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MetaCyc Enzyme: indole-3-glycerol phosphate synthase / phosphoribosylanthranilate isomerase

Gene: trpC Accession Numbers: EG11026 (MetaCyc), b1262, ECK1256

Synonyms: trpF, trpCF

Species: Escherichia coli K-12 substr. MG1655

Summary:
Bifunctional phosphoribosylanthranilate isomerase / indole-3-glycerol phosphate synthase (TrpC) carries out the third and fourth steps in the tryptophan biosynthesis pathway.

The phosphoribosylanthranilate isomerase activity of TrpC catalyzes the Amadori rearrangement of its substrate into carboxyphenylaminodeoxyribulose phosphate [White82, Smith67]. The indole-glycerol phosphate synthase activity of TrpC catalyzes the ring closure of this product to yield indole-3-glycerol phosphate [White82, Smith67, Creighton66].

Early mutant studies identified N-(5'-phosphoribosyl)-anthranilate (PRA) [Doy61] and 1-(o-carboxyphenylamino)-1'-deoxyribulose-5'-phosphate (CDRP) [Smith60] as intermediates in the biosynthesis of tryptophan and provided evidence that a single polypeptide chain catalyzes both the conversion of PRA to CDRP and CDRP to indole-3-glycerol-phosphate (IGP) [Smith67]. These observations were confirmed by kinetic and mutant complementation studies which further demonstrated that the two reactions occur at two distinct, non-overlapping sites on the polypeptide and that CDRP is a free intermediate [Creighton70].

Subsequent kinetic and ligand binding studies of the Escherichia coli enzyme, an excised PRA isomerase domain of this enzyme, and the naturally monofunctional PRA isomerase of Saccharomyces cerevisiae led to a proposed mechanism for the PRA isomerase reaction. Interestingly, in this mechanism, the spontaneous conversion of putative enol and keto tautomers of CDRP may limit the rate of tryptophan biosynthesis [Hommel95]. In addition, studies involving expression of engineered monofunctional domains of the E. coli enzyme suggested that the PRA isomerase domain may stabilize the IGP synthase domain [Eberhard95]. Structural and kinetic studies of mutants allowed identification of catalytically important residues for the IGP synthase reaction [Darimont98].

A number of structural studies show that TrpC has two individual domains, each catalyzing one of its two activities. Crystal structures to 2, 2.8, and 4 Å resolution, as well as protease studies, show that the two TrpC domains are distinct, each with a folding pattern of an 8-fold parallel β-α barrel [Kirschner80, Priestle87, Eberhard89, Wilmanns90, Wilmanns92]. The amino-terminal domain carries out the synthase activity and the carboxy-terminal domain carries out the isomerase activity [Eberhard89]. The two active sites face away from each other, presumably precluding direct transfer of carboxyphenylaminodeoxyribulose phosphate from the isomerase site to the synthase site [Priestle87]. The isolated synthase domain is unstable, suggesting that the combined domains may mutually stabilize each other [Kirschner80, Priestle87].

Like the α subunit of E. coli tryptophan synthase (TrpA), both the PRA isomerase and IGP synthase domains of E. coli TrpC contain the common (β/α)8-barrel (TIM barrel) protein fold (in [Darimont98]). The PRA isomerase domain is of interest in the study of protein folding/unfolding pathways and their intermediates [Akanuma05] as well as in studies of molecular evolution [Akanuma08]. In addition, this fold in the IGP synthase domain has been used in studies of protein stability [Yang09a].

TrpC is unique among the five enzymes in the tryptophan biosynthesis pathway in that it is not part of a multisubunit enzyme complex [Christie80].

Locations: cytosol

Map Position: [1,316,451 <- 1,317,809]

Molecular Weight of Polypeptide: 49.361 kD (from nucleotide sequence), 45.0 kD (experimental) [Creighton66 ]

pI: 5.94

Unification Links: ASAP:ABE-0004238 , CGSC:72 , EchoBASE:EB1019 , EcoGene:EG11026 , EcoliWiki:b1262 , ModBase:P00909 , OU-Microarray:b1262 , PortEco:trpC , PR:PRO_000024119 , Pride:P00909 , Protein Model Portal:P00909 , RefSeq:NP_415778 , RegulonDB:EG11026 , SMR:P00909 , String:511145.b1262 , UniProt:P00909

Relationship Links: InterPro:IN-FAMILY:IPR001240 , InterPro:IN-FAMILY:IPR001468 , InterPro:IN-FAMILY:IPR011060 , InterPro:IN-FAMILY:IPR013785 , InterPro:IN-FAMILY:IPR013798 , PDB:Structure:1JCM , PDB:Structure:1PII , PDB:Structure:2KZH , Pfam:IN-FAMILY:PF00218 , Pfam:IN-FAMILY:PF00697 , Prosite:IN-FAMILY:PS00614

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0000162 - tryptophan biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11, Smith67]
GO:0006568 - tryptophan metabolic process Inferred by computational analysis [GOA01]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11]
GO:0009073 - aromatic amino acid family biosynthetic process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0004425 - indole-3-glycerol-phosphate synthase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Creighton66]
GO:0004640 - phosphoribosylanthranilate isomerase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Hommel95, Smith67]
GO:0003824 - catalytic activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11]
GO:0016831 - carboxy-lyase activity Inferred by computational analysis [UniProtGOA11]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

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: indole-3-glycerol phosphate synthase

Synonyms: IGP synthase, indole-3-glycerol phosphate synthetase, indoleglycerol phosphate synthase

EC Number: 4.1.1.48

1-(o-carboxyphenylamino)-1'-deoxyribulose 5'-phosphate + H+ <=> (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O

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 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 the indole-glycerol phosphate synthase reaction catalyzed by TrpC the substrate 1-(o-carboxyphenylamino)-1'-deoxyribulose-5'-phosphate undergoes an irreversible ring closure to yield indole-3-glycerol-phosphate, carbon dioxide and water (in [Darimont98]).

No cofactors or metal ions have been identified as essential for catalysis [Eberhard89].

Inhibitors (Unknown Mechanism): 3-methylanthranilate [Smith62a] , 4-methylanthranilate [Smith62a] , 5-methylanthranilate [Smith62a] , 5-fluoroanthranilate [Smith62a] , rCdRP [Priestle87] , anthranilate [Smith62a]

Kinetic Parameters:

Substrate
Km (μM)
Citations
1-(o-carboxyphenylamino)-1'-deoxyribulose 5'-phosphate
5.0
[Creighton66]


Enzymatic reaction of: phosphoribosylanthranilate isomerase

Synonyms: PRA isomerase, PRAI, N-(5'-phosphoribosyl) anthranilate isomerase, phosphoribosyl anthranilate isomerase

EC Number: 5.3.1.24

N-(5-phosphoribosyl)-anthranilate <=> 1-(o-carboxyphenylamino)-1'-deoxyribulose 5'-phosphate

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 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 N-(5'-phosphoribosyl)-anthranilate isomerase reaction catalyzed by TrpC is an intramolecular redox reaction, also known as an Amadori rearrangement. The proposed mechanism favors the direction of 1-(o-carboxyphenylamino)-1'-deoxyribulose-5'-phosphate formation (in [Hommel95]).


Sequence Features

Feature Class Location Citations Comment
Protein-Segment 1 -> 256
[UniProt10a]
UniProt: Indole-3-glycerol phosphate synthase; Sequence Annotation Type: region of interest;
Sequence-Conflict 30
[Yanofsky81, UniProt10]
Alternate sequence: missing; UniProt: (in Ref. 3; CAA23673);
Sequence-Conflict 94
[Christie80, Yanofsky81, UniProt10]
Alternate sequence: R; UniProt: (in Ref. 1; CAA23664/AAA57299 and 3; CAA23673);
Protein-Segment 257 -> 452
[UniProt10a]
UniProt: N-(5'-phosphoribosyl)anthranilate isomerase; Sequence Annotation Type: region of interest;
Sequence-Conflict 284
[Yanofsky81, UniProt10]
Alternate sequence: missing; UniProt: (in Ref. 3; CAA23673);
Sequence-Conflict 293
[Yanofsky81, UniProt10]
Alternate sequence: D; UniProt: (in Ref. 3; CAA23673);
Sequence-Conflict 329
[Christie80, Yanofsky81, UniProt10]
Alternate sequence: V; UniProt: (in Ref. 1; CAA23664/AAA57299 and 3; CAA23673);
Sequence-Conflict 398
[Milkman93, Christie80, Yanofsky81, UniProt10]
Alternate sequence: T; UniProt: (in Ref. 1; CAA23664/AAA57299, 3; CAA23673 and 4; AAB60033);

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b1262 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11026; confirmed by SwissProt match.


References

Akanuma05: Akanuma S, Miyagawa H, Kitamura K, Yamagishi A (2005). "A detailed unfolding pathway of a (beta/alpha)8-barrel protein as studied by molecular dynamics simulations." Proteins 58(3);538-46. PMID: 15614829

Akanuma08: Akanuma S, Yamagishi A (2008). "Experimental evidence for the existence of a stable half-barrel subdomain in the (beta/alpha)8-barrel fold." J Mol Biol 382(2);458-66. PMID: 18674541

Christie80: Christie GE, Platt T (1980). "Gene structure in the tryptophan operon of Escherichia coli. Nucleotide sequence of trpC and the flanking intercistronic regions." J Mol Biol 1980;142(4);519-30. PMID: 7007653

Creighton66: Creighton TE, Yanofsky C (1966). "Indole-3-glycerol phosphate synthetase of Escherichia coli, an enzyme of the tryptophan operon." J Biol Chem 241(20);4616-24. PMID: 5332729

Creighton70: Creighton TE (1970). "N-(5'-phosphoribosyl)anthranilate isomerase-indol-3-ylglycerol phosphate synthetase of tryptophan biosynthesis. Relationship between the two activities of the enzyme from Escherichia coli." Biochem J 120(4);699-707. PMID: 4924490

Darimont98: Darimont B, Stehlin C, Szadkowski H, Kirschner K (1998). "Mutational analysis of the active site of indoleglycerol phosphate synthase from Escherichia coli." Protein Sci 7(5);1221-32. PMID: 9605328

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

Doy61: Doy CH, Rivera A, Srinivasan PR (1961). "Evidence for the enzymatic synthesis of N-(5'-phosphoribosyl) anthranilic acid, a new intermediate in tryptophan biosynthesis." Biochem Biophys Res Commun 4;83-8. PMID: 13724174

Eberhard89: Eberhard M, Kirschner K (1989). "Modification of a catalytically important residue of indoleglycerol-phosphate synthase from Escherichia coli." FEBS Lett 1989;245(1-2);219-22. PMID: 2494074

Eberhard95: Eberhard M, Tsai-Pflugfelder M, Bolewska K, Hommel U, Kirschner K (1995). "Indoleglycerol phosphate synthase-phosphoribosyl anthranilate isomerase: comparison of the bifunctional enzyme from Escherichia coli with engineered monofunctional domains." Biochemistry 34(16);5419-28. PMID: 7727400

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.

Hommel95: Hommel U, Eberhard M, Kirschner K (1995). "Phosphoribosyl anthranilate isomerase catalyzes a reversible amadori reaction." Biochemistry 34(16);5429-39. PMID: 7727401

Kirschner80: Kirschner K, Szadkowski H, Henschen A, Lottspeich F (1980). "Limited proteolysis of N-(5'-phosphoribosyl)anthranilate isomerase: indoleglycerol phosphate synthase from Escherichia coli yields two different enzymically active, functional domains." J Mol Biol 143(4);395-409. PMID: 7014916

Milkman93: Milkman R, Bridges MM (1993). "Molecular evolution of the Escherichia coli chromosome. IV. Sequence comparisons." Genetics 133(3);455-68. PMID: 8095913

Priestle87: Priestle JP, Grutter MG, White JL, Vincent MG, Kania M, Wilson E, Jardetzky TS, Kirschner K, Jansonius JN (1987). "Three-dimensional structure of the bifunctional enzyme N-(5'-phosphoribosyl)anthranilate isomerase-indole-3-glycerol-phosphate synthase from Escherichia coli." Proc Natl Acad Sci U S A 1987;84(16);5690-4. PMID: 3303031

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Smith60: Smith OH, Yanofsky C (1960). "1-(o-Carboxyphenylamino)-1-deoxyribulose 5-phosphate, a new intermediate in the biosynthesis of tryptophan." J Biol Chem 235;2051-7. PMID: 13832114

Smith62a: Smith OH, Yanofsky C "Enzymes involved in the biosynthesis of tryptophan." Methods in Enzymology 1962; V:794-806.

Smith67: Smith OH (1967). "Structure of the trpC cistron specifying indoleglycerol phosphate synthetase, and its localization in the tryptophan operon of Escherichia coli." Genetics 57(1);95-105. PMID: 4865047

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

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

White82: White JL, Grutter MG, Wilson E, Thaller C, Ford GC, Smit JDG, Jansonius JN, Kirschner K "Crystallization and preliminary X-ray crystallographic data of the bifunctional enzyme phosphoribosyl-anthranilate isomerase-indole-3-glycerol-phosphate synthase from Escherichia coli." FEBS Lett 1982;148:87-90.

Wilmanns90: Wilmanns M, Schlagenhauf E, Fol B, Jansonius JN (1990). "Crystallization and structure solution at 4 A resolution of the recombinant synthase domain of N-(5'-phosphoribosyl)anthranilate isomerase:indole-3-glycerol-phosphate synthase from Escherichia coli complexed to a substrate analogue." Protein Eng 3(3);173-80. PMID: 2184433

Wilmanns92: Wilmanns M, Priestle JP, Niermann T, Jansonius JN (1992). "Three-dimensional structure of the bifunctional enzyme phosphoribosylanthranilate isomerase: indoleglycerolphosphate synthase from Escherichia coli refined at 2.0 A resolution." J Mol Biol 223(2);477-507. PMID: 1738159

Yang09a: Yang X, Kathuria SV, Vadrevu R, Matthews CR (2009). "Betaalpha-hairpin clamps brace betaalphabeta modules and can make substantive contributions to the stability of TIM barrel proteins." PLoS One 4(9);e7179. PMID: 19787060

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


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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 Tue Nov 25, 2014, BIOCYC13B.