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Escherichia coli K-12 substr. MG1655 Protein: ModE transcriptional dual regulator



Gene: modE Accession Numbers: G6395 (EcoCyc), b0761, ECK0750

Synonyms: chlD, modR, ModE-MoO42-, Molybdate-responsive transcription factor

Regulation Summary Diagram: ?

Component of: ModE-MoO42- DNA-binding transcriptional dual regulator (extended summary available)

Subunit composition of ModE transcriptional dual regulator = [ModE]2

Locations: inner membrane, cytosol

Map Position: [793,079 <- 793,867] (17.09 centisomes)
Length: 789 bp / 262 aa

Molecular Weight of Polypeptide: 28.281 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0002585 , EchoBASE:EB3017 , EcoGene:EG13227 , EcoliWiki:b0761 , ModBase:P0A9G8 , OU-Microarray:b0761 , PortEco:modE , PR:PRO_000023270 , Pride:P0A9G8 , Protein Model Portal:P0A9G8 , RefSeq:NP_415282 , RegulonDB:G6395 , SMR:P0A9G8 , String:511145.b0761 , UniProt:P0A9G8

Relationship Links: InterPro:IN-FAMILY:IPR000847 , InterPro:IN-FAMILY:IPR003725 , InterPro:IN-FAMILY:IPR004606 , InterPro:IN-FAMILY:IPR005116 , InterPro:IN-FAMILY:IPR008995 , InterPro:IN-FAMILY:IPR011991 , InterPro:IN-FAMILY:IPR016462 , PDB:Structure:1B9M , PDB:Structure:1B9N , PDB:Structure:1H9R , PDB:Structure:1H9S , PDB:Structure:1O7L , Pfam:IN-FAMILY:PF00126 , Pfam:IN-FAMILY:PF03459

In Reactions of unknown directionality:

Not in pathways:
ModE + molybdate = ModE-MoO42-

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0006777 - Mo-molybdopterin cofactor biosynthetic process
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0015689 - molybdate ion transport Inferred by computational analysis [GOA01]
GO:0055085 - transmembrane transport Inferred by computational analysis [GOA01]
Molecular Function: GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01]
GO:0005524 - ATP binding Inferred by computational analysis [GOA01]
GO:0015098 - molybdate ion transmembrane transporter activity Inferred by computational analysis [GOA01]
GO:0016820 - hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances Inferred by computational analysis [GOA01]
GO:0030151 - molybdenum ion binding Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]
GO:0043190 - ATP-binding cassette (ABC) transporter complex Inferred by computational analysis [GOA01]

MultiFun Terms: information transfer RNA related Transcription related
metabolism biosynthesis of building blocks cofactors, small molecule carriers molybdenum
regulation genetic unit regulated operon
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level repressor

Essentiality data for modE 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]

Subunit of: ModE-MoO42- DNA-binding transcriptional dual regulator

Synonyms: ModE

Subunit composition of ModE-MoO42- DNA-binding transcriptional dual regulator = [(ModE)2][molybdate]
         ModE transcriptional dual regulator = (ModE)2

Summary:
The transcription factor ModE, for "Molybdenum," is the principal regulator that controls the transcription of operons involved in the transport of molybdenum and synthesis of molybdoenzymes and molybdate-related functions, among others [Walkenhorst95, McNicholas96, Grunden96, Anderson97, Grunden99, Self99, Hasona98, Anderson00, McNicholas02, Tao05]. The regulatory effect of ModE is induced when E. coli is grown under anaerobic growth conditions and when the physiological inducer, molybdenum, binds to ModE and promotes the dimerization of the ModE-Mo complex [Grunden99, Self99, Anderson97, Kuper03]. The ModE dimer binds two molecules of molybdenum with a Kd of 0.8 mM. Tungsten can act as a substitute for Mo in ModE binding to the modABCD promoter in vitro, but the complex may be biologically inactive [Anderson00].

The binding targets for ModE consist of inverted repeat sequences that possess conserved motifs; each monomer binds to one of these conserved sequences [Studholme03, Grunden99, Anderson97, Self99].

A crystal structure of ModE has been solved at 2.1Å resolution [Hall99].

The monomer of this transcription factor contains two domains: the N-terminal domain is responsible for binding DNA and the dimerization and also contains a winged helix-turn-helix motif [Hall99]. The C-terminal domain is indispensable for molybdate binding and possibly is involved in the DNA binding [Gourley01, McNicholas96, Hall99, Schuttelkopf03]. Tentatively, this transcription factor is classified as a member of the LysR family [Anderson97].

A microarray analysis for ModE of E. coli was done by [Tao05].

Citations: [McNicholas98, McNicholas98a, McNicholas97, Stewart03]

Sequence Length: 262 AAs

In Reactions of unknown directionality:

Not in pathways:
ModE + molybdate = ModE-MoO42-

GO Terms:

Biological Process: GO:2000143 - negative regulation of DNA-templated transcription, initiation Inferred from experiment [Grunden96]
Molecular Function: GO:0000986 - bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding Inferred from experiment [Grunden96]
GO:0030151 - molybdenum ion binding Inferred from experiment [Grunden99]

MultiFun Terms: information transfer RNA related Transcription related
metabolism biosynthesis of building blocks cofactors, small molecule carriers molybdenum
regulation genetic unit regulated operon
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level repressor

DNA binding site length: 24 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: CGtTATATaattaatTATATAaCG

Regulated Transcription Units (9 total): ?

Notes:


Sequence Features

Feature Class Location Citations Comment
Protein-Segment 1 -> 121
[UniProt10]
UniProt: I; Sequence Annotation Type: region of interest;
DNA-Binding-Region 33 -> 79
[UniProt10a]
UniProt: H-T-H motif winged-type;
Mutagenesis-Variant 76
[Grunden96, UniProt11]
Alternate sequence: A → V; UniProt: Partial loss of repression by modE.
Protein-Segment 122 -> 183
[UniProt10]
UniProt: IIA (MOP1A); Sequence Annotation Type: region of interest;
Mutagenesis-Variant 125
[Grunden96, UniProt11]
Alternate sequence: T → I; UniProt: Transcription repression by modE even in the absence of molybdate.
Protein-Segment 125 -> 133
[UniProt10]
UniProt: Required for dimer formation and molybdate binding; Sequence Annotation Type: region of interest;
Mutagenesis-Variant 133
[Grunden96, UniProt11]
Alternate sequence: G → D; UniProt: Transcription repression by modE even in the absence of molybdate.
Protein-Segment 184 -> 255
[UniProt10]
UniProt: IIB (MOP2); Sequence Annotation Type: region of interest;
Mutagenesis-Variant 216 -> 262
[Grunden96, UniProt11]
Alternate sequence: QCEVLMALPDGQTLCATVPVNEATSLQQGQNVTAYFNADSVIIATLC → missing; UniProt: Transcription repression by modE even in the absence of molybdate.
Protein-Segment 256 -> 262
[UniProt10]
UniProt: IIA (MOP1B); Sequence Annotation Type: region of interest;


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

Anderson00: Anderson LA, McNairn E, Lubke T, Pau RN, Boxer DH, Leubke T (2000). "ModE-dependent molybdate regulation of the molybdenum cofactor operon moa in Escherichia coli." J Bacteriol 2000;182(24);7035-43. PMID: 11092866

Anderson97: Anderson LA, Palmer T, Price NC, Bornemann S, Boxer DH, Pau RN (1997). "Characterisation of the molybdenum-responsive ModE regulatory protein and its binding to the promoter region of the modABCD (molybdenum transport) operon of Escherichia coli." Eur J Biochem 246(1);119-26. PMID: 9210473

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

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."

Gourley01: Gourley DG, Schuttelkopf AW, Anderson LA, Price NC, Boxer DH, Hunter WN (2001). "Oxyanion binding alters conformation and quaternary structure of the c-terminal domain of the transcriptional regulator mode. Implications for molybdate-dependent regulation, signaling, storage, and transport." J Biol Chem 276(23);20641-7. PMID: 11259434

Grunden96: Grunden AM, Ray RM, Rosentel JK, Healy FG, Shanmugam KT (1996). "Repression of the Escherichia coli modABCD (molybdate transport) operon by ModE." J Bacteriol 1996;178(3);735-44. PMID: 8550508

Grunden99: Grunden AM, Self WT, Villain M, Blalock JE, Shanmugam KT (1999). "An analysis of the binding of repressor protein ModE to modABCD (molybdate transport) operator/promoter DNA of Escherichia coli." J Biol Chem 1999;274(34);24308-15. PMID: 10446207

Hall99: Hall DR, Gourley DG, Leonard GA, Duke EM, Anderson LA, Boxer DH, Hunter WN (1999). "The high-resolution crystal structure of the molybdate-dependent transcriptional regulator (ModE) from Escherichia coli: a novel combination of domain folds." EMBO J 18(6);1435-46. PMID: 10075916

Hasona98: Hasona A, Self WT, Ray RM, Shanmugam KT (1998). "Molybdate-dependent transcription of hyc and nar operons of Escherichia coli requires MoeA protein and ModE-molybdate." FEMS Microbiol Lett 169(1);111-6. PMID: 9851041

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Kuper03: Kuper J, Meyer zu Berstenhorst S, Vodisch B, Mendel RR, Schwarz G, Boxer DH (2003). "In vivo detection of molybdate-binding proteins using a competition assay with ModE in Escherichia coli." FEMS Microbiol Lett 218(1);187-93. PMID: 12583917

McNicholas02: McNicholas PM, Gunsalus RP (2002). "The molybdate-responsive Escherichia coli ModE transcriptional regulator coordinates periplasmic nitrate reductase (napFDAGHBC) operon expression with nitrate and molybdate availability." J Bacteriol 184(12);3253-9. PMID: 12029041

McNicholas96: McNicholas PM, Chiang RC, Gunsalus RP (1996). "The Escherichia coli modE gene: effect of modE mutations on molybdate dependent modA expression." FEMS Microbiol Lett 145(1);117-23. PMID: 8931336

McNicholas97: McNicholas PM, Rech SA, Gunsalus RP (1997). "Characterization of the ModE DNA-binding sites in the control regions of modABCD and moaABCDE of Escherichia coli." Mol Microbiol 1997;23(3);515-24. PMID: 9044285

McNicholas98: McNicholas PM, Chiang RC, Gunsalus RP (1998). "Anaerobic regulation of the Escherichia coli dmsABC operon requires the molybdate-responsive regulator ModE." Mol Microbiol 27(1);197-208. PMID: 9466267

McNicholas98a: McNicholas PM, Mazzotta MM, Rech SA, Gunsalus RP (1998). "Functional dissection of the molybdate-responsive transcription regulator, ModE, from Escherichia coli." J Bacteriol 180(17);4638-43. PMID: 9721306

Schuttelkopf03: Schuttelkopf AW, Boxer DH, Hunter WN (2003). "Crystal structure of activated ModE reveals conformational changes involving both oxyanion and DNA-binding domains." J Mol Biol 326(3);761-7. PMID: 12581638

Self99: Self WT, Grunden AM, Hasona A, Shanmugam KT (1999). "Transcriptional regulation of molybdoenzyme synthesis in Escherichia coli in response to molybdenum: ModE-molybdate, a repressor of the modABCD (molybdate transport) operon is a secondary transcriptional activator for the hyc and nar operons." Microbiology 1999;145 ( Pt 1);41-55. PMID: 10206709

Stewart03: Stewart V, Bledsoe PJ, Williams SB (2003). "Dual overlapping promoters control napF (periplasmic nitrate reductase) operon expression in Escherichia coli K-12." J Bacteriol 185(19);5862-70. PMID: 13129959

Studholme03: Studholme DJ, Pau RN (2003). "A DNA element recognised by the molybdenum-responsive transcription factor ModE is conserved in Proteobacteria, green sulphur bacteria and Archaea." BMC Microbiol 3;24. PMID: 14641908

Tao05: Tao H, Hasona A, Do PM, Ingram LO, Shanmugam KT (2005). "Global gene expression analysis revealed an unsuspected deo operon under the control of molybdate sensor, ModE protein, in Escherichia coli." Arch Microbiol 184(4);225-33. PMID: 16205910

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.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 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."

Walkenhorst95: Walkenhorst HM, Hemschemeier SK, Eichenlaub R (1995). "Molecular analysis of the molybdate uptake operon, modABCD, of Escherichia coli and modR, a regulatory gene." Microbiol Res 1995;150(4);347-61. PMID: 8564363


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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