Escherichia coli K-12 substr. MG1655 Enzyme: O-succinylhomoserine(thiol)-lyase / O-succinylhomoserine lyase

Gene: metB Accession Numbers: EG10582 (EcoCyc), b3939, ECK3931

Synonyms: met-1

Regulation Summary Diagram: ?

Regulation summary diagram for metB

Subunit composition of O-succinylhomoserine(thiol)-lyase / O-succinylhomoserine lyase = [MetB]4

This pyridoxal 5'-phosphate (PLP) dependent enzyme catalyzes a γ-replacement reaction that produces L-cystathionine and succinate from the substrates O-succinylhomoserine and L-cysteine in the transsulfuration pathway for methionine biosynthesis (see pathway L-methionine biosynthesis I). In the absence of L-cysteine it can catalyze a γ-elimination (deamination) reaction of O-succinylhomoserine to produce 2-oxobutanoate (α-ketobutyrate), ammonia and succinate, although this is considered to be a non-physiological reaction [Holbrook90].

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

The enzyme was first purified from Salmonella typhimurium [Guggenheim69]. The native enzyme was later purified from Escherichia coli and characterized as a homotetramer, similar to the Salmonella enzyme [Tran83]. The recombinant enzyme was overproduced in E. coli, purified, and characterized both structurally and kinetically. It contained one PLP binding site per subunit and absorption spectra showed the PLP to be in a Schiff base form with lysine 198 [Holbrook90, Martel87]. The PLP binding sites of purified, native E. coli cystathionine γ-synthase (MetB) and cystathionine β-lyase (MetC) were localized on phosphopyridoxal peptides. The amino acid sequences of these peptides were found to be homologous with the PLP binding site of rat liver cystathionine γ-lyase (γ-cystathionase) [Martel87]. MetB also shares 30% identity and 36% overall amino acid sequence homology with MetC, suggesting a common evolutionary origin [Belfaiza86].

Steady-state kinetic analysis of the enzyme showed a ping-pong mechanism [Holbrook90]. However, later steady state kinetic analysis using continuous assays that employed coupling enzymes suggested that the enzyme has an ordered mechanism at L-cysteine concentrations greater than its Km and a ping-pong mechanism at L-cysteine concentrations lower that its Km [Aitken03]. Spectroscopic analysis techniques showed that the γ-replacement and γ-elimination reactions go through a common intermediate that was identified as an α-imino-β,γ-unsaturated pyridoxamine derivative [Brzovic90].

Site-directed mutagenesis studies probed the role of acidic residues D45 and E325 as determinants of reaction specificity. Substitutions D45F and E325Y interconverted the corresponding residues found in MetC. Although mutations in either position had reduced catalytic efficiency which showed that they are required for substrate binding, complementation experiments suggested that the in vivo reaction specificity was not altered relative to wild-type enzyme. Therefore further work is necessary to define the determinants of reaction specificity [Farsi09].

The crystal structure of the recombinant enzyme has been determined at 1.5 Å resolution [Clausen98].

The apparent molecular mass of the protein complex was determined by gel filtration chromatography [Tran83] or sedimentation equilibrium analysis [Holbrook90] and the apparent molecular mass of the subunit was determined by SDS-PAGE [Tran83, Holbrook90].

Citations: [Duchange83]

Gene Citations: [Greene84]

Locations: cytosol

Map Position: [4,126,695 -> 4,127,855] (88.94 centisomes, 320°)
Length: 1161 bp / 386 aa

Molecular Weight of Polypeptide: 41.55 kD (from nucleotide sequence), 40.0 kD (experimental) [Tran83 ]

Molecular Weight of Multimer: 160.0 kD (experimental) [Tran83]

pI: 6.43

Unification Links: ASAP:ABE-0012887 , CGSC:515 , DIP:DIP-10192N , EchoBASE:EB0577 , EcoGene:EG10582 , EcoliWiki:b3939 , ModBase:P00935 , OU-Microarray:b3939 , PortEco:metB , PR:PRO_000023209 , Pride:P00935 , Protein Model Portal:P00935 , RefSeq:NP_418374 , RegulonDB:EG10582 , SMR:P00935 , String:511145.b3939 , UniProt:P00935

Relationship Links: InterPro:IN-FAMILY:IPR000277 , InterPro:IN-FAMILY:IPR011821 , InterPro:IN-FAMILY:IPR015421 , InterPro:IN-FAMILY:IPR015422 , InterPro:IN-FAMILY:IPR015424 , Panther:IN-FAMILY:PTHR11808 , PDB:Structure:1CS1 , Pfam:IN-FAMILY:PF01053 , Prosite:IN-FAMILY:PS00868

In Paralogous Gene Group: 478 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for metB

GO Terms:

Biological Process: GO:0009086 - methionine biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Greene84]
GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0003962 - cystathionine gamma-synthase activity Inferred from experiment Inferred by computational analysis [GOA01, Holbrook90]
GO:0030170 - pyridoxal phosphate binding Inferred from experiment Inferred by computational analysis [GOA01a, Holbrook90]
GO:0042802 - identical protein binding Inferred from experiment [Holbrook90, Tran83]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism biosynthesis of building blocks amino acids methionine
metabolism carbon utilization amino acids
metabolism central intermediary metabolism threonine catabolism

Essentiality data for metB 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 No 37 Aerobic 7.2 0.35 No [Joyce06]
MOPS medium with 0.4% glucose Indeterminate 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
No [Feist07, Comment 4]

Last-Curated ? 26-Apr-2011 by Fulcher C , SRI International

Enzymatic reaction of: O-succinylhomoserine(thiol)-lyase

Synonyms: cystathionine γ-synthase, O-succinyl-L-homoserine succinate-lyase (adding cysteine), OSHS

EC Number:

L-cysteine + O-succinyl-L-homoserine <=> succinate + L-cystathionine + H+

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.

Alternative Substrates for O-succinyl-L-homoserine: O-acetyl-L-homoserine [Hacham03 ]

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

In this γ-replacement reaction the succinyl group of O-succinyl-L-homoserine is displaced by the thiol of L-cysteine to produce L-cystathionine [Aitken03]. There was no product inhibition with either L-cystathionine or succinate [Holbrook90].

Cofactors or Prosthetic Groups: pyridoxal 5'-phosphate [Holbrook90]

Cofactor Binding Comment: There is one pyridoxal phosphate cofactor per monomer. [Holbrook90, Martel87]

Kinetic Parameters:

Km (μM)

pH(opt): 7.8 [Holbrook90]

Enzymatic reaction of: O-succinylhomoserine lyase

EC Number: 4.3.1.-

O-succinyl-L-homoserine + H2O <=> 2-oxobutanoate + succinate + ammonium + H+

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 physiologically favored in the direction shown.

Alternative Substrates for O-succinyl-L-homoserine: vinylglycine [Holbrook90 ]

This γ-elimination (deamination) reaction occurs in the absence of L-cysteine. O-succinyl-L-homoserine is hydrolyzed to succinate, ammonia and 2-oxobutanoate (α-ketobutyrate) [Holbrook90, Aitken03].

Kinetic Parameters:

Km (μM)

pH(opt): 7.4 [Aitken03]

Sequence Features

Protein sequence of MetB with features indicated

Feature Class Location Citations Comment
N6-pyridoxal-phosphate-Lys-Modification 198
[Martel87, UniProt11a]
UniProt: N6-(pyridoxal phosphate)lysine.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b3939 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10582.


Aitken03: Aitken SM, Kim DH, Kirsch JF (2003). "Escherichia coli cystathionine gamma-synthase does not obey ping-pong kinetics. Novel continuous assays for the elimination and substitution reactions." Biochemistry 42(38);11297-306. PMID: 14503880

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

Brzovic90: Brzovic P, Holbrook EL, Greene RC, Dunn MF (1990). "Reaction mechanism of Escherichia coli cystathionine gamma-synthase: direct evidence for a pyridoxamine derivative of vinylglyoxylate as a key intermediate in pyridoxal phosphate dependent gamma-elimination and gamma-replacement reactions." Biochemistry 1990;29(2);442-51. PMID: 2405904

Clausen98: Clausen T, Huber R, Prade L, Wahl MC, Messerschmidt A (1998). "Crystal structure of Escherichia coli cystathionine gamma-synthase at 1.5 A resolution." EMBO J 17(23);6827-38. PMID: 9843488

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

Duchange83: Duchange N, Zakin MM, Ferrara P, Saint-Girons I, Park I, Tran SV, Py MC, Cohen GN (1983). "Structure of the metJBLF cluster in Escherichia coli K12. Sequence of the metB structural gene and of the 5'- and 3'-flanking regions of the metBL operon." J Biol Chem 1983;258(24);14868-71. PMID: 6361020

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

Farsi09: Farsi A, Lodha PH, Skanes JE, Los H, Kalidindi N, Aitken SM (2009). "Interconversion of a pair of active-site residues in Escherichia coli cystathionine gamma-synthase, E. coli cystathionine beta-lyase, and Saccharomyces cerevisiae cystathionine gamma-lyase and development of tools for the investigation of their mechanisms and reaction specificity." Biochem Cell Biol 87(2);445-57. PMID: 19370061

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

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."

Greene84: Greene RC, Smith AA (1984). "Insertion mutagenesis of the metJBLF gene cluster of Escherichia coli K-12: evidence for an metBL operon." J Bacteriol 1984;159(2);767-9. PMID: 6086586

Guggenheim69: Guggenheim S, Flavin M (1969). "Cystathionine gamma-synthase from Salmonella. Beta elimination and replacement reactions and inhibition by O-succinylserine." J Biol Chem 244(13);3722-7. PMID: 4893684

Hacham03: Hacham Y, Gophna U, Amir R (2003). "In vivo analysis of various substrates utilized by cystathionine gamma-synthase and O-acetylhomoserine sulfhydrylase in methionine biosynthesis." Mol Biol Evol 20(9);1513-20. PMID: 12832650

Holbrook90: Holbrook EL, Greene RC, Krueger JH (1990). "Purification and properties of cystathionine gamma-synthase from overproducing strains of Escherichia coli." Biochemistry 1990;29(2);435-42. PMID: 2405903

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

Martel87: Martel A, Bouthier de la Tour C, Le Goffic F (1987). "Pyridoxal 5'phosphate binding site of Escherichia coli beta cystathionase and cystathionine gamma synthase comparison of their sequences." Biochem Biophys Res Commun 1987;147(2);565-71. PMID: 3307782

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

Tran83: Tran SV, Schaeffer E, Bertrand O, Mariuzza R, Ferrara P (1983). "Appendix. Purification, molecular weight, and NH2-terminal sequence of cystathionine gamma-synthase of Escherichia coli." J Biol Chem 1983;258(24);14872-3. PMID: 6361021

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

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

Other References Related to Gene Regulation

Drazic13: Drazic A, Miura H, Peschek J, Le Y, Bach NC, Kriehuber T, Winter J (2013). "Methionine oxidation activates a transcription factor in response to oxidative stress." Proc Natl Acad Sci U S A 110(23);9493-8. PMID: 23690622

Gebendorfer12: Gebendorfer KM, Drazic A, Le Y, Gundlach J, Bepperling A, Kastenmuller A, Ganzinger KA, Braun N, Franzmann TM, Winter J (2012). "Identification of a Hypochlorite-specific Transcription Factor from Escherichia coli." J Biol Chem 287(9);6892-903. PMID: 22223481

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

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

Monsieurs05: Monsieurs P, De Keersmaecker S, Navarre WW, Bader MW, De Smet F, McClelland M, Fang FC, De Moor B, Vanderleyden J, Marchal K (2005). "Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium." J Mol Evol 60(4);462-74. PMID: 15883881

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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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