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Escherichia coli K-12 substr. MG1655 Enzyme: amidophosphoribosyl transferase



Gene: purF Accession Numbers: EG10794 (EcoCyc), b2312, ECK2306

Synonyms: ade(ub), ade, purC

Regulation Summary Diagram: ?

Subunit composition of amidophosphoribosyl transferase = [PurF]4

Summary:
Amidophosphoribosyl transferase catalyzes the committed step in purine de novo biosynthesis. In this reaction an amino group derived from glutamine is added to the C-1 of 5-phospho-α-D-ribose 1-diphosphate (PRPP), the diphosphoryl group is displaced, and glutamate is produced. The enzyme can use ammonia in place of glutamine and it was also shown to have glutaminase activity in the absence of other substrates [Messenger79].

The enzyme belongs to the class II (purF-type) glutamine amidotransferases in which the glutamine and ammonia binding sites are on a single subunit. In contrast, in class I (trpG-type) enzymes the sites are on distinct subunits. PurF was initially determined to be either a homotetramer, or a homotrimer based on native apparent molecular masses of 194 kDa by sedimentation equilibrium centrifugation, or 224 kDa by gel filtration chromatography. The apparent molecular mass of the subunit was 57 kDa by SDS-PAGE [Messenger79]. The crystal structure showed a homotetramer [Muchmore98].

The purified enzyme was shown to lack iron and other trace metals. Affinity labeling studies showed the amino-terminal cysteine to be the active site residue necessary for glutamine amide transfer [Tso82]. A catalytic triad of Cys1-His101-Asp29 was identified by site-directed mutagenesis [Mei89]. The glutamine amide transfer domain was localized to residues 1-237, a region not obligatory for ammonia-dependent activity [Mei90]. Both the glutamine-dependent and ammonia-dependent activities were shown to be feedback-regulated by GMP and AMP synergistically, and sites involved were identified [Zhou93, Zhou94].

Crystal structure analysis and analog binding studies defined sites involved in catalysis and regulation and suggested two separate catalytic domains. One domain contains the active site involved in the abstraction of nitrogen from the glutamine amide group. The nitrogen (ammonia) is then translocated through a channel (intramolecular tunnel) to the active site for the PRPP acceptor substrate in the second domain [Kim95, Kim96a, Krahn97, Muchmore98]. The mechanism of interdomain signaling has also been studied [Bera99, Bera00], and ammonia channel function has been computationally modeled [Wang09b].

In the area of metabolic engineering, a feedback-resistant mutant of PurF (Lys326Gln [Zhou94]) was used to increase yield in an inosine-producing strain of E. coli [Shimaoka07]. In another study, overexpressed his6-tagged PurF was shown to have promiscuous phosphoribosylanthranilate isomerase activity, which was evolved to a higher efficiency enzyme by random mutagenesis and selection [Patrick08].

Reviews: Jensen, K.F., G. Dandanell, B. Hove-Jensen, and M. Willemoes (2008) "Nucleotides, Nucleosides and Nucleobases" EcoSal 3.6.2 [ECOSAL] and [Smith98a]

Gene Citations: [Makaroff85, Rolfes88a, Tso82a, Sampei88, Meng90]

Locations: cytosol

Map Position: [2,426,743 <- 2,428,260] (52.3 centisomes)
Length: 1518 bp / 505 aa

Molecular Weight of Polypeptide: 56.488 kD (from nucleotide sequence), 57.0 kD (experimental) [Messenger79 ]

pI: 6.13

Unification Links: ASAP:ABE-0007631 , CGSC:340 , DisProt:DP00578 , EchoBASE:EB0787 , EcoGene:EG10794 , EcoliWiki:b2312 , ModBase:P0AG16 , OU-Microarray:b2312 , PortEco:purF , Pride:P0AG16 , Protein Model Portal:P0AG16 , RefSeq:NP_416815 , RegulonDB:EG10794 , SMR:P0AG16 , String:511145.b2312 , Swiss-Model:P0AG16 , UniProt:P0AG16

Relationship Links: InterPro:IN-FAMILY:IPR000583 , InterPro:IN-FAMILY:IPR000836 , InterPro:IN-FAMILY:IPR005854 , InterPro:IN-FAMILY:IPR017932 , PDB:Structure:1ECB , PDB:Structure:1ECC , PDB:Structure:1ECF , PDB:Structure:1ECG , PDB:Structure:1ECJ , Pfam:IN-FAMILY:PF00156 , Pfam:IN-FAMILY:PF00310 , Prosite:IN-FAMILY:PS00103 , Prosite:IN-FAMILY:PS51278

In Paralogous Gene Group: 554 (3 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006164 - purine nucleotide biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Tso82]
GO:0006541 - glutamine metabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Tso82, Mei90]
GO:0006189 - 'de novo' IMP biosynthetic process Inferred by computational analysis [UniProtGOA12]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
GO:0009113 - purine nucleobase biosynthetic process Inferred by computational analysis [GOA01a]
GO:0009116 - nucleoside metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0004044 - amidophosphoribosyltransferase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Tso82, Messenger79]
GO:0016757 - transferase activity, transferring glycosyl groups Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Tso82]
GO:0042802 - identical protein binding Inferred from experiment [Messenger79, Muchmore98]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Tso82]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Zhang07, Lasserre06]

MultiFun Terms: metabolism biosynthesis of building blocks nucleotides purine biosynthesis

Essentiality data for purF 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:
Last-Curated ? 10-Jan-2012 by Fulcher C , SRI International


Enzymatic reaction of: amidophosphoribosyl transferase

Synonyms: P-ribosyl-pp amido transferase, PRPP amidotransferase, glutamine phosphoribosylpyrophosphate amidotransferase, glutamine 5-phosphoribosylamine:pyrophosphate phosphoribosyltransferase, phosphoribosyldiphosphate 5-amidotransferase, 5-phosphoribosylamine:glutamine pyrophosphate phosphoribosyltransferase, glutamine PRPP amidotrnasferase

EC Number: 2.4.2.14

5-phospho-α-D-ribose 1-diphosphate + L-glutamine + H2O <=> 5-phospho-β-D-ribosylamine + L-glutamate + diphosphate

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 L-glutamine: ammonia [Messenger79 ]

In Pathways: superpathway of 5-aminoimidazole ribonucleotide biosynthesis , superpathway of histidine, purine, and pyrimidine biosynthesis , superpathway of purine nucleotides de novo biosynthesis II , 5-aminoimidazole ribonucleotide biosynthesis I , 5-aminoimidazole ribonucleotide biosynthesis II

Summary:
This reaction is composed of two half-reactions involving the hydrolysis of glutamine to produce glutamate and ammonia, and the amination of 5-phospho-α-D-ribose 1-diphosphate (PRPP) to produce 5-phospho-β-D-ribosyl-amine (PRA) and diphosphate.

The glutamine and ammonia-dependent activities are subject to end-product inhibiton by AMP and GMP. Inhibition was competitive with respect to PRPP, but only GMP showed cooperativity for PRPP binding. GMP was more effective as an inhibitor than AMP. When used in combination, AMP and GMP acted synergystically. The glutamine-dependent activity was oxygen-sensitive and was also inactivated by p-mercuribenzoate and iodoacetamide [Messenger79].

The glutamine-dependent activity showed pH optima of 6.6-7.7 in phosphate buffer and 7.8-8.6 in Tris buffer. The pH optimum of 8.5 for the ammonia-dependent activity indicated that ammonia, rather than ammonium, is the substrate for PRA synthesis [Messenger79].

Cofactors or Prosthetic Groups: Mg2+ [Messenger79]

Activators (Unknown Mechanism): GDP [Messenger79] , GTP [Messenger79]

Inhibitors (Allosteric): GMP [Messenger79, Zhou94]

Inhibitors (Competitive): GMP [Messenger79] , AMP [Messenger79, Comment 5]

Inhibitors (Unknown Mechanism): XMP [Messenger79] , ADP [Messenger79] , IMP [Messenger79] , iodoacetamide [Messenger79] , p-mercuribenzoate [Messenger79] , L-2-amino-4-oxo-5-chloropentanoate [Messenger79] , 6-diazo-5-oxonorleucine [Messenger79]

Primary Physiological Regulators of Enzyme Activity: GMP , AMP

Kinetic Parameters:

Substrate
Km (μM)
Citations
L-glutamine
1720.0, 2100.0, 7340.0
[Kim96a, BRENDA14]
L-glutamine
1700.0
[Messenger79, BRENDA14]
5-phospho-α-D-ribose 1-diphosphate
53.0
[Kim95, BRENDA14]
5-phospho-α-D-ribose 1-diphosphate
67.0
[Messenger79, BRENDA14]

pH(opt): 6.6 [BRENDA14, Messenger79], 7.8 [BRENDA14, Messenger79], 8.5 [BRENDA14, Messenger79]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Tso82, UniProt11]
UniProt: Removed.
Active-Site 2
[UniProt10]
UniProt: For GATase activity;
Conserved-Region 2 -> 236
[UniProt09]
UniProt: Glutamine amidotransferase type-2;
Chain 2 -> 505
[UniProt09]
UniProt: Amidophosphoribosyltransferase;
Sequence-Conflict 45 -> 46
[Tso82a, Zalkin83, UniProt10]
Alternate sequence: LR → SL; UniProt: (in Ref. 2 and 3);
Sequence-Conflict 50
[Tso82a, Zalkin83, UniProt10]
Alternate sequence: G → A; UniProt: (in Ref. 2 and 3);
Sequence-Conflict 213 -> 230
[Tso82a, Zalkin83, UniProt10]
Alternate sequence: ALDTLGFDFLRDVAPGEA → GSIRWALISCVTSRRAR; UniProt: (in Ref. 2 and 3);
Sequence-Conflict 277
[Tso82a, Zalkin83, UniProt10]
Alternate sequence: V → A; UniProt: (in Ref. 2 and 3);
Sequence-Conflict 283
[Tso82a, Zalkin83, UniProt10]
Alternate sequence: L → V; UniProt: (in Ref. 2 and 3);
Sequence-Conflict 337
[Zalkin83, UniProt10]
Alternate sequence: M → I; UniProt: (in Ref. 2; AAA24453);
Metal-Binding-Site 367
[UniProt10]
UniProt: Magnesium;
Metal-Binding-Site 368
[UniProt10]
UniProt: Magnesium;
Sequence-Conflict 386
[Sampei88, UniProt10]
Alternate sequence: A → R; UniProt: (in Ref. 1; CAA30971);
Sequence-Conflict 494
[Tso82a, Zalkin83, UniProt10]
Alternate sequence: N → S; UniProt: (in Ref. 2 and 3);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b2312 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10794; 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

Bera00: Bera AK, Smith JL, Zalkin H (2000). "Dual role for the glutamine phosphoribosylpyrophosphate amidotransferase ammonia channel. Interdomain signaling and intermediate channeling." J Biol Chem 275(11);7975-9. PMID: 10713115

Bera99: Bera AK, Chen S, Smith JL, Zalkin H (1999). "Interdomain signaling in glutamine phosphoribosylpyrophosphate amidotransferase." J Biol Chem 274(51);36498-504. PMID: 10593947

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

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

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

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."

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Kim95: Kim JH, Wolle D, Haridas K, Parry RJ, Smith JL, Zalkin H (1995). "A stable carbocyclic analog of 5-phosphoribosyl-1-pyrophosphate to probe the mechanism of catalysis and regulation of glutamine phosphoribosylpyrophosphate amidotransferase." J Biol Chem 270(29);17394-9. PMID: 7542237

Kim96a: Kim JH, Krahn JM, Tomchick DR, Smith JL, Zalkin H (1996). "Structure and function of the glutamine phosphoribosylpyrophosphate amidotransferase glutamine site and communication with the phosphoribosylpyrophosphate site." J Biol Chem 271(26);15549-57. PMID: 8663035

Krahn97: Krahn JM, Kim JH, Burns MR, Parry RJ, Zalkin H, Smith JL (1997). "Coupled formation of an amidotransferase interdomain ammonia channel and a phosphoribosyltransferase active site." Biochemistry 36(37);11061-8. PMID: 9333323

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Makaroff85: Makaroff CA, Zalkin H (1985). "Regulation of Escherichia coli purF. Analysis of the control region of a pur regulon gene." J Biol Chem 1985;260(18);10378-87. PMID: 2991286

Mei89: Mei B, Zalkin H (1989). "A cysteine-histidine-aspartate catalytic triad is involved in glutamine amide transfer function in purF-type glutamine amidotransferases." J Biol Chem 264(28);16613-9. PMID: 2674138

Mei90: Mei BG, Zalkin H (1990). "Amino-terminal deletions define a glutamine amide transfer domain in glutamine phosphoribosylpyrophosphate amidotransferase and other PurF-type amidotransferases." J Bacteriol 1990;172(6);3512-4. PMID: 2188964

Meng90: Meng LM, Kilstrup M, Nygaard P (1990). "Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli." Eur J Biochem 1990;187(2);373-9. PMID: 2404765

Messenger79: Messenger LJ, Zalkin H (1979). "Glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli. Purification and properties." J Biol Chem 1979;254(9);3382-92. PMID: 372191

Muchmore98: Muchmore CR, Krahn JM, Kim JH, Zalkin H, Smith JL (1998). "Crystal structure of glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli." Protein Sci 1998;7(1);39-51. PMID: 9514258

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

Patrick08: Patrick WM, Matsumura I (2008). "A study in molecular contingency: glutamine phosphoribosylpyrophosphate amidotransferase is a promiscuous and evolvable phosphoribosylanthranilate isomerase." J Mol Biol 377(2);323-36. PMID: 18272177

Rolfes88a: Rolfes RJ, Zalkin H (1988). "Regulation of Escherichia coli purF. Mutations that define the promoter, operator, and purine repressor gene." J Biol Chem 1988;263(36);19649-52. PMID: 3058703

Sampei88: Sampei G, Mizobuchi K (1988). "Nucleotide sequence of the Escherichia coli purF gene encoding amidophosphoribosyltransferase for de novo purine nucleotide synthesis." Nucleic Acids Res 16(17);8717. PMID: 3047685

Shimaoka07: Shimaoka M, Takenaka Y, Kurahashi O, Kawasaki H, Matsui H (2007). "Effect of amplification of desensitized purF and prs on inosine accumulation in Escherichia coli." J Biosci Bioeng 103(3);255-61. PMID: 17434429

Smith98a: Smith JL (1998). "Glutamine PRPP amidotransferase: snapshots of an enzyme in action." Curr Opin Struct Biol 8(6);686-94. PMID: 9914248

Tso82: Tso JY, Hermodson MA, Zalkin H (1982). "Glutamine phosphoribosylpyrophosphate amidotransferase from cloned Escherichia coli purF. NH2-terminal amino acid sequence, identification of the glutamine site, and trace metal analysis." J Biol Chem 1982;257(7);3532-6. PMID: 7037784

Tso82a: Tso JY, Zalkin H, van Cleemput M, Yanofsky C, Smith JM (1982). "Nucleotide sequence of Escherichia coli purF and deduced amino acid sequence of glutamine phosphoribosylpyrophosphate amidotransferase." J Biol Chem 1982;257(7);3525-31. PMID: 6277938

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: 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.

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."

Wang09b: Wang XS, Roitberg AE, Richards NG (2009). "Computational studies of ammonia channel function in glutamine 5'-phosphoribosylpyrophosphate amidotransferase." Biochemistry 48(51);12272-82. PMID: 19921932

Zalkin83: Zalkin H (1983). "Structure, function, and regulation of amidophosphoribosyltransferase from prokaryotes." Adv Enzyme Regul 21;225-37. PMID: 6443594

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111

Zhou93: Zhou G, Charbonneau H, Colman RF, Zalkin H (1993). "Identification of sites for feedback regulation of glutamine 5-phosphoribosylpyrophosphate amidotransferase by nucleotides and relationship to residues important for catalysis." J Biol Chem 268(14);10471-81. PMID: 7683680

Zhou94: Zhou G, Smith JL, Zalkin H (1994). "Binding of purine nucleotides to two regulatory sites results in synergistic feedback inhibition of glutamine 5-phosphoribosylpyrophosphate amidotransferase." J Biol Chem 269(9);6784-9. PMID: 8120039

Other References Related to Gene Regulation

Cho11: Cho BK, Federowicz SA, Embree M, Park YS, Kim D, Palsson BO (2011). "The PurR regulon in Escherichia coli K-12 MG1655." Nucleic Acids Res 39(15);6456-64. PMID: 21572102

He90: He B, Shiau A, Choi KY, Zalkin H, Smith JM (1990). "Genes of the Escherichia coli pur regulon are negatively controlled by a repressor-operator interaction." J Bacteriol 1990;172(8);4555-62. PMID: 2198266

Maciag11: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

Mitchell03: Mitchell JE, Zheng D, Busby SJ, Minchin SD (2003). "Identification and analysis of 'extended -10' promoters in Escherichia coli." Nucleic Acids Res 31(16);4689-95. PMID: 12907708

Nonet87: Nonet ML, Marvel CC, Tolan DR (1987). "The hisT-purF region of the Escherichia coli K-12 chromosome. Identification of additional genes of the hisT and purF operons." J Biol Chem 262(25);12209-17. PMID: 3040734

Rolfes88: Rolfes RJ, Zalkin H (1988). "Escherichia coli gene purR encoding a repressor protein for purine nucleotide synthesis. Cloning, nucleotide sequence, and interaction with the purF operator." J Biol Chem 263(36);19653-61. PMID: 3058704


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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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