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Escherichia coli K-12 substr. MG1655 Enzyme: N5-carboxyaminoimidazole ribonucleotide mutase



Gene: purE Accession Numbers: EG10793 (EcoCyc), b0523, ECK0516

Synonyms: ade(f), Pur2, ade3, ade, purE1 peptide, catalytic subunit, AIR carboxylase subunit, catalytic subunit, AIR carboxylase

Regulation Summary Diagram: ?

Subunit composition of N5-carboxyaminoimidazole ribonucleotide mutase = [PurE]8

Summary:
PurE and PurK were previously thought to be two subunits of AIR carboxylase [Tiedeman89], although later studies showed the enzymes to be subunits of a distinct mutase and carboxylase, respectively [Mueller94].

PurE catalyzes an unusual transformation, the reversible interconversion of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) and 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate (CAIR). Direct transfer of the carboxylate group of the carbamate of N5-CAIR produces CAIR [Hoskins07, Meyer99].

A crystal structure of PurE determined at 1.5Å resolution with and without the substrate CAIR revealed an octameric quaternary structure. The mononucleotide binding site is located in a a cleft at the interface of two subunits [Mathews99]. Subsequent crystal structures of the wild-type enzyme co-crystallized with a CAIR analog, and structures of His45Asn and His45Gln mutant enzymes crystallized with CAIR or an analog, provided insight into substrate binding. A reaction mechanism involving the essential His45 residue, and an enzyme-bound aminoimidazole ribonucleotide and carbon dioxide intermediate was proposed [Hoskins07].

A high concentration of bicarbonate partially rescues the defect of a purK mutant during growth in the absence of purines, probably by perturbing the balance of AIR toward N5-CAIR. An overproduction of PurE further increases rescue in the presence of bicarbonate [Firestine94].

The overproduction and purification of PurE has been reported [Meyer92].

Analysis of the purE locus at the nucleotide sequence level revealed that the purE1 and purE2 cistrons correspond to two distinct, overlapping genes, purE and purK [Watanabe89].

Two classes of PurE exist. Class I enzymes require N5-CAIR, the product of PurK, as substrate. Class II enzymes found in higher eukaryotes catalyze the direct carboxylation of 5-amino-1-(5-phospho-D-ribosyl)imidazole (AIR) to produce CAIR [Zhang08b, Firestine94].

Review: [Zhang08b]

Gene Citations: [Koduri80, Meng90]

Locations: cytosol

Map Position: [551,814 <- 552,323] (11.89 centisomes)
Length: 510 bp / 169 aa

Molecular Weight of Polypeptide: 17.78 kD (from nucleotide sequence), 17.0 kD (experimental) [Meyer92 ]

Molecular Weight of Multimer: 126.0 kD (experimental) [Meyer92]

Unification Links: ASAP:ABE-0001796 , CGSC:341 , EchoBASE:EB0786 , EcoGene:EG10793 , EcoliWiki:b0523 , OU-Microarray:b0523 , PortEco:purE , PR:PRO_000023640 , Pride:P0AG18 , Protein Model Portal:P0AG18 , RefSeq:NP_415056 , RegulonDB:EG10793 , SMR:P0AG18 , String:511145.b0523 , Swiss-Model:P0AG18 , UniProt:P0AG18

Relationship Links: InterPro:IN-FAMILY:IPR000031 , InterPro:IN-FAMILY:IPR024694 , PDB:Structure:1D7A , PDB:Structure:1QCZ , PDB:Structure:2ATE , PDB:Structure:2NSH , PDB:Structure:2NSJ , PDB:Structure:2NSL , Pfam:IN-FAMILY:PF00731 , Smart:IN-FAMILY:SM01001

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006164 - purine nucleotide biosynthetic process Inferred by computational analysis [UniProtGOA11a]
GO:0006189 - 'de novo' IMP biosynthetic process Inferred by computational analysis [UniProtGOA12, GOA01a]
Molecular Function: GO:0034023 - 5-(carboxyamino)imidazole ribonucleotide mutase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Mueller94]
GO:0042802 - identical protein binding Inferred from experiment [Meyer92]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05, Lasserre06]

MultiFun Terms: metabolism biosynthesis of building blocks nucleotides purine biosynthesis

Essentiality data for purE knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes et al., 2003, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba et al., 2006, 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 No 37 Aerobic 7.2 0.22 No [Baba et al., 2006, Comment 2]
No [Feist07, Comment 4]

Credits:
Last-Curated ? 16-Dec-2011 by Fulcher C , SRI International


Enzymatic reaction of: N5-carboxyaminoimidazole ribonucleotide mutase

Synonyms: 5-(carboxyamino)imidazole ribonucleotide mutase, N5-CAIR mutase

EC Number: 5.4.99.18

N5-carboxyaminoimidazole ribonucleotide <=> 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate

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 histidine, purine, and pyrimidine biosynthesis , superpathway of purine nucleotides de novo biosynthesis II , inosine-5'-phosphate biosynthesis I

Summary:
The reverse reaction converting AIR to N5-CAIR has been studied in vitro. The physiological substrate N5-CAIR is an unstable intermediate produced by PurK [Mueller94, Meyer99].

Inhibitors (Unknown Mechanism): 4-nitro-5-aminoimidazole ribonucleotide [Firestine94]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
N5-carboxyaminoimidazole ribonucleotide
15.5
[Hoskins07, BRENDA14]
5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate
22.6
15.6
[Hoskins07, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Meyer92, UniProt11a]
UniProt: Removed.
Chain 2 -> 169
[UniProt09]
UniProt: Phosphoribosylaminoimidazole carboxylase catalytic subunit;
Amino-Acid-Sites-That-Bind 16
[UniProt10]
UniProt: Substrate;
Amino-Acid-Sites-That-Bind 19
[UniProt10]
UniProt: Substrate;
Amino-Acid-Sites-That-Bind 46
[UniProt10]
UniProt: Substrate;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b0523 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10793; confirmed by SwissProt match.


References

Baba et al., 2006: 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

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

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

Firestine94: Firestine SM, Poon SW, Mueller EJ, Stubbe J, Davisson VJ (1994). "Reactions catalyzed by 5-aminoimidazole ribonucleotide carboxylases from Escherichia coli and Gallus gallus: a case for divergent catalytic mechanisms." Biochemistry 1994;33(39);11927-34. PMID: 7918411

Gerdes et al., 2003: 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."

Hoskins07: Hoskins AA, Morar M, Kappock TJ, Mathews II, Zaugg JB, Barder TE, Peng P, Okamoto A, Ealick SE, Stubbe J (2007). "N5-CAIR mutase: role of a CO2 binding site and substrate movement in catalysis." Biochemistry 46(10);2842-55. PMID: 17298082

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

Koduri80: Koduri RK, Gots JS (1980). "A DNA-binding protein with specificity for pur genes in Escherichia coli." J Biol Chem 1980;255(20);9594-8. PMID: 7000760

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

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

Mathews99: Mathews II, Kappock TJ, Stubbe J, Ealick SE (1999). "Crystal structure of Escherichia coli PurE, an unusual mutase in the purine biosynthetic pathway." Structure Fold Des 1999;7(11);1395-406. PMID: 10574791

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

Meyer92: Meyer E, Leonard NJ, Bhat B, Stubbe J, Smith JM (1992). "Purification and characterization of the purE, purK, and purC gene products: identification of a previously unrecognized energy requirement in the purine biosynthetic pathway." Biochemistry 1992;31(21);5022-32. PMID: 1534690

Meyer99: Meyer E, Kappock TJ, Osuji C, Stubbe J (1999). "Evidence for the direct transfer of the carboxylate of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) to generate 4-carboxy-5-aminoimidazole ribonucleotide catalyzed by Escherichia coli PurE, an N5-CAIR mutase." Biochemistry 1999;38(10);3012-8. PMID: 10074353

Mueller94: Mueller EJ, Meyer E, Rudolph J, Davisson VJ, Stubbe J (1994). "N5-carboxyaminoimidazole ribonucleotide: evidence for a new intermediate and two new enzymatic activities in the de novo purine biosynthetic pathway of Escherichia coli." Biochemistry 1994;33(8);2269-78. PMID: 8117684

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

Tiedeman89: Tiedeman AA, Keyhani J, Kamholz J, Daum HA, Gots JS, Smith JM (1989). "Nucleotide sequence analysis of the purEK operon encoding 5'-phosphoribosyl-5-aminoimidazole carboxylase of Escherichia coli K-12." J Bacteriol 1989;171(1);205-12. PMID: 2464576

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.

UniProt11a: 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."

Watanabe89: Watanabe W, Sampei G, Aiba A, Mizobuchi K (1989). "Identification and sequence analysis of Escherichia coli purE and purK genes encoding 5'-phosphoribosyl-5-amino-4-imidazole carboxylase for de novo purine biosynthesis." J Bacteriol 1989;171(1);198-204. PMID: 2644189

Zhang08b: Zhang Y, Morar M, Ealick SE (2008). "Structural biology of the purine biosynthetic pathway." Cell Mol Life Sci 65(23);3699-724. PMID: 18712276

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

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


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Tue Nov 25, 2014, BIOCYC14B.