Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

MetaCyc Enzyme: tryptophan synthase, β subunit dimer

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

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

Species: Escherichia coli K-12 substr. MG1655

Component of: tryptophan synthase (summary available)

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

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.

Locations: cytosol

Map Position: [1,315,246 <- 1,316,439]

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

Unification Links: ASAP:ABE-0004234 , CGSC:73 , EchoBASE:EB1018 , EcoGene:EG11025 , EcoliWiki:b1261 , Mint:MINT-7711989 , ModBase:P0A879 , OU-Microarray:b1261 , PortEco:trpB , PR:PRO_000024118 , Pride:P0A879 , Protein Model Portal:P0A879 , RefSeq:NP_415777 , RegulonDB:EG11025 , 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

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0000162 - tryptophan biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProt-GOA, 2011, GOA06, GOA et al., 2001, Zhao93]
GO:0009073 - aromatic amino acid family biosynthetic process Inferred from experiment Inferred by computational analysis [UniProt-GOA, 2011, Zhao93]
GO:0006568 - tryptophan metabolic process Inferred by computational analysis [GOA et al., 2001]
GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProt-GOA, 2011]
Molecular Function: GO:0004834 - tryptophan synthase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA et al., 2001, 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 [UniProt-GOA, 2011]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Murphy69]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [Diaz-Mejia et al., 2009, LopezCampistrou05]

MultiFun Terms: metabolism biosynthesis of building blocks amino acids tryptophan

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: tryptophan synthase

EC Number: 4.2.1.122

L-serine + indole <=> L-tryptophan + 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 , superpathway of tryptophan biosynthesis , tryptophan biosynthesis

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Summary:
In this reaction indole condenses with L-serine to produce L-tryptophan. The ability of the isolated, purified holo-β2-subunit of tryptophan synthase (containing two molecules of pyridoxal 5'-phosphate bound per dimer) to catalyze this reaction was shown in experiments that compared the activities of native holo-β2-subunit and holo-β2-subunit proteolytically nicked at E-296 [Kaufmann91].

This β subunit-catalyzed partial reaction is considered to be practically irreversible (in [Lane91]).

Cofactors or Prosthetic Groups: pyridoxal 5'-phosphate [Kaufmann91]

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

pH(opt): 8 [BRENDA14, Zhao11a]


Subunit of: tryptophan synthase

Species: Escherichia coli K-12 substr. MG1655

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]

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , 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 , superpathway of tryptophan biosynthesis , tryptophan biosynthesis

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

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]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Higgins80, Link97, UniProt11]
UniProt: Removed.
Chain 2 -> 397
[UniProt, 2009]
UniProt: Tryptophan synthase beta chain;
Active-Site 62
[Higgins80, UniProt11]
UniProt: Nucleophile.
Sequence-Conflict 78
[Higgins80, UniProt, 2010]
Alternate sequence: K; UniProt: (in Ref. 7; AA sequence);
Active-Site 86
[UniProt10]
UniProt: Proton donor; Non-Experimental Qualifier: probably;
N6-pyridoxal-phosphate-Lys-Modification 87
[UniProt11a]
UniProt: N6-(pyridoxal phosphate)lysine; Non-Experimental Qualifier: by similarity.
Extrinsic-Sequence-Variant 281
[UniProt, 2010]
Alternate sequence: R; UniProt: (in mutant TRPB8);
Sequence-Conflict 365
[Cotton72, UniProt11]
Alternate sequence: Z; UniProt: (in Ref. 10; AA sequence).
Sequence-Conflict 368 -> 369
[Cotton72, UniProt11]
Alternate sequence: BK; UniProt: (in Ref. 10; AA sequence).

History:
10/20/97 Gene b1261 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11025; confirmed by SwissProt match.


References

Adachi74: Adachi O, Kohn LD, Miles EW (1974). "Crystalline alpha2 beta2 complexes of tryptophan synthetase of Escherichia coli. A comparison between the native complex and the reconstituted complex." J Biol Chem 249(24);7756-63. PMID: 4609974

Bang83: Bang WG, Lang S, Sahm H, Wagner F (1983). "Production L-tryptophan by Escherichia coli cells." Biotechnol Bioeng 25(4);999-1011. PMID: 18548715

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

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

Cotton72: Cotton RG, Crawford IP (1972). "Tryptophan synthetase B 2 subunit. Application of genetic analysis to the study of primary structure." J Biol Chem 247(6);1883-91. PMID: 4552018

Crawford58: Crawford IP, Yanofsky C (1958). "ON THE SEPARATION OF THE TRYPTOPHAN SYNTHETASE OF ESCHERICHIA COLI INTO TWO PROTEIN COMPONENTS." Proc Natl Acad Sci U S A 44(12);1161-70. PMID: 16590328

Diaz-Mejia et al., 2009: 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

Dunn08: Dunn MF, Niks D, Ngo H, Barends TR, Schlichting I (2008). "Tryptophan synthase: the workings of a channeling nanomachine." Trends Biochem Sci 33(6);254-64. PMID: 18486479

Dunn90: Dunn MF, Aguilar V, Brzovic P, Drewe WF, Houben KF, Leja CA, Roy M (1990). "The tryptophan synthase bienzyme complex transfers indole between the alpha- and beta-sites via a 25-30 A long tunnel." Biochemistry 29(37);8598-607. PMID: 2271543

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

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

Gschwind79: Gschwind HP, Gschwind U, Paul CH, Kirschner K (1979). "Affinity chromatography of tryptophan synthase from Escherichia coli. Systematic studies with immobilized tryptophanol phosphate." Eur J Biochem 96(2);403-16. PMID: 378665

Hathaway70: Hathaway GM, Crawford IP (1970). "Studies on the association of beta-chain monomers of Escherichia coli tryptophan synthetase." Biochemistry 9(8);1801-8. PMID: 4909082

Higgins78: Higgins W, Miles EW (1978). "Affinity labeling of the pyridoxal phosphate binding site of the beta2 subunit of Escherichia coli tryptophan synthase." J Biol Chem 253(13);4648-52. PMID: 350880

Higgins80: Higgins W, Miles EW, Fairwell T (1980). "Location of three active site residues in the NH2-terminal sequence of the beta 2 subunit tryptophan synthase from Escherichia coli." J Biol Chem 255(2);512-7. PMID: 6985892

Kaufmann91: Kaufmann M, Schwarz T, Jaenicke R, Schnackerz KD, Meyer HE, Bartholmes P (1991). "Limited proteolysis of the beta 2-dimer of tryptophan synthase yields an enzymatically active derivative that binds alpha-subunits." Biochemistry 30(17);4173-9. PMID: 2021608

Kirschner91: Kirschner K, Lane AN, Strasser AW (1991). "Reciprocal communication between the lyase and synthase active sites of the tryptophan synthase bienzyme complex." Biochemistry 1991;30(2);472-8. PMID: 1899027

Lane83: Lane AN, Kirschner K (1983). "The catalytic mechanism of tryptophan synthase from Escherichia coli. Kinetics of the reaction of indole with the enzyme--L-serine complexes." Eur J Biochem 129(3);571-82. PMID: 6402362

Lane91: Lane AN, Kirschner K (1991). "Mechanism of the physiological reaction catalyzed by tryptophan synthase from Escherichia coli." Biochemistry 30(2);479-84. PMID: 1899028

Lim91a: Lim WK, Shin HJ, Milton DL, Hardman JK (1991). "Relative activities and stabilities of mutant Escherichia coli tryptophan synthase alpha subunits." J Bacteriol 1991;173(6);1886-93. PMID: 2001993

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

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Miles01: Miles EW (2001). "Tryptophan synthase: a multienzyme complex with an intramolecular tunnel." Chem Rec 1(2);140-51. PMID: 11893063

Miles77: Miles EW, Moriguchi M (1977). "Tryptophan synthase of Escherichia coli. Removal of pyridoxal 5'-phosphate and separation of the alpha and beta2 subunits." J Biol Chem 1977;252(19);6594-9. PMID: 330534

Miles99: Miles EW, Rhee S, Davies DR (1999). "The molecular basis of substrate channeling." J Biol Chem 274(18);12193-6. PMID: 10212181

Murphy69: Murphy TM, Mills SE (1969). "Immunochemical and enzymatic comparisons of the tryptophan synthase alpha subunits from five species of Enterobacteriaceae." J Bacteriol 97(3);1310-20. PMID: 4887511

Nishio10: Nishio K, Ogasahara K, Morimoto Y, Tsukihara T, Lee SJ, Yutani K (2010). "Large conformational changes in the Escherichia coli tryptophan synthase beta(2) subunit upon pyridoxal 5'-phosphate binding." FEBS J 277(9);2157-70. PMID: 20370823

Planchenault96: Planchenault T, Navon A, Schulze AJ, Goldberg ME (1996). "Transient non-native interactions in early folding intermediates do not influence the folding kinetics of Escherichia coli tryptophan synthase beta 2 subunits." Eur J Biochem 240(3);615-21. PMID: 8856062

Tanizawa83: Tanizawa K, Miles EW (1983). "L-serine binds to arginine-148 of the beta 2 subunit of Escherichia coli tryptophan synthase." Biochemistry 22(15);3594-603. PMID: 6412746

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

UniProt, 2010: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

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

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

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


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Thu Dec 18, 2014, biocyc11.