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Escherichia coli K-12 substr. MG1655 Enzyme: tryptophan synthase

Subunit composition of tryptophan synthase = [TrpA]2[(TrpB)2]
         tryptophan synthase, α subunit = TrpA (extended summary available)
         tryptophan synthase, β subunit dimer = (TrpB)2 (extended summary available)
                 tryptophan synthase, β subunit = TrpB

Summary:
The physiologically active form of tryptophan synthase is a tetrameric α22 complex consisting of two α subunits (the protein product of the trpA gene) and a dimer of two β subunits (the protein product of the trpB gene). This complex catalyzes the last two steps in the biosynthesis of tryptophan [Lane91].

Although the α22 complex from Escherichia coli has been well studied, the purified α22 complex from Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella typhimurium) provided crystals suitable for X-ray crystallography. Thus, the complex from this species has been studied in greater detail (reviewed in [Miles01, Dunn08]).

Molecular Weight: 146.5 kD (experimental) [Adachi74 ]

Gene-Reaction Schematic: ?

Credits:
Last-Curated ? 12-Feb-2010 by Fulcher C , SRI International


Enzymatic reaction of: tryptophan synthase

Synonyms: tryptophan desmolase, tryptophan synthetase

EC Number: 4.2.1.20

(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine <=> L-tryptophan + D-glyceraldehyde 3-phosphate + H2O

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. [Kirschner91]

In Pathways: superpathway of chorismate metabolism , superpathway of phenylalanine, tyrosine, and tryptophan biosynthesis , tryptophan biosynthesis

Summary:
The overall tryptophan synthase reaction consists of a sequence of two partial reactions. The α subunit of the complex carries out the aldol cleavage of indole-3-glycerol phosphate to indole + glyceraldehyde-3-phosphate. The β subunit is responsible for the synthesis of L-tryptophan from indole + L-serine. The α22 complex, which alone catalyzes the overall reaction, proceeds at two independent α/β sites via catalysis of the α reaction on the α subunit component, channeling the product (indole) to the pyridoxal 5'-phosphate site on the β component, where, in the presence of L-serine, it is converted to tryptophan [Lane83, Dunn90] and reviewed in [Miles99]. Indole does not appear in solution and is not a free intermediate [Crawford58]. There is apparent subunit communication mediated by transduced conformational changes between the subunits, whereby the rates of the α and β reactions are strongly enhanced by, respectively, the β and α subunits [Lim91a, Kirschner91].

The partial reaction catalyzed by the α subunit is reversible [Yutani87], whereas the partial reaction catalyzed by the β subunit and the overall reaction catalyzed by the α22 complex are considered to be practically irreversible (in [Kirschner91]).

Cofactors or Prosthetic Groups: pyridoxal 5'-phosphate [Miles77]

Cofactor Binding Comment: Pyridoxal phosphate derivatives are much more strongly bound to the complex than to the beta subunit. This finding indicates that strong binding forces, in addition to the Schiff base linkage, exist in the complex, but not in the beta subunit. When this bond is broken during the formation of a derivative, the derivative is only weakly bound to the beta subunit, but is stongly bound to the complex by additional forces.[Miles77]

T(opt): 40 °C [Bang83, BRENDA14, Zhao11a]

pH(opt): 8 [BRENDA14, Zhao11a]


Component enzyme of tryptophan synthase : tryptophan synthase, α subunit

Synonyms: Try, TrpA, α subunit, TSase α, A protein

Gene: trpA Accession Numbers: EG11024 (EcoCyc), b1260, ECK1254

Locations: cytosol

Sequence Length: 268 AAs

Molecular Weight: 28.724 kD (from nucleotide sequence)

Molecular Weight: 30.0 kD (experimental) [Gschwind79]

pI: 5.54

GO Terms:

Biological Process: GO:0000162 - tryptophan biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, GOA06, Yanofsky93]
GO:0009073 - aromatic amino acid family biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Yanofsky93]
GO:0006568 - tryptophan metabolic process Inferred by computational analysis [GOA01a]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0016829 - lyase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Kirschner91]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0004834 - tryptophan synthase activity Inferred by computational analysis [GOA06, GOA01, GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Murphy69]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]

MultiFun Terms: metabolism biosynthesis of building blocks amino acids tryptophan

Unification Links: DIP:DIP-35957N , DisProt:DP00252 , EcoliWiki:b1260 , ModBase:P0A877 , PR:PRO_000024117 , Pride:P0A877 , Protein Model Portal:P0A877 , RefSeq:NP_415776 , SMR:P0A877 , String:511145.b1260 , UniProt:P0A877

Relationship Links: InterPro:IN-FAMILY:IPR002028 , InterPro:IN-FAMILY:IPR011060 , InterPro:IN-FAMILY:IPR013785 , InterPro:IN-FAMILY:IPR018204 , PDB:Structure:1V7Y , PDB:Structure:1WQ5 , PDB:Structure:1XC4 , PDB:Structure:1XCF , Pfam:IN-FAMILY:PF00290 , Prosite:IN-FAMILY:PS00167

Catalyzes:
(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate ↔ indole + D-glyceraldehyde 3-phosphate

Summary:
The TrpA polypeptide (TSase α) functions as the α subunit of the tetrameric (α22) tryptophan synthase complex [Miles77]. As a purified protein, the α subunit is a monomer. TSase α contains the binding site for indole-3-glycerol-phosphate (InGP) and can carry out the cleavage reaction of InGP to indole and glyceraldehyde-3-phosphate, also termed the α reaction. Within the physiological complex with the β subunit, the reaction rate is increased by 1-2 orders of magnitude (in [Kirschner91]).

TrpA has been shown to lack tryptophan residues [Henning62]. Numerous TrpA mutant studies have examined structure-function relationships in this protein. Mutations that affect catalytic activity [Hiraga96, Sarker95, Lim91, Milton86, Yutani87, Yee96, Yanofsky93, Lim91a], subunit interactions [Swift92, Lim91a], conformational stability [Hiraga96a, Lim92] and folding [Kim01a, Lim91a] have been identified.

The crystal structure of the wild-type TrpA protein has been reported at 2.8 Å resolution [Jeong04a, Jeong04], 2.5 Å resolution [Jeong05] and 2.3 Å resolution [Nishio05]. The crystal structure of a double mutant TrpA protein has been reported at 1.8 Å resolution [Jeong04, Jeong05].

The TrpA protein has been structurally classified as a (beta alpha)(8) TIM barrel protein, a member of the common TIM barrel superfamily. Nuclear magnetic resonance spectroscopic techniques have been used to investigate its equilibrium folding mechanism in order to obtain insights into the development of structure and stability [Vadrevu08]. Many previous studies of the folding mechanism of recombinant wild-type and mutant TrpA proteins using various biophysical techniques identified intermediates in the folding pathway, for example [Beasty86, Choi95, Gualfetti99, Jeong03, Wintrode05, Wu05b, Wu07].

Essentiality data for trpA 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]

Component enzyme of tryptophan synthase : tryptophan synthase, β subunit dimer

Synonyms: β subunit, TSase β2, B protein, β2 protein

Gene: trpB Accession Numbers: EG11025 (EcoCyc), b1261, ECK1255

Locations: cytosol

Subunit composition of tryptophan synthase, β subunit dimer = [TrpB]2
         tryptophan synthase, β subunit = TrpB

Map Position: [1,315,246 <- 1,316,439] (28.35 centisomes)
Length: 1194 bp / 397 aa

Molecular Weight of Polypeptide: 42.983 kD (from nucleotide sequence), 44.0 kD (experimental) [Gschwind79 ]

Molecular Weight of Multimer: 89.0 kD (experimental) [Adachi74]

pI: 6.04

GO Terms:

Biological Process: GO:0000162 - tryptophan biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, GOA06, GOA01a, Zhao93]
GO:0009073 - aromatic amino acid family biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Zhao93]
GO:0006568 - tryptophan metabolic process Inferred by computational analysis [GOA01a]
GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0004834 - tryptophan synthase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Kaufmann91]
GO:0030170 - pyridoxal phosphate binding Inferred from experiment [Higgins78]
GO:0042802 - identical protein binding Inferred from experiment [Nishio10]
GO:0042803 - protein homodimerization activity Inferred from experiment [Hathaway70]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Murphy69]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, LopezCampistrou05]

MultiFun Terms: metabolism biosynthesis of building blocks amino acids tryptophan

Unification Links: EcoliWiki:b1261 , Mint:MINT-7711989 , ModBase:P0A879 , PR:PRO_000024118 , Pride:P0A879 , Protein Model Portal:P0A879 , RefSeq:NP_415777 , SMR:P0A879 , String:511145.b1261 , Swiss-Model:P0A879 , UniProt:P0A879

Relationship Links: InterPro:IN-FAMILY:IPR001926 , InterPro:IN-FAMILY:IPR006653 , InterPro:IN-FAMILY:IPR006654 , InterPro:IN-FAMILY:IPR023026 , Panther:IN-FAMILY:PTHR10314:SF3 , PDB:Structure:2DH5 , PDB:Structure:2DH6 , Pfam:IN-FAMILY:PF00291 , Prosite:IN-FAMILY:PS00168

Catalyzes:
indole + L-serine → L-tryptophan + H2O

Summary:
The TrpB polypeptide functions as the β subunit of the tetrameric (α22) tryptophan synthase complex [Hathaway70]. The TrpB protein forms a homodimer (TSase β2) in which each subunit contains a molecule of the cofactor pyridoxal 5'-phosphate (PLP) covalently linked to the ε-amino group of a lysine residue via a Schiff base [Bartholmes76]. This complex catalyzes the synthesis of L-tryptophan from indole and L-serine, also termed the β reaction.

The β2 subunit possesses binding sites for L-serine and PLP and can catalyze a variety of reactions involving these compounds [Tanizawa83].

The apo-β2 subunit has been used as a model system to study the mechanism of folding of protein oligomers [Planchenault96].

The crystal structure of the holo-tryptophan synthase β-subunit from Escherichia coli has been determined (see links to PDB: 2DH5, 2DH6), but a paper has not yet been published.

Gene Citations: [Yanofsky81, Yanofsky66, Imamoto65, Imamoto66]

Essentiality data for trpB 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]

References

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Bartholmes76: Bartholmes P, Kirschner K, Gschwind HP (1976). "Cooperative and noncooperative binding of pyridoxal 5'-phosphate to tryptophan synthase from Escherichia coli." Biochemistry 15(21);4712-7. PMID: 788781

Beasty86: Beasty AM, Hurle MR, Manz JT, Stackhouse T, Onuffer JJ, Matthews CR (1986). "Effects of the phenylalanine-22----leucine, glutamic acid-49----methionine, glycine-234----aspartic acid, and glycine-234----lysine mutations on the folding and stability of the alpha subunit of tryptophan synthase from Escherichia coli." Biochemistry 25(10);2965-74. PMID: 2872918

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Wu07: Wu Y, Vadrevu R, Kathuria S, Yang X, Matthews CR (2007). "A tightly packed hydrophobic cluster directs the formation of an off-pathway sub-millisecond folding intermediate in the alpha subunit of tryptophan synthase, a TIM barrel protein." J Mol Biol 366(5);1624-38. PMID: 17222865

Yanofsky66: Yanofsky C, Ito J (1966). "Nonsense codons and polarity in the tryptophan operon." J Mol Biol 21(2);313-34. PMID: 5339605

Yanofsky81: Yanofsky C, Platt T, Crawford IP, Nichols BP, Christie GE, Horowitz H, VanCleemput M, Wu AM (1981). "The complete nucleotide sequence of the tryptophan operon of Escherichia coli." Nucleic Acids Res 1981;9(24);6647-68. PMID: 7038627

Yanofsky93: Yanofsky C, Yee MC, Horn V (1993). "Partial revertants of tryptophan synthetase alpha chain active site mutant Asp60-->Asn." J Biol Chem 268(11);8213-20. PMID: 8463331

Yee96: Yee MC, Horn V, Yanofsky C (1996). "On the role of helix 0 of the tryptophan synthetase alpha chain of Escherichia coli." J Biol Chem 271(25);14754-63. PMID: 8662916

Yutani87: Yutani K, Ogasahara K, Tsujita T, Kanemoto K, Matsumoto M, Tanaka S, Miyashita T, Matsushiro A, Sugino Y, Miles EW (1987). "Tryptophan synthase alpha subunit glutamic acid 49 is essential for activity. Studies with 19 mutants at position 49." J Biol Chem 262(28);13429-33. PMID: 2888759

Zhao11a: Zhao G, Liu J, Dong K, Zhang F, Zhang H, Liu Q, Jiao Q (2011). "Enzymatic synthesis of L-tryptophan from hair acid hydrolysis industries wastewater with tryptophan synthase." Bioresour Technol 102(3);3554-7. PMID: 20884203

Zhao93: Zhao GP, Somerville RL (1993). "A single amino acid switch within the "hinge" region of the tryptophan synthase beta subunit of Escherichia coli that leads to diminished association with alpha subunit and arrested conversion of ESII to product." J Biol Chem 268(20);14921-31. PMID: 8325869


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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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