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Escherichia coli K-12 substr. MG1655 Protein: MetJ-S-adenosylmethionine DNA-binding transcriptional repressor



Gene: metJ Accession Numbers: EG10588 (EcoCyc), b3938, ECK3930

Regulation Summary Diagram: ?

Subunit composition of MetJ-S-adenosylmethionine DNA-binding transcriptional repressor = [(MetJ)(S-adenosyl-L-methionine)]2
         MetJ-S-adenosylmethionine = (MetJ)(S-adenosyl-L-methionine)
                 MetJ transcriptional repressor = MetJ

Summary:
MetJ represses the expression of genes involved in biosynthesis and transport of methionine [Marincs06, Weissbach91].

MetJ belongs to the ribbon-helix-helix family of regulatory proteins. The typical motif of members of this family, the ribbon-helix-helix motif for DNA binding, has been observed in the crystalline structure of MetJ [Somers92]. This motif is composed of a two-stranded antiparallel β-ribbon that lies along the DNA major groove, two outer α-helices that interact with adjacent proteins along the DNA, and two inner β-helices that form the subunit interface [Somers92].

MetJ as a homodimer [Smith85b, Somers92] recognizes and binds to an 8-bp DNA sequence called the met-box, which varies around a perfect palindromic consensus sequence [SaintGirons84, Phillips89, Belfaiza86]. MetJ finds its target sites rapidly by facilitated diffusion [Augustus09]. The affinity of MetJ to this site is enhanced by S-adenosyl methionine (AdoMet) [Phillips89, Hyre95], which is the end product of methionine biosynthesis and which binds MetJ to act as a corepressor [LaMonte06]. The binding of AdoMet to MetJ creates an unusually long-range electrostatic interaction with the phosphodiester backbone of the DNA, raising the DNA affinity by at least 100-fold [Phillips94, Parsons95]. In addition to AdoMet, the metabolites 5-deoxy-5-(methylthio)adenosine (MTA) and adenine (Ade) also bind with high affinity to MetJ, but the biological effects of this binding are not known [MartiArbona12].

The genes regulated by MetJ contain in their regulatory region two to five continuous met-boxes [Old91], in which MetJ dimers interact with each other [Phillips89, Somers92].

The metJ gene, which is autoregulated, is transcribed divergently from the metBL operon, which is repressed by MetJ [SaintGirons84].

Reviews: [Old91, Weissbach91].

Citations: [Cai89, Liu01]

Gene Citations: [Smith84a]

Map Position: [4,126,101 <- 4,126,418] (88.93 centisomes)
Length: 318 bp / 105 aa

Unification Links: ASAP:ABE-0012874 , CGSC:508 , EchoBASE:EB0583 , EcoGene:EG10588 , OU-Microarray:b3938 , PortEco:metJ , RegulonDB:EG10588

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0045892 - negative regulation of transcription, DNA-templated Inferred from experiment [Marincs06]
Molecular Function: GO:0000986 - bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding Inferred from experiment [Marincs06]
GO:0042803 - protein homodimerization activity Inferred from experiment [Smith85b]

MultiFun Terms: information transfer RNA related Transcription related
metabolism biosynthesis of building blocks amino acids methionine
regulation genetic unit regulated operon
regulation type of regulation transcriptional level repressor

DNA binding site length: 16 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: AGACGTCTAGACGTCT

Regulated Transcription Units (11 total): ?

Notes:

Credits:
Created 28-Apr-2009 by Gama-Castro S , UNAM


Subunit of MetJ-S-adenosylmethionine DNA-binding transcriptional repressor: MetJ-S-adenosylmethionine

Synonyms: B3938, MetJ, MetJ-SAM

Sequence Length: 105 AAs

Molecular Weight: 12.141 kD (from nucleotide sequence)

MultiFun Terms: information transfer RNA related Transcription related
metabolism biosynthesis of building blocks amino acids methionine
regulation genetic unit regulated operon
regulation type of regulation transcriptional level repressor

Relationship Links: PDB:STRUCTURE:1CMC , Pfam:IN-FAMILY:PF01340

In Reactions of unknown directionality:

Not in pathways:
MetJ + S-adenosyl-L-methionine = MetJ-S-adenosylmethionine


Subunit of MetJ-S-adenosylmethionine: MetJ transcriptional repressor

Synonyms: MetJ

Gene: metJ Accession Numbers: EG10588 (EcoCyc), b3938, ECK3930

Locations: cytosol

Sequence Length: 105 AAs

Molecular Weight: 12.141 kD (from nucleotide sequence)

pI: 5.42

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:0006555 - methionine metabolic process Inferred by computational analysis [GOA01]
GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11]
GO:0009086 - methionine biosynthetic process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0002055 - adenine binding
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003700 - sequence-specific DNA binding transcription factor activity 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]

MultiFun Terms: information transfer RNA related Transcription related
metabolism biosynthesis of building blocks amino acids methionine
regulation genetic unit regulated operon
regulation type of regulation transcriptional level repressor

Unification Links: DIP:DIP-47929N , EcoliWiki:b3938 , Mint:MINT-1265451 , PR:PRO_000023215 , Pride:P0A8U6 , Protein Model Portal:P0A8U6 , RefSeq:NP_418373 , SMR:P0A8U6 , String:511145.b3938 , UniProt:P0A8U6

Relationship Links: InterPro:IN-FAMILY:IPR002084 , InterPro:IN-FAMILY:IPR010985 , InterPro:IN-FAMILY:IPR023453 , PDB:Structure:1CMA , PDB:Structure:1CMB , PDB:Structure:1CMC , PDB:Structure:1MJ2 , PDB:Structure:1MJK , PDB:Structure:1MJL , PDB:Structure:1MJM , PDB:Structure:1MJO , PDB:Structure:1MJP , PDB:Structure:1MJQ , Pfam:IN-FAMILY:PF01340 , ProDom:IN-FAMILY:PD020365

In Reactions of unknown directionality:

Not in pathways:
MetJ + adenine = MetJ-adenine
MetJ + S-methyl-5'-thioadenosine = MetJ-MTA
MetJ + S-adenosyl-L-methionine = MetJ-S-adenosylmethionine

Essentiality data for metJ 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]


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3938 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10588; confirmed by SwissProt match.


References

Augustus09: Augustus AM, Reardon PN, Spicer LD (2009). "MetJ repressor interactions with DNA probed by in-cell NMR." Proc Natl Acad Sci U S A 106(13);5065-9. PMID: 19289840

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

Belfaiza86: Belfaiza J, Parsot C, Martel A, de la Tour CB, Margarita D, Cohen GN, Saint-Girons I (1986). "Evolution in biosynthetic pathways: two enzymes catalyzing consecutive steps in methionine biosynthesis originate from a common ancestor and possess a similar regulatory region." Proc Natl Acad Sci U S A 83(4);867-71. PMID: 3513164

Cai89: Cai XY, Maxon ME, Redfield B, Glass R, Brot N, Weissbach H (1989). "Methionine synthesis in Escherichia coli: effect of the MetR protein on metE and metH expression." Proc Natl Acad Sci U S A 1989;86(12);4407-11. PMID: 2543976

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."

Hyre95: Hyre DE, Spicer LD (1995). "Thermodynamic evaluation of binding interactions in the methionine repressor system of Escherichia coli using isothermal titration calorimetry." Biochemistry 34(10);3212-21. PMID: 7880815

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

LaMonte06: LaMonte BL, Hughes JA (2006). "In vivo hydrolysis of S-adenosylmethionine induces the met regulon of Escherichia coli." Microbiology 152(Pt 5);1451-9. PMID: 16622061

Liu01: Liu R, Blackwell TW, States DJ (2001). "Conformational model for binding site recognition by the E.coli MetJ transcription factor." Bioinformatics 17(7);622-33. PMID: 11448880

Marincs06: Marincs F, Manfield IW, Stead JA, McDowall KJ, Stockley PG (2006). "Transcript analysis reveals an extended regulon and the importance of protein-protein co-operativity for the Escherichia coli methionine repressor." Biochem J 396(2);227-34. PMID: 16515535

MartiArbona12: Marti-Arbona R, Teshima M, Anderson PS, Nowak-Lovato KL, Hong-Geller E, Unkefer CJ, Unkefer PJ (2012). "Identification of new ligands for the methionine biosynthesis transcriptional regulator (MetJ) by FAC-MS." J Mol Microbiol Biotechnol 22(4);205-14. PMID: 22890386

Old91: Old IG, Phillips SE, Stockley PG, Saint Girons I (1991). "Regulation of methionine biosynthesis in the Enterobacteriaceae." Prog Biophys Mol Biol 56(3);145-85. PMID: 1771231

Parsons95: Parsons ID, Persson B, Mekhalfia A, Blackburn GM, Stockley PG (1995). "Probing the molecular mechanism of action of co-repressor in the E. coli methionine repressor-operator complex using surface plasmon resonance (SPR)." Nucleic Acids Res 23(2);211-6. PMID: 7862523

Phillips89: Phillips SE, Manfield I, Parsons I, Davidson BE, Rafferty JB, Somers WS, Margarita D, Cohen GN, Saint-Girons I, Stockley PG (1989). "Cooperative tandem binding of met repressor of Escherichia coli." Nature 341(6244);711-5. PMID: 2677754

Phillips94: Phillips K, Phillips SE (1994). "Electrostatic activation of Escherichia coli methionine repressor." Structure 2(4);309-16. PMID: 8087557

SaintGirons84: Saint-Girons I, Duchange N, Cohen GN, Zakin MM (1984). "Structure and autoregulation of the metJ regulatory gene in Escherichia coli." J Biol Chem 1984;259(22);14282-5. PMID: 6094549

Smith84a: Smith AA, Greene RC (1984). "Cloning of the methionine regulatory gene, metJ, of Escherichia coli K12 and identification of its product." J Biol Chem 259(22);14279-81. PMID: 6389545

Smith85b: Smith AA, Greene RC, Kirby TW, Hindenach BR (1985). "Isolation and characterization of the product of the methionine-regulatory gene metJ of Escherichia coli K-12." Proc Natl Acad Sci U S A 82(18);6104-8. PMID: 2994061

Somers92: Somers WS, Phillips SE (1992). "Crystal structure of the met repressor-operator complex at 2.8 A resolution reveals DNA recognition by beta-strands." Nature 1992;359(6394);387-93. PMID: 1406951

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."

Weissbach91: Weissbach H, Brot N (1991). "Regulation of methionine synthesis in Escherichia coli." Mol Microbiol 1991;5(7);1593-7. PMID: 1943695

Other References Related to Gene Regulation

Kirby86: Kirby TW, Hindenach BR, Greene RC (1986). "Regulation of in vivo transcription of the Escherichia coli K-12 metJBLF gene cluster." J Bacteriol 1986;165(3);671-7. PMID: 2419307

Stojiljkovic94: Stojiljkovic I, Baumler AJ, Hantke K (1994). "Fur regulon in gram-negative bacteria. Identification and characterization of new iron-regulated Escherichia coli genes by a fur titration assay." J Mol Biol 236(2);531-45. PMID: 8107138


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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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