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Escherichia coli K-12 substr. MG1655 Enzyme: cobalamin-independent homocysteine transmethylase



Gene: metE Accession Numbers: EG10584 (EcoCyc), b3829, ECK3823

Synonyms: metB12

Regulation Summary Diagram: ?

Summary:
In the absence of exogenously supplied vitamin B12 (cobalamin), E. coli MetE catalyzes the final step of de novo methionine biosynthesis. In the presence of the vitamin B12 cofactor, MetH functions in this reaction and synthesis of MetE is repressed (see pathway methionine biosynthesis I). The metE and metH genes lack similarity in their deduced amino acid sequences, suggesting that these proteins arose by convergent evolution [Gonzalez92a].

MetE was shown to utilize only the triglutamate form of folate (5-methyltetrahydropteroyltri-L-glutamate) whereas MetH utilized either the monoglutamate (5-methyl-tetrahydrofolate) or the triglutamate forms of folate [Foster64].

Early studies utilized unpurified or partially purified enzyme [Foster64, Guest64]. The enzyme was later purified from extracts of E. coli K-12 and characterized [Whitfield70]. The metE gene was cloned and expressed [Chu85, Old88] and the expression of MetE was shown to be repressed by methionine and vitamin B12 [Old88]. Recombinant enzyme has also been purified and characterized [Gonzalez92a].

MetE contains zinc which is necessary for its activity. Cys643 and Cys726 have been identified as two of the zinc ligands and a third may be His641 [Zhou99]. Evidence suggested that the sulfur of the homocysteine substrate binds directly to the zinc ion [Peariso01]. Modeling of the structure of E. coli MetE based on the crystal structure of MetE from Thermotoga maritima showed a double-barrel structure that likely evolved by gene duplication [Pejchal05].

Inactivation of MetE has been shown in E. coli cells growing under conditions of transient oxidative stress, resulting in a methionine auxotrophy. Under these conditions MetE protein is found at high levels. A possible mechanism involving reversible inactivation of MetE by oxidized glutathione was proposed and glutathionylation of Cys645 at the entrance to the active site was demonstrated. Thiol-trapping experiments provided direct evidence of MetE oxidation in vivo [Hondorp04]. It was subsequently shown that a Cys645Ala mutant eliminated the methionine auxotrophy imposed by oxidative stress, suggesting that modulation of MetE activity by Cys645 oxidation has physiological significance under these conditions. Control of methionine availability may modulate cellular growth during oxidative stress [Hondorp09].

The MetE reaction mechanism has been studied with respect to the kinetic pathway for binding of substrates 5-methyltetrahydropteroyltri-L-glutamate and homocysteine. Binding of these substrates was found to be synergistic. Evidence also suggested that activation of 5-methyltetrahydropteroyltri-L-glutamate for methyl group transfer occurs by protonation of N5, which occurs upon formation of the ternary MetE, homocysteine, 5-methyltetrahydropteroyltri-L-glutamate complex [Taurog06a, Taurog06].

Adaptation of E. coli to anaerobic growth has been shown to involve the action of a conserved, anaerobically induced small regulatory RNA named FnrS which negatively regulates a set of genes that includes metE (see the illustration above and click on FnrS). FnrS expression is strictly dependent on the anaerobic transcriptional regulator FNR. It was suggested that FnrS-mediated post-transcriptional control may play a role in rapid adaptation during anaerobic-to-aerobic transitions [Boysen10].

MetJ and MetR are involved in the overexpression of MetE, which is strongly induced by GroE depletion [Fujiwara12].

Review: Hondrop, E.R. and R.G. Matthews (2006) "Methionine" EcoSal 3.6.1.7 [ECOSAL].

Review: [Smith71a]

Locations: cytosol

Map Position: [4,011,076 -> 4,013,337] (86.45 centisomes)
Length: 2262 bp / 753 aa

Molecular Weight of Polypeptide: 84.673 kD (from nucleotide sequence)

pI: 5.98 [Neidhardt96], 6.6 [Daniels92]

Unification Links: ASAP:ABE-0012520 , CGSC:512 , DIP:DIP-6847N , EchoBASE:EB0579 , EcoGene:EG10584 , EcoliWiki:b3829 , Mint:MINT-1280694 , OU-Microarray:b3829 , PortEco:metE , PR:PRO_000023211 , Pride:P25665 , Protein Model Portal:P25665 , RefSeq:NP_418273 , RegulonDB:EG10584 , SMR:P25665 , String:511145.b3829 , Swiss-Model:P25665 , UniProt:P25665

Relationship Links: InterPro:IN-FAMILY:IPR002629 , InterPro:IN-FAMILY:IPR006276 , InterPro:IN-FAMILY:IPR013215 , Pfam:IN-FAMILY:PF01717 , Pfam:IN-FAMILY:PF08267

Gene-Reaction Schematic: ?

Instance reaction of [L-homocysteine + an N5-methyl-tetrahydrofolate → L-methionine + a tetrahydrofolate] (2.1.1.13):
i1: L-homocysteine + N5-methyl--tetrahydropteroyl tri-L-glutamate → L-methionine + tetrahydropteroyl tri-L-glutamate (2.1.1.14)

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0009086 - methionine biosynthetic process Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0003871 - 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Whitfield70]
GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Arifuzzaman, 2006]
GO:0008270 - zinc ion binding Inferred from experiment Inferred by computational analysis [GOA01a, Zhou99]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: metabolism biosynthesis of building blocks amino acids methionine

Essentiality data for metE 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 0.4% glucose No 37 Aerobic 7.2 0.27 No [Patrick07, Comment 3]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 4]
MOPS medium with 0.4% glucose Indeterminate 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
No [Feist07, Comment 5]

Credits:
Last-Curated ? 29-Apr-2011 by Fulcher C , SRI International


Enzymatic reaction of: cobalamin-independent homocysteine transmethylase

Synonyms: methionine synthase, tetrahydropteroyltriglutamate methyltransferase, homocysteine methylase, 5-methyltetrahydropteroyltri-L-glutamate:L-homocysteine S-methyltransferase, cobalamin-independent methionine synthase, 5-methyltetrahydropteroyltriglutamate-homocysteine-S-methyltransferase, 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase, 5-methyltetrahydropteroyltriglutamate-homocysteine transmethylase

EC Number: 2.1.1.14

L-homocysteine + N5-methyl--tetrahydropteroyl tri-L-glutamate <=> L-methionine + tetrahydropteroyl tri-L-glutamate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

In Pathways: superpathway of S-adenosyl-L-methionine biosynthesis , homoserine and methionine biosynthesis , superpathway of lysine, threonine and methionine biosynthesis I , aspartate superpathway , S-adenosyl-L-methionine cycle I , methionine biosynthesis I

Summary:
Enzyme activity required the presence of inorganic phosphate in the reaction mixture and was stimulated by the divalent cations Mg2+ or Mn2+. Ca2+ was less effective and Ba2+ Co2+ Fe2+ and Zn2+ were not effective. Enzyme activity was nonspecifically inhibited by high ionic strength. Monoglutamate and diglutamate folate derivatives could not replace the triglutamate folate derivative as a methyl donor. Cysteine, β-mercaptoethanol, or dithiothreitol could not replace homocysteine as a methyl acceptor [Whitfield70, Guest64].

Cofactors or Prosthetic Groups: Zn2+ [Comment 6, Zhou99]

Inhibitors (Competitive): pteroyl-γ-glutamyl-γ-glutamylglutamate [Whitfield70] , tetrahydropteroyl-α-glutamylglutamate [Whitfield70]

Inhibitors (Unknown Mechanism): 5-methyl-tetrahydropteroyl-α-glutamylglutamate [Whitfield70] , EDTA [Whitfield70]

Kinetic Parameters:

Substrate
Km (μM)
Citations
L-homocysteine
69.0
[Zhou00a, BRENDA, 2014]

pH(opt): 7.5 [BRENDA, 2014, Whitfield70], 8.1 [BRENDA, 2014, Guest64], 7.5-7.8 [Whitfield70]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Link97, UniProt11]
UniProt: Removed.
Repeat 2 -> 370
[UniProt09]
UniProt: Approximate;
Chain 2 -> 753
[UniProt09]
UniProt: 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase;
Sequence-Conflict 363
[Gonzalez92a, UniProt10a]
Alternate sequence: L → V; UniProt: (in Ref. 1; AAA23544);
Repeat 371 -> 753
[UniProt09]
UniProt: Approximate;
Sequence-Conflict 605
[Plunkett93, UniProt10a]
Alternate sequence: E → Q; UniProt: (in Ref. 3; AAA67625);
Mutagenesis-Variant 641
[Zhou99, UniProt11]
Alternate sequence: H → Q; UniProt: Impaired activity, lower affinity for zinc binding. Binds homocysteine 2-4x more weakly than wild-type.
Alternate sequence: H → N; UniProt: Impaired activity, lower affinity for zinc binding.
Metal-Binding-Site 641
[UniProt10a]
UniProt: Zinc;
Mutagenesis-Variant 643
[Zhou99, UniProt11]
Alternate sequence: C → S; UniProt: Impaired activity, lower affinity for zinc binding. Binds homocysteine 7x tighter than wild-type.
Metal-Binding-Site 643
[UniProt10a]
UniProt: Zinc;
Sequence-Conflict 659
[Plunkett93, UniProt10a]
Alternate sequence: A → R; UniProt: (in Ref. 3; AAA67625);
Mutagenesis-Variant 726
[Zhou99, Gonzalez96, UniProt11]
Alternate sequence: C → S; UniProt: Impaired activity, lower affinity for zinc binding. Binds homocysteine 2-4x more weakly than wild-type.
Metal-Binding-Site 726
[UniProt10a]
UniProt: Zinc;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3829 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10584; confirmed by SwissProt match.


References

Arifuzzaman, 2006: Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H (2006). "Large-scale identification of protein-protein interaction of Escherichia coli K-12." Genome Res 16(5);686-91. PMID: 16606699

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

Boysen10: Boysen A, Moller-Jensen J, Kallipolitis B, Valentin-Hansen P, Overgaard M (2010). "Translational regulation of gene expression by an anaerobically induced small non-coding RNA in Escherichia coli." J Biol Chem 285(14);10690-702. PMID: 20075074

BRENDA, 2014: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Chu85: Chu J, Shoeman R, Hart J, Coleman T, Mazaitis A, Kelker N, Brot N, Weissbach H (1985). "Cloning and expression of the metE gene in Escherichia coli." Arch Biochem Biophys 239(2);467-74. PMID: 2988449

Daniels92: Daniels DL, Plunkett G, Burland V, Blattner FR (1992). "Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes." Science 1992;257(5071);771-8. PMID: 1379743

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

ECOSAL: "Escherichia coli and Salmonella: Cellular and Molecular Biology." Online edition.

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Foster64: Foster MA, Tejerina G, Guest JR, Woods DD (1964). "Two enzymic mechanisms for the methylation of homocysteine by extracts of Escherichia coli." Biochem J 92:476-488. PMID: 5319971

Fujiwara12: Fujiwara K, Taguchi H (2012). "Mechanism of methionine synthase overexpression in chaperonin-depleted Escherichia coli." Microbiology 158(Pt 4);917-24. PMID: 22262097

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, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Gonzalez92a: Gonzalez JC, Banerjee RV, Huang S, Sumner JS, Matthews RG (1992). "Comparison of cobalamin-independent and cobalamin-dependent methionine synthases from Escherichia coli: two solutions to the same chemical problem." Biochemistry 1992;31(26);6045-56. PMID: 1339288

Gonzalez96: Gonzalez JC, Peariso K, Penner-Hahn JE, Matthews RG (1996). "Cobalamin-independent methionine synthase from Escherichia coli: a zinc metalloenzyme." Biochemistry 35(38);12228-34. PMID: 8823155

Guest64: Guest JR, Friedman S, Foster MA, Tejerina G, Woods DD (1964). "Transfer of the methyl group from N5-methyltetrahydrofolates to homocysteine in Escherichia coli." Biochem J 92(3);497-504. PMID: 5319972

Hondorp04: Hondorp ER, Matthews RG (2004). "Oxidative stress inactivates cobalamin-independent methionine synthase (MetE) in Escherichia coli." PLoS Biol 2(11);e336. PMID: 15502870

Hondorp09: Hondorp ER, Matthews RG (2009). "Oxidation of cysteine 645 of cobalamin-independent methionine synthase causes a methionine limitation in Escherichia coli." J Bacteriol 191(10);3407-10. PMID: 19286805

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

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

Neidhardt96: Neidhardt FC, Curtiss III R, Ingraham JL, Lin ECC, Low Jr KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE "Escherichia coli and Salmonella, Cellular and Molecular Biology, Second Edition." American Society for Microbiology, Washington, D.C., 1996.

Old88: Old IG, Hunter MG, Wilson DT, Knight SM, Weatherston CA, Glass RE (1988). "Cloning and characterization of the genes for the two homocysteine transmethylases of Escherichia coli." Mol Gen Genet 211(1);78-87. PMID: 2830470

Patrick07: Patrick WM, Quandt EM, Swartzlander DB, Matsumura I (2007). "Multicopy suppression underpins metabolic evolvability." Mol Biol Evol 24(12);2716-22. PMID: 17884825

Peariso01: Peariso K, Zhou ZS, Smith AE, Matthews RG, Penner-Hahn JE (2001). "Characterization of the zinc sites in cobalamin-independent and cobalamin-dependent methionine synthase using zinc and selenium X-ray absorption spectroscopy." Biochemistry 40(4);987-93. PMID: 11170420

Pejchal05: Pejchal R, Ludwig ML (2005). "Cobalamin-independent methionine synthase (MetE): a face-to-face double barrel that evolved by gene duplication." PLoS Biol 3(2);e31. PMID: 15630480

Plunkett93: Plunkett G, Burland V, Daniels DL, Blattner FR (1993). "Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes." Nucleic Acids Res 1993;21(15);3391-8. PMID: 8346018

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Smith71a: Smith DA (1971). "S-amino acid metabolism and its regulation in Escherichia coli and Salmonella typhimurium." Adv Genet 1971;16;141-65. PMID: 4947102

Taurog06: Taurog RE, Matthews RG (2006). "Activation of methyltetrahydrofolate by cobalamin-independent methionine synthase." Biochemistry 45(16);5092-102. PMID: 16618098

Taurog06a: Taurog RE, Jakubowski H, Matthews RG (2006). "Synergistic, random sequential binding of substrates in cobalamin-independent methionine synthase." Biochemistry 45(16);5083-91. PMID: 16618097

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 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.

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

Whitfield70: Whitfield CD, Steers EJ, Weisbach H (1970). "Purification and properties of 5-methyltetrahydropteroyltriglutamate-homocysteine transmethylase." J Biol Chem 1970;245(2);390-401. PMID: 4904482

Zhou00a: Zhou ZS, Smith AE, Matthews RG (2000). "L-Selenohomocysteine: one-step synthesis from L-selenomethionine and kinetic analysis as substrate for methionine synthases." Bioorg Med Chem Lett 10(21);2471-5. PMID: 11078203

Zhou99: Zhou ZS, Peariso K, Penner-Hahn JE, Matthews RG (1999). "Identification of the zinc ligands in cobalamin-independent methionine synthase (MetE) from Escherichia coli." Biochemistry 1999;38(48);15915-26. PMID: 10625458

Other References Related to Gene Regulation

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

Cai89a: Cai XY, Redfield B, Maxon M, Weissbach H, Brot N (1989). "The effect of homocysteine on MetR regulation of metE, metR and metH expression in vitro." Biochem Biophys Res Commun 163(1);79-83. PMID: 2673243

Jafri95: Jafri S, Urbanowski ML, Stauffer GV (1995). "A mutation in the rpoA gene encoding the alpha subunit of RNA polymerase that affects metE-metR transcription in Escherichia coli." J Bacteriol 177(3);524-9. PMID: 7836282

Lorenz95: Lorenz E, Stauffer GV (1995). "Characterization of the MetR binding sites for the glyA gene of Escherichia coli." J Bacteriol 1995;177(14);4113-20. PMID: 7608086

Maxon89: Maxon ME, Redfield B, Cai XY, Shoeman R, Fujita K, Fisher W, Stauffer G, Weissbach H, Brot N (1989). "Regulation of methionine synthesis in Escherichia coli: effect of the MetR protein on the expression of the metE and metR genes." Proc Natl Acad Sci U S A 1989;86(1);85-9. PMID: 2643109

Urbanowski89a: Urbanowski ML, Stauffer GV (1989). "Genetic and biochemical analysis of the MetR activator-binding site in the metE metR control region of Salmonella typhimurium." J Bacteriol 1989;171(10);5620-9. PMID: 2676984

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


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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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