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Escherichia coli K-12 substr. MG1655 Enzyme: anthranilate synthase component II



Gene: trpD Accession Numbers: EG11027 (EcoCyc), b1263, ECK1257

Synonyms: trpGD

Regulation Summary Diagram: ?

Component of: anthranilate synthase (extended summary available)

Summary:
Anthranilate phosphoribosyl transferase (TrpD) catalyzes the second step in the pathway of tryptophan biosynthesis.

TrpD catalyzes a phosphoribosyltransferase reaction that generates N-(5'-phosphoribosyl)-anthranilate [Gonzalez86].

The phosphoribosyl transferase and anthranilate synthase contributing portions of TrpD are present in different portions of the protein. The anthranilate synthase reaction requires the amino-terminal portion of the protein, whereas the phosphoribosyltransferase reaction requires the carboxy-terminal region [Jackson74].

Gene Citations: [Imamoto66, Imamoto65, Yanofsky66]

Locations: cytosol

Map Position: [1,317,813 <- 1,319,408] (28.4 centisomes)
Length: 1596 bp / 531 aa

Molecular Weight of Polypeptide: 56.87 kD (from nucleotide sequence)

pI: 6.47

Unification Links: ASAP:ABE-0004241 , CGSC:71 , EchoBASE:EB1020 , EcoGene:EG11027 , EcoliWiki:b1263 , ModBase:P00904 , OU-Microarray:b1263 , PortEco:trpD , PR:PRO_000024120 , Pride:P00904 , Protein Model Portal:P00904 , RefSeq:NP_415779 , RegulonDB:EG11027 , SMR:P00904 , String:511145.b1263 , Swiss-Model:P00904 , UniProt:P00904

Relationship Links: InterPro:IN-FAMILY:IPR000312 , InterPro:IN-FAMILY:IPR005940 , InterPro:IN-FAMILY:IPR006221 , InterPro:IN-FAMILY:IPR017459 , InterPro:IN-FAMILY:IPR017926 , Pfam:IN-FAMILY:PF00117 , Pfam:IN-FAMILY:PF00591 , Pfam:IN-FAMILY:PF02885 , Prosite:IN-FAMILY:PS51273

In Paralogous Gene Group: 9 (5 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0000162 - tryptophan biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, GOA06, GOA01a, Ito66, Gonzalez86, Ito69]
GO:0006541 - glutamine metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11a]
GO:0009073 - aromatic amino acid family biosynthetic process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0004048 - anthranilate phosphoribosyltransferase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Gonzalez86]
GO:0004049 - anthranilate synthase activity Inferred from experiment Inferred by computational analysis [GOA01, Ito69]
GO:0000287 - magnesium ion binding Inferred by computational analysis [GOA06]
GO:0003824 - catalytic activity Inferred by computational analysis [UniProtGOA11a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016757 - transferase activity, transferring glycosyl groups Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol

MultiFun Terms: metabolism biosynthesis of building blocks amino acids tryptophan

Essentiality data for trpD 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]

Credits:
Curated 01-Jul-2008 by Shearer A , SRI International
Last-Curated ? 12-Feb-2010 by Fulcher C , SRI International


Enzymatic reaction of: anthranilate phosphoribosyl transferase (anthranilate synthase component II)

Synonyms: N-(5-phospho-D-ribosyl)-anthranilate:pyrophosphate phospho-α-D-ribosyltransferase, phosphoribosyl-anthranilate pyrophosphorylase

EC Number: 2.4.2.18

N-(5-phosphoribosyl)-anthranilate + diphosphate <=> anthranilate + 5-phospho-α-D-ribose 1-diphosphate

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 opposite direction.

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

Summary:
Tryptophan is a competitive inhibitor with respect to 5-phosphoribosyl 1-pyrophosphate. The Ki for this inhibition is 0.5 µM [Gonzalez86].

Kinetic Parameters:

Substrate
Km (μM)
Citations
anthranilate
0.58
[Gonzalez86]
5-phospho-α-D-ribose 1-diphosphate
50.0
[Gonzalez86]


Subunit of: anthranilate synthase

Subunit composition of anthranilate synthase = [TrpE]2[TrpD]2
         anthranilate synthase component I = TrpE
         anthranilate synthase component II = TrpD (summary available)

Summary:
Anthranilate synthase (TrpDE) catalyzes the first step in the pathway of tryptophan biosynthesis, and is subject to feedback regulation by the end product of the pathway, L-tryptophan [Pabst73]. One of its component monomers also catalyzes the second step in the same pathway.

TrpDE catalyzes the glutamine amidotransferase reaction that adds an amine group from glutamine to chorismate to yield anthranilate and glutamate [Baker66, Ito69]. TrpE on its own can carry out an alternate version of this reaction, using ammonium sulfate rather than glutamine as an amino donor [Ito69]. TrpD dramatically increases the affinity of TrpE for glutamine over TrpE alone [Ito69a].

TrpDE functions as a as complex comprising two TrpD and two TrpE monomers [Li74]. In line with their role in synthesizing tryptophan, the components of this complex contain almost no tryptophan, with one residue in TrpD and none in TrpE [Nichols81].

Translation of TrpE and TrpD is coordinated via a specialized intercistronic sequence between trpE and trpD. If the latter portion of the trpE mRNA is not translated, trpD mRNA translation is markedly reduced [Nichols81].

The complex from Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella typhimurium) has also been extensively studied. More recent reports have included its crystal structure 1.9 Å resolution [Morollo01], the thermodynamics of complex-catalyzed reactions [Byrnes00], intersubunit communication mechanisms [Caligiuri91], and aminodeoxyisochorismate as an enzyme-bound reaction intermediate [Morollo93].

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


Enzymatic reaction of: anthranilate synthase

Synonyms: ASase, anthranilate synthetase

EC Number: 4.1.3.27

chorismate + L-glutamine <=> anthranilate + pyruvate + L-glutamate + 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 L-glutamine: ammonia [Ito69 ]

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

Summary:
Both tryptophan and 7-methyltryptophan are competitive inhibitors with respect to chorismate [Baker66, Held70].

Cofactors or Prosthetic Groups: Mg2+ [Ito69a]

Alternative Cofactors for Mg2+: Co2+ , Fe2+

Inhibitors (Competitive): 7-methyl-L-tryptophan [Held70] , L-tryptophan [Baker66, Comment 5]

Inhibitors (Noncompetitive): L-tryptophan [Baker66, Comment 6]

Primary Physiological Regulators of Enzyme Activity: L-tryptophan

Kinetic Parameters:

Substrate
Km (μM)
Citations
chorismate
1.2
[Baker66, BRENDA14]
chorismate
29.0
[Holden02, BRENDA14]
chorismate
5.5
[Ito69a]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Li74a, UniProt11]
UniProt: Removed.
Chain 2 -> 531
[UniProt09]
UniProt: Anthranilate synthase component II;
Conserved-Region 3 -> 196
[UniProt09]
UniProt: Glutamine amidotransferase type-1;
Protein-Segment 57 -> 59
[UniProt14]
UniProt: Glutamine binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Sequence-Conflict 61
[Horowitz82, UniProt10a]
Alternate sequence: P → A; UniProt: (in Ref. 2);
Amino-Acid-Sites-That-Bind 84
[UniProt14]
UniProt: Glutamine; Non-Experimental Qualifier: by similarity.
Active-Site 84
[UniProt10]
UniProt: For GATase activity; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 88
[UniProt14]
UniProt: Glutamine; Non-Experimental Qualifier: by similarity.
Protein-Segment 134 -> 135
[UniProt14]
UniProt: Glutamine binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Active-Site 170
[UniProt10]
UniProt: For GATase activity; Non-Experimental Qualifier: by similarity;
Active-Site 172
[UniProt10]
UniProt: For GATase activity; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 192
[Horowitz82, Yanofsky81, UniProt10a]
Alternate sequence: Q → H; UniProt: (in Ref. 1 and 2);
Protein-Segment 202 -> 531
[UniProt10]
UniProt: Anthranilate phosphoribosyltransferase; Sequence Annotation Type: region of interest;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b1263 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11027; 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

Baker66: Baker TI, Crawford IP (1966). "Anthranilate synthetase. Partial purification and some kinetic studies on the enzyme from Escherichia coli." J Biol Chem 241(23);5577-84. PMID: 5333199

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

Byrnes00: Byrnes WM, Goldberg RN, Holden MJ, Mayhew MP, Tewari YB (2000). "Thermodynamics of reactions catalyzed by anthranilate synthase." Biophys Chem 84(1);45-64. PMID: 10723544

Caligiuri91: Caligiuri MG, Bauerle R (1991). "Subunit communication in the anthranilate synthase complex from Salmonella typhimurium." Science 252(5014);1845-8. PMID: 2063197

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."

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

Gonzalez86: Gonzalez JE, Somerville RL (1986). "The anthranilate aggregate of Escherichia coli: kinetics of inhibition by tryptophan of phosphoribosyltransferase." Biochem Cell Biol 64(7);681-91. PMID: 2428387

Held70: Held WA, Smith OH (1970). "Mechanism of 3-methylanthranilic acid derepression of the tryptophan operon in Escherichia coli." J Bacteriol 101(1);209-17. PMID: 4904235

Holden02: Holden MJ, Mayhew MP, Gallagher DT, Vilker VL (2002). "Chorismate lyase: kinetics and engineering for stability." Biochim Biophys Acta 1594(1);160-7. PMID: 11825618

Horowitz82: Horowitz H, Christie GE, Platt T (1982). "Nucleotide sequence of the trpD gene, encoding anthranilate synthetase component II of Escherichia coli." J Mol Biol 1982;156(2);245-56. PMID: 6283099

Imamoto65: Imamoto F, Morikawa N, Sato K (1965). "On the transcription of the tryptophan operon in Escherichia coli. 3. Multicistronic messenger RNA and polarity for transcription." J Mol Biol 13(1);169-82. PMID: 5323613

Imamoto66: Imamoto F, Ito J, Yanofsky C (1966). "Polarity in the tryptophan operon of E. coli." Cold Spring Harb Symp Quant Biol 31;235-49. PMID: 4866380

Ito66: Ito J, Yanofsky C (1966). "The nature of the anthranilic acid synthetase complex of Escherichia coli." J Biol Chem 241(17);4112-4. PMID: 5331787

Ito69: Ito J, Cox EC, Yanofsky C (1969). "Anthranilate synthetase, an enzyme specified by the tryptophan operon of Escherichia coli: purification and characterization of component I." J Bacteriol 97(2):725-33. PMID: 4886289

Ito69a: Ito J, Yanofsky C (1969). "Anthranilate synthetase, an enzyme specified by the tryptophan operon of Escherichia coli: Comparative studies on the complex and the subunits." J Bacteriol 1969;97(2);734-42. PMID: 4886290

Jackson74: Jackson EN, Yanofsky C (1974). "Localization of two functions of the phosphoribosyl anthranilate transferase of Escherichia coli to distinct regions of the polypeptide chain." J Bacteriol 117(2);502-8. PMID: 4590474

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

Li74: Li SL, Hanlon J, Yanofsky C (1974). "Separation of anthranilate synthetase components I and II of Escherichia coli, Salmonella typhimurium, and Serratia marcescens and determination of their amino-terminal sequences by automatic Edman degradation." Biochemistry 1974;13(8);1736-44. PMID: 4598537

Li74a: Li SL, Hanlon J, Yanofsky C (1974). "Structural homology of the glutamine amidotransferase subunits of the anthranilate synthetases of Escherichia coli, Salmonella typhimurium and Serratia marcescens." Nature 248(443);48-50. PMID: 4594441

Morollo01: Morollo AA, Eck MJ (2001). "Structure of the cooperative allosteric anthranilate synthase from Salmonella typhimurium." Nat Struct Biol 8(3);243-7. PMID: 11224570

Morollo93: Morollo AA, Bauerle R (1993). "Characterization of composite aminodeoxyisochorismate synthase and aminodeoxyisochorismate lyase activities of anthranilate synthase." Proc Natl Acad Sci U S A 90(21);9983-7. PMID: 8234345

Nichols81: Nichols BP, van Cleemput M, Yanofsky C (1981). "Nucleotide sequence of Escherichia coli trpE. Anthranilate synthetase component I contains no tryptophan residues." J Mol Biol 1981;146(1);45-54. PMID: 7021857

Pabst73: Pabst MJ, Kuhn JC, Somerville RL (1973). "Feedback regulation in the anthranilate aggregate from wild type and mutant strains of Escherichia coli." J Biol Chem 248(3);901-14. PMID: 4567790

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

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.

UniProt14: UniProt Consortium (2014). "UniProt version 2014-01 released on 2014-01-01 00:00:00." Database.

UniProtGOA11a: 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."

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

Other References Related to Gene Regulation

Bass87a: Bass S, Sugiono P, Arvidson DN, Gunsalus RP, Youderian P (1987). "DNA specificity determinants of Escherichia coli tryptophan repressor binding." Genes Dev 1(6);565-72. PMID: 3315854

Bertrand76: Bertrand K, Squires C, Yanofsky C (1976). "Transcription termination in vivo in the leader region of the tryptophan operon of Escherichia coli." J Mol Biol 103(2);319-37. PMID: 781269

Bertrand76a: Bertrand K, Yanofsky C (1976). "Regulation of transcription termination in the leader region of the tryptophan operon of Escherichia coli involves tryptophan or its metabolic product." J Mol Biol 103(2);339-49. PMID: 781270

Bertrand77: Bertrand K, Korn LJ, Lee F, Yanofsky C (1977). "The attenuator of the tryptophan operon of Escherichia coli. Heterogeneous 3'-OH termini in vivo and deletion mapping of functions." J Mol Biol 117(1);227-47. PMID: 340702

Fisher85: Fisher RF, Das A, Kolter R, Winkler ME, Yanofsky C (1985). "Analysis of the requirements for transcription pausing in the tryptophan operon." J Mol Biol 182(3);397-409. PMID: 2409288

Grandori98: Grandori R, Khalifah P, Boice JA, Fairman R, Giovanielli K, Carey J (1998). "Biochemical characterization of WrbA, founding member of a new family of multimeric flavodoxin-like proteins." J Biol Chem 273(33);20960-6. PMID: 9694845

Gunsalus80a: Gunsalus RP, Yanofsky C (1980). "Nucleotide sequence and expression of Escherichia coli trpR, the structural gene for the trp aporepressor." Proc Natl Acad Sci U S A 1980;77(12);7117-21. PMID: 7012834

Hiraga73: Hiraga S, Yanofsky C (1973). "Inhibition of the progress of transcription on the tryptophan operon of Escherichia coli." J Mol Biol 79(2);339-49. PMID: 4586412

Imamoto68: Imamoto F (1968). "On the initiation of transcription of the tryptophan operon in Escherichia coli." Proc Natl Acad Sci U S A 60(1);305-12. PMID: 4872441

Jackson73: Jackson EN, Yanofsky C (1973). "Thr region between the operator and first structural gene of the tryptophan operon of Escherichia coli may have a regulatory function." J Mol Biol 76(1);89-101. PMID: 4578102

Jeeves99: Jeeves M, Evans PD, Parslow RA, Jaseja M, Hyde EI (1999). "Studies of the Escherichia coli Trp repressor binding to its five operators and to variant operator sequences." Eur J Biochem 1999;265(3);919-28. PMID: 10518785

Klig88: Klig LS, Carey J, Yanofsky C (1988). "trp repressor interactions with the trp aroH and trpR operators. Comparison of repressor binding in vitro and repression in vivo." J Mol Biol 1988;202(4);769-77. PMID: 3050131

Kumamoto87: Kumamoto AA, Miller WG, Gunsalus RP (1987). "Escherichia coli tryptophan repressor binds multiple sites within the aroH and trp operators." Genes Dev 1(6);556-64. PMID: 3315853

Landick85: Landick R, Carey J, Yanofsky C (1985). "Translation activates the paused transcription complex and restores transcription of the trp operon leader region." Proc Natl Acad Sci U S A 82(14);4663-7. PMID: 2991886

Oxender79: Oxender DL, Zurawski G, Yanofsky C (1979). "Attenuation in the Escherichia coli tryptophan operon: role of RNA secondary structure involving the tryptophan codon region." Proc Natl Acad Sci U S A 76(11);5524-8. PMID: 118451

Platt76: Platt T, Squires C, Yanofsky C (1976). "Ribosome-protected regions in the leader-trpE sequence of Escherichia coli tryptophan operon messenger RNA." J Mol Biol 103(2);411-20. PMID: 781274

Salmon03: Salmon K, Hung SP, Mekjian K, Baldi P, Hatfield GW, Gunsalus RP (2003). "Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR." J Biol Chem 278(32);29837-55. PMID: 12754220

Squires76: Squires C, Lee F, Bertrand K, Squires CL, Bronson MJ, Yanofsky C (1976). "Nucleotide sequence of the 5' end of tryptophan messenger RNA of Escherichia coli." J Mol Biol 103(2);351-81. PMID: 781271

Stauffer78: Stauffer GV, Zurawski G, Yanofsky C (1978). "Single base-pair alterations in the Escherichia coli trp operon leader region that relieve transcription termination at the trp attenuator." Proc Natl Acad Sci U S A 75(10);4833-7. PMID: 368800

Stoltzfus88: Stoltzfus A, Leslie JF, Milkman R (1988). "Molecular evolution of the Escherichia coli chromosome. I. Analysis of structure and natural variation in a previously uncharacterized region between trp and tonB." Genetics 120(2);345-58. PMID: 3058546

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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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