQSPIIIITGEQLSSYEYGLLQVPIFGALIAGNLLLARLTSRRTVRSLIIMGGWPIMIGLLVAAAATVISSHAYLWMTAGLSIYAFGIGLANAGLVRLTLFASDMSKGTVSAAMGMLQMLIF

54 -> 72

VPTSMTAYLAGGMFLQWLL

UniProt: Helical.

59 -> 59

UniProt: In Ref. 2; CAA69997..

Type

Positions

Sequence

Comment

15 -> 32

ALLFPLCLVLYEFSTYIG

UniProt: Helical.

26 -> 39

EFSTYIGNDMIQPG

conserved in MdfA orthologs

27 -> 361

54 -> 72

VPTSMTAYLAGGMFLQWLL

UniProt: Helical.

59 -> 59

UniProt: In Ref. 2; CAA69997..

73 -> 83

GPLSDRIGRRP

identified in MFS antiporters and symporters

83 -> 103

PVMLAGVVWFIVTCLAILLAQ

UniProt: Helical.

108 -> 116

FTLLRFLQG

identified in MFS antiporters and symporters

110 -> 130

LLRFLQGISLCFIGAVGYAAI

UniProt: Helical.

127 -> 127

Y → F: significant reduction in chloramphenicol transport

145 -> 165

LMANVALIAPLLGPLVGAAWI

UniProt: Helical.

146 -> 146

M → A: significant reduction in chloramphenicol transport

154 -> 162

PLLGPLVGA

antiporter-specific motif

167 -> 187

VLPWEGMFVLFAALAAISFFG

UniProt: Helical.

170 -> 170

W → A: significant reduction in chloramphenicol transport

225 -> 240

ALALGFVSLPLLAWIA

UniProt: In Ref. 1; AAC44147..

227 -> 247

ALGFVSLPLLAWIAQSPIIII

UniProt: Helical.

256 -> 276

EYGLLQVPIFGALIAGNLLLA

UniProt: Helical.

288 -> 308

IIMGGWPIMIGLLVAAAATVI

UniProt: Helical.

315 -> 335

WMTAGLSIYAFGIGLANAGLV

UniProt: Helical.

347 -> 367

GTVSAAMGMLQMLIFTVGIEI

UniProt: Helical.

379 -> 399

LFNLFNLVNGILWLSLMVIFL

UniProt: Helical.

Multifun Terms (GenProtEC)

4 - transport --> 4.2 - Electrochemical potential driven transporters --> 4.2.A - Porters (Uni-, Sym- and Antiporters)

5 - cell processes --> 5.6 - protection --> 5.6.4 - drug resistance/sensitivity

6 - cell structure --> 6.1 - membrane

Gene Ontology Terms (GO)

cellular_component

GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane

molecular_function

GO:0022857 - transmembrane transporter activity
GO:0015299 - solute:proton antiporter activity
GO:0015385 - sodium:proton antiporter activity
GO:0015386 - potassium:proton antiporter activity

biological_process

GO:1990961 - xenobiotic detoxification by transmembrane export across the plasma membrane
GO:0046677 - response to antibiotic
GO:0030641 - regulation of cellular pH
GO:0055085 - transmembrane transport
GO:0035725 - sodium ion transmembrane transport
GO:0071805 - potassium ion transmembrane transport
GO:0098656 - anion transmembrane transport

	Type	Name	Post Left	Post Right	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
	promoter	TSS_990	883505		reverse	nd	[RS-EPT-CBR]	[12]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

TSS_990

883505

reverse

[RS-EPT-CBR]

[12]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Evidence

[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] Alon Cudkowicz N., Schuldiner S., 2019, Deletion of the major Escherichia coli multidrug transporter AcrB reveals transporter plasticity and redundancy in bacterial cells., PLoS One 14(6):e0218828
[2] Edgar R., Bibi E., 1999, A single membrane-embedded negative charge is critical for recognizing positively charged drugs by the Escherichia coli multidrug resistance protein MdfA., EMBO J 18(4):822-32
[3] Heng J., Liu M., Liu Y., Fan J., Wang X., Zhao Y., Zhang XC., 2015, Substrate-bound structure of the E. coli multidrug resistance transporter MdfA., Cell Res 25(9):1060-73
[4] Jaenecke F., Nakada-Nakura Y., Nagarathinam K., Ogasawara S., Liu K., Hotta Y., Iwata S., Nomura N., Tanabe M., 2018, Generation of Conformation-Specific Antibody Fragments for Crystallization of the Multidrug Resistance Transporter MdfA., Methods Mol Biol 1700:97-109
[5] Lee A., Mao W., Warren MS., Mistry A., Hoshino K., Okumura R., Ishida H., Lomovskaya O., 2000, Interplay between efflux pumps may provide either additive or multiplicative effects on drug resistance., J Bacteriol 182(11):3142-50
[6] Nagarathinam K., Jaenecke F., Nakada-Nakura Y., Hotta Y., Liu K., Iwata S., Stubbs MT., Nomura N., Tanabe M., 2017, The multidrug-resistance transporter MdfA from Escherichia coli: crystallization and X-ray diffraction analysis., Acta Crystallogr F Struct Biol Commun 73(Pt 7):423-430
[7] Schuldiner S., 2018, The Escherichia coli effluxome., Res Microbiol 169(7-8):357-362
[8] Shuster Y., Steiner-Mordoch S., Alon Cudkowicz N., Schuldiner S., 2016, A Transporter Interactome Is Essential for the Acquisition of Antimicrobial Resistance to Antibiotics., PLoS One 11(4):e0152917
[9] Sigal N., Lewinson O., Wolf SG., Bibi E., 2007, E. coli multidrug transporter MdfA is a monomer., Biochemistry 46(17):5200-8
[10] Wu HH., Symersky J., Lu M., 2019, Structure of an engineered multidrug transporter MdfA reveals the molecular basis for substrate recognition., Commun Biol 2:210
[11] Zomot E., Yardeni EH., Vargiu AV., Tam HK., Malloci G., Ramaswamy VK., Perach M., Ruggerone P., Pos KM., Bibi E., 2018, A New Critical Conformational Determinant of Multidrug Efflux by an MFS Transporter., J Mol Biol 430(9):1368-1385
[12] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

Reference(s)

[1] Alon Cudkowicz N., Schuldiner S., 2019, Deletion of the major Escherichia coli multidrug transporter AcrB reveals transporter plasticity and redundancy in bacterial cells., PLoS One 14(6):e0218828

[2] Edgar R., Bibi E., 1999, A single membrane-embedded negative charge is critical for recognizing positively charged drugs by the Escherichia coli multidrug resistance protein MdfA., EMBO J 18(4):822-32

[3] Heng J., Liu M., Liu Y., Fan J., Wang X., Zhao Y., Zhang XC., 2015, Substrate-bound structure of the E. coli multidrug resistance transporter MdfA., Cell Res 25(9):1060-73

[4] Jaenecke F., Nakada-Nakura Y., Nagarathinam K., Ogasawara S., Liu K., Hotta Y., Iwata S., Nomura N., Tanabe M., 2018, Generation of Conformation-Specific Antibody Fragments for Crystallization of the Multidrug Resistance Transporter MdfA., Methods Mol Biol 1700:97-109

[5] Lee A., Mao W., Warren MS., Mistry A., Hoshino K., Okumura R., Ishida H., Lomovskaya O., 2000, Interplay between efflux pumps may provide either additive or multiplicative effects on drug resistance., J Bacteriol 182(11):3142-50

[6] Nagarathinam K., Jaenecke F., Nakada-Nakura Y., Hotta Y., Liu K., Iwata S., Stubbs MT., Nomura N., Tanabe M., 2017, The multidrug-resistance transporter MdfA from Escherichia coli: crystallization and X-ray diffraction analysis., Acta Crystallogr F Struct Biol Commun 73(Pt 7):423-430

[7] Schuldiner S., 2018, The Escherichia coli effluxome., Res Microbiol 169(7-8):357-362

[8] Shuster Y., Steiner-Mordoch S., Alon Cudkowicz N., Schuldiner S., 2016, A Transporter Interactome Is Essential for the Acquisition of Antimicrobial Resistance to Antibiotics., PLoS One 11(4):e0152917

[9] Sigal N., Lewinson O., Wolf SG., Bibi E., 2007, E. coli multidrug transporter MdfA is a monomer., Biochemistry 46(17):5200-8

[10] Wu HH., Symersky J., Lu M., 2019, Structure of an engineered multidrug transporter MdfA reveals the molecular basis for substrate recognition., Commun Biol 2:210

[11] Zomot E., Yardeni EH., Vargiu AV., Tam HK., Malloci G., Ramaswamy VK., Perach M., Ruggerone P., Pos KM., Bibi E., 2018, A New Critical Conformational Determinant of Multidrug Efflux by an MFS Transporter., J Mol Biol 430(9):1368-1385

[12] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.