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Escherichia coli K-12 substr. MG1655 Enzyme: cobalamin-dependent methionine synthase



Gene: metH Accession Numbers: EG10587 (EcoCyc), b4019, ECK4011

Regulation Summary Diagram: ?

Summary:
Cobalamin-dependent methionine synthase (MetH) is a large modular protein that catalyzes the transfer of a methyl group from 5-methyl-tetrahydrofolate to homocysteine to form methionine in the final step of de novo methionine biosynthesis [Whitfield70]. MetH first catalyzes methyl transfer from enzyme-bound methylcobalamin to homocysteine to produce methionine and cob(I)alamin [Frasca88]. Methyltetrahydrofolate then remethylates cob(I)alamin to regenerate methylcobalamin and tetrahydrofolate. The cobalamin cofactor, which serves as both acceptor and donor of the methyl group, is oxidized once every approximately 2,000 catalytic cycles and must be reactivated by the uptake of an electron from reduced flavodoxin [Fujii74] and a methyl group from S-adenosyl-L-methionine (AdoMet) [Taylor67]. Glu61 of flavodoxin is required to bind to Lys959 of the C-terminal activation domain of the enzyme [Hall00]. Zinc is required for catalysis of methyl transfer from methylcobalamin to homocysteine [Goulding97a].

The enzyme undergoes large conformational changes to allow the cobalamin-binding domain to react with three different substrates: homocysteine, methyltetrahydrofolate, AdoMet [Drummond93, Fleischhacker07, Liptak08]. The His759 residue helps maintaining equilibria between different conformations of the enzyme [Liptak07].

The reaction can be catalyzed by either of two transmethylases encoded by metE or metH. This enzyme, the metH gene product, is dependent on vitamin B12 as a cofactor, whereas the metE gene product is not [Banerjee89]. MetH can utilize either the mono- or triglutamate forms of folate in contrast to MetE, which can use only the triglutamate form [Gonzalez92]. The MetR-dependent activation of metE and metH genes require different C terminal domain residues and orientiation of the alpha subunit of RNA polymerase [Fritsch00].

MetH is composed of four functionally distinct modules that are arranged linearly with single interdomain linkers. The N-terminal module binds and activates homocysteine while the second module binds and activates methyl-tetrahydrofolate. The third module binds the cobalamin cofactor and the last module is necessary for the reductive methylation of MetH, as it binds and activates AdoMet [Goulding97].

Crystals of the cobalamine-binding domain of MetH are available [Luschinsky92]. An X-ray structure of the C-terminal fragment of methionine synthase in the reactivation conformation was observed recently [Datta08].

Gene Citations: [Marconi91, Wehmeier92]

Locations: cytosol

Map Position: [4,221,851 -> 4,225,534] (90.99 centisomes)
Length: 3684 bp / 1227 aa

Molecular Weight of Polypeptide: 136.0 kD (from nucleotide sequence)

pI: 5.26

Unification Links: ASAP:ABE-0013140 , CGSC:509 , EchoBASE:EB0582 , EcoGene:EG10587 , EcoliWiki:b4019 , Entrez-gene:948522 , ModBase:P13009 , OU-Microarray:b4019 , PortEco:metH , Pride:P13009 , Protein Model Portal:P13009 , RefSeq:NP_418443 , RegulonDB:EG10587 , SMR:P13009 , String:511145.b4019 , UniProt:P13009

Relationship Links: InterPro:IN-FAMILY:IPR000489 , InterPro:IN-FAMILY:IPR003726 , InterPro:IN-FAMILY:IPR003759 , InterPro:IN-FAMILY:IPR004223 , InterPro:IN-FAMILY:IPR006158 , InterPro:IN-FAMILY:IPR011005 , InterPro:IN-FAMILY:IPR011822 , Panther:IN-FAMILY:PTHR21091:SF9 , PDB:Structure:1BMT , PDB:Structure:1K7Y , PDB:Structure:1K98 , PDB:Structure:1MSK , PDB:Structure:3BUL , PDB:Structure:3IV9 , PDB:Structure:3IVA , Pfam:IN-FAMILY:PF00809 , Pfam:IN-FAMILY:PF02310 , Pfam:IN-FAMILY:PF02574 , Pfam:IN-FAMILY:PF02607 , Pfam:IN-FAMILY:PF02965 , Prosite:IN-FAMILY:PS50970 , Prosite:IN-FAMILY:PS50972 , Prosite:IN-FAMILY:PS50974 , Prosite:IN-FAMILY:PS51332 , Prosite:IN-FAMILY:PS51337 , Smart:IN-FAMILY:SM01018

In Paralogous Gene Group: 79 (2 members)

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 [UniProtGOA11]
GO:0009086 - methionine biosynthetic process Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11]
GO:0042558 - pteridine-containing compound metabolic process Inferred by computational analysis [GOA01]
GO:0044237 - cellular metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0008270 - zinc ion binding Inferred from experiment Inferred by computational analysis [GOA01, Goulding97a]
GO:0008705 - methionine synthase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Goulding97, Hall00]
GO:0031419 - cobalamin binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Banerjee90]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11]
GO:0008898 - S-adenosylmethionine-homocysteine S-methyltransferase activity Inferred by computational analysis [GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11, GOA01]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Jarrett97, Banerjee89]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005622 - intracellular Inferred by computational analysis [GOA01]

MultiFun Terms: metabolism biosynthesis of building blocks amino acids methionine

Essentiality data for metH 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]
Yes [Feist07, Comment 4]

Credits:
Reviewed 26-Feb-2010 by Sarker M


Enzymatic reaction of: methionine synthase

Synonyms: 5-methyltetrahydrofolate-homocysteine-S-methyltransferase, 5-methyltetrahydrofolate:L-homocysteine S-methyltransferase, cobalamine-dependent homocysteine transmethylase, homocysteine methylase, cobalamin-dependent methionine synthase, B12-dependent methionine synthase, 5-methyltetrahydrofolate--homocysteine methyl transferase, homocysteine-N5-methyltetrahydrofolate transmethylase

EC Number: 2.1.1.13

L-homocysteine + an N5-methyl-tetrahydrofolate <=> L-methionine + a tetrahydrofolate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is irreversible in the direction shown. [Banerjee90]

Alternative Substrates for an N5-methyl-tetrahydrofolate: N5-methyl-tetrahydropteroyl mono-L-glutamate

In Pathways: S-adenosyl-L-methionine cycle I , superpathway of S-adenosyl-L-methionine biosynthesis , homoserine and methionine biosynthesis , superpathway of lysine, threonine and methionine biosynthesis I , aspartate superpathway , methionine biosynthesis I , N10-formyl-tetrahydrofolate biosynthesis

Summary:
During catalysis, an enzyme-bound cobalamine prosthetic group is used as an intermediate methyl donor and acceptor. At different points during the reaction cycle, the coordination to the cobalt of the cobalamine changes. Corodination of the His-759 residue to the cobalt center is necessary for the interconversion betwee the reactivation and catalytic conformations [Liptak07]. Zinc is required for catalysis of methyl transfer from methylcobalamin to homocysteine [Goulding97a]. Mutations of Cys310 or Cys311 to either alanine or serine result in loss of catalytic activity [Goulding97]. The equilibria between various conformations of MetH are sensitive to temparature, the presence or absence of ligands including methyl-tetrahydrofolate, and the beta-ligand of the cobalamine prosthetic group [Fleischhacker07].

The reaction involves an ordered sequential mechanism in which methyltetrahydrofolate binding precedes binding of homocysteine and release of methionine precedes release of tetrahydrofolate [Banerjee90].

Cofactors or Prosthetic Groups: cob(I)alamin [Frasca88, Banerjee89, Banerjee90], Zn2+ [Comment 5, Goulding97a]

Inhibitors (Other): L-methionine [Banerjee90] , tetrahydropteroyl mono-L-glutamate [Banerjee90]

Kinetic Parameters:

Substrate
Km (μM)
Citations
L-homocysteine
69.0
[Zhou00, BRENDA14]
L-homocysteine
0.8
[Banerjee90]
an N5-methyl-tetrahydrofolate
27.8
[Banerjee90]

T(opt): 45 °C [BRENDA14, Luschinsky92]

pH(opt): 7.2 [Banerjee90]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Goulding97, UniProt11]
UniProt: Removed.
Conserved-Region 2 -> 325
[UniProt09]
UniProt: Hcy-binding;
Chain 2 -> 1227
[UniProt09]
UniProt: Methionine synthase;
Sequence-Conflict 113
[Banerjee89, Old90, UniProt10a]
Alternate sequence: A → R; UniProt: (in Ref. 1 and 2);
Metal-Binding-Site 247
[UniProt10a]
UniProt: Zinc;
Mutagenesis-Variant 310
[Goulding97, UniProt11]
Alternate sequence: C → S; UniProt: Loss of zinc binding. Loss of catalytic activity.
Alternate sequence: C → A; UniProt: Loss of zinc binding. Loss of catalytic activity.
Metal-Binding-Site 310
[UniProt10a]
UniProt: Zinc;
Mutagenesis-Variant 311
[Goulding97, UniProt11]
Alternate sequence: C → S; UniProt: Loss of zinc binding. Loss of catalytic activity.
Alternate sequence: C → A; UniProt: Loss of zinc binding. Loss of catalytic activity.
Metal-Binding-Site 311
[UniProt10a]
UniProt: Zinc;
Conserved-Region 356 -> 617
[UniProt09]
UniProt: Pterin-binding;
Sequence-Conflict 641
[Banerjee89, Old90, UniProt10a]
Alternate sequence: S → T; UniProt: (in Ref. 1 and 2);
Conserved-Region 650 -> 744
[UniProt09]
UniProt: B12-binding N-terminal;
Conserved-Region 746 -> 881
[UniProt09]
UniProt: B12-binding;
Mutagenesis-Variant 757
[Jarrett96, UniProt11]
Alternate sequence: D → N; UniProt: Decreases activity by about 45%.
Alternate sequence: D → E; UniProt: Decreases activity by about 70%.
Mutagenesis-Variant 759
[Jarrett96, UniProt11]
Alternate sequence: H → G; UniProt: Loss of catalytic activity.
Metal-Binding-Site 759
[Drennan94, UniProt11]
UniProt: Cobalt (cobalamin axial ligand).
Amino-Acid-Sites-That-Bind 804
[UniProt10a]
UniProt: Cobalamin;
Mutagenesis-Variant 810
[Jarrett96, UniProt11]
Alternate sequence: S → A; UniProt: Decreases activity by about 40%.
Protein-Segment 834 -> 835
[UniProt10]
UniProt: Cobalamin-binding; Sequence Annotation Type: region of interest;
Conserved-Region 897 -> 1227
[UniProt09]
UniProt: AdoMet activation;
Amino-Acid-Sites-That-Bind 946
[UniProt10a]
UniProt: S-adenosyl-L-methionine;
Sequence-Conflict 1079 -> 1080
[Old90, UniProt10a]
Alternate sequence: QH → HD; UniProt: (in Ref. 1; CAA34601);
Amino-Acid-Sites-That-Bind 1134
[UniProt10a]
UniProt: S-adenosyl-L-methionine; via carbonyl oxygen;
Amino-Acid-Sites-That-Bind 1138
[UniProt10a]
UniProt: Cobalamin; via carbonyl oxygen;
Protein-Segment 1189 -> 1190
[UniProt10]
UniProt: S-adenosyl-L-methionine binding; Sequence Annotation Type: region of interest;
Sequence-Conflict 1195 -> 1227
[Old90, UniProt10a]
Alternate sequence: IQRDQVEDYARRKGMSVTEVERWLAPNLGYDAD → TSARSG; UniProt: (in Ref. 1; CAA34601);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b4019 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10587; confirmed by SwissProt match.


References

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

Banerjee89: Banerjee RV, Johnston NL, Sobeski JK, Datta P, Matthews RG (1989). "Cloning and sequence analysis of the Escherichia coli metH gene encoding cobalamin-dependent methionine synthase and isolation of a tryptic fragment containing the cobalamin-binding domain." J Biol Chem 1989;264(23);13888-95. PMID: 2668277

Banerjee90: Banerjee RV, Frasca V, Ballou DP, Matthews RG (1990). "Participation of cob(I) alamin in the reaction catalyzed by methionine synthase from Escherichia coli: a steady-state and rapid reaction kinetic analysis." Biochemistry 1990;29(50);11101-9. PMID: 2271698

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Datta08: Datta S, Koutmos M, Pattridge KA, Ludwig ML, Matthews RG (2008). "A disulfide-stabilized conformer of methionine synthase reveals an unexpected role for the histidine ligand of the cobalamin cofactor." Proc Natl Acad Sci U S A 105(11);4115-20. PMID: 18332423

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

Drennan94: Drennan CL, Huang S, Drummond JT, Matthews RG, Lidwig ML (1994). "How a protein binds B12: A 3.0 A X-ray structure of B12-binding domains of methionine synthase." Science 266(5191);1669-74. PMID: 7992050

Drummond93: Drummond JT, Huang S, Blumenthal RM, Matthews RG (1993). "Assignment of enzymatic function to specific protein regions of cobalamin-dependent methionine synthase from Escherichia coli." Biochemistry 32(36);9290-5. PMID: 8369297

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

Fleischhacker07: Fleischhacker AS, Matthews RG (2007). "Ligand trans influence governs conformation in cobalamin-dependent methionine synthase." Biochemistry 46(43);12382-92. PMID: 17924667

Frasca88: Frasca V, Banerjee RV, Dunham WR, Sands RH, Matthews RG (1988). "Cobalamin-dependent methionine synthase from Escherichia coli B: electron paramagnetic resonance spectra of the inactive form and the active methylated form of the enzyme." Biochemistry 27(22);8458-65. PMID: 2853966

Fritsch00: Fritsch PS, Urbanowski ML, Stauffer GV (2000). "Role of the RNA polymerase alpha subunits in MetR-dependent activation of metE and metH: important residues in the C-terminal domain and orientation requirements within RNA polymerase." J Bacteriol 182(19);5539-50. PMID: 10986259

Fujii74: Fujii K, Huennekens FM (1974). "Activation of methionine synthetase by a reduced triphosphopyridine nucleotide-dependent flavoprotein system." J Biol Chem 249(21);6745-53. PMID: 4154078

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."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Gonzalez92: 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

Goulding97: Goulding CW, Postigo D, Matthews RG (1997). "Cobalamin-dependent methionine synthase is a modular protein with distinct regions for binding homocysteine, methyltetrahydrofolate, cobalamin, and adenosylmethionine." Biochemistry 36(26);8082-91. PMID: 9201956

Goulding97a: Goulding CW, Matthews RG (1997). "Cobalamin-dependent methionine synthase from Escherichia coli: involvement of zinc in homocysteine activation." Biochemistry 1997;36(50);15749-57. PMID: 9398304

Hall00: Hall DA, Jordan-Starck TC, Loo RO, Ludwig ML, Matthews RG (2000). "Interaction of flavodoxin with cobalamin-dependent methionine synthase." Biochemistry 39(35);10711-9. PMID: 10978155

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

Jarrett96: Jarrett JT, Amaratunga M, Drennan CL, Scholten JD, Sands RH, Ludwig ML, Matthews RG (1996). "Mutations in the B12-binding region of methionine synthase: how the protein controls methylcobalamin reactivity." Biochemistry 35(7);2464-75. PMID: 8652590

Jarrett97: Jarrett JT, Goulding CW, Fluhr K, Huang S, Matthews RG (1997). "Purification and assay of cobalamin-dependent methionine synthase from Escherichia coli." Methods Enzymol 281;196-213. PMID: 9250984

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

Liptak07: Liptak MD, Fleischhacker AS, Matthews RG, Brunold TC (2007). "Probing the role of the histidine 759 ligand in cobalamin-dependent methionine synthase." Biochemistry 46(27);8024-35. PMID: 17567043

Liptak08: Liptak MD, Datta S, Matthews RG, Brunold TC (2008). "Spectroscopic study of the cobalamin-dependent methionine synthase in the activation conformation: effects of the Y1139 residue and S-adenosylmethionine on the B12 cofactor." J Am Chem Soc 130(48);16374-81. PMID: 19006389

Luschinsky92: Luschinsky CL, Drummond JT, Matthews RG, Ludwig ML (1992). "Crystallization and preliminary X-ray diffraction studies of the cobalamin-binding domain of methionine synthase from Escherichia coli." J Mol Biol 1992;225(2);557-60. PMID: 1593636

Marconi91: Marconi R, Wigboldus J, Weissbach H, Brot N (1991). "Transcriptional start and MetR binding sites on the Escherichia coli metH gene." Biochem Biophys Res Commun 175(3);1057-63. PMID: 2025237

Old90: Old IG, Margarita D, Glass RE, Saint Girons I (1990). "Nucleotide sequence of the metH gene of Escherichia coli K-12 and comparison with that of Salmonella typhimurium LT2." Gene 1990;87(1);15-21. PMID: 2185137

Taylor67: Taylor RT, Weissbach H (1967). "N5-methyltetrahydrofolate-homocysteine transmethylase. Role of S-adenosylmethionine in vitamin B12-dependent methionine synthesis." J Biol Chem 242(7);1517-21. PMID: 5337044

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

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."

Wehmeier92: Wehmeier UF, Nobelmann B, Lengeler JW (1992). "Cloning of the Escherichia coli sor genes for L-sorbose transport and metabolism and physical mapping of the genes near metH and iclR." J Bacteriol 1992;174(23);7784-90. PMID: 1447144

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

Zhou00: 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

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

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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