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MetaCyc Enzyme: N5-carboxyaminoimidazole ribonucleotide synthetase

Gene: purK Accession Numbers: EG10796 (MetaCyc), b0522, ECK0515

Synonyms: purE2, purE2 peptide, CO2-binding subunit, CO2 subunit, AIR carboxylase

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of N5-carboxyaminoimidazole ribonucleotide synthetase = [PurK]2
         N5-carboxyaminoimidazole ribonucleotide synthetase monomer = PurK

Summary:
PurK and PurE were previously thought to be two subunits of AIR carboxylase [Tiedeman89], although later studies showed the enzymes to be subunits of a distinct carboxylase and mutase, respectively [Mueller94a].

PurK converts 5-amino-1-(5-phospho-D-ribosyl)imidazole (AIR) to the unstable intermediate N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) (the carbamate of AIR) in an ATP-dependent manner by the ligation of bicarbonate to the N5 amino group of AIR [Mueller94a, Zhang08c].

Crystal structures have been determined for PurK in complex with sulfate and MgADP [Thoden99b]. A later report refined the crystal structure for PurK to 1.6 Å resolution with MgATP, or MgADP/P(i) bound to the active site. The proposed reaction mechanism involves a carboxyphosphate intermediate. The enzyme is not found in humans and is of interest as a target for the design of antimicrobial drugs [Thoden08]. While this three domain protein is a member of the ATP grasp superfamily, it lacks conservation within the substrate specificity (Ω) loop [Thoden99b] .

PurK exhibits AIR-dependent ATPase activity that does not show bicarbonate dependence and AIR is not carboxylated during ATP hydrolysis [Meyer92]. 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]. Nonenzymatic carboxylation of AIR occurs, although under physiological conditions ATP must be added as a second substrate for the AIR carboxylation reaction to occur. PurK is required for AIR conversion to 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate (CAIR) under low bicarbonate concentrations [Meyer92].

The overproduction and purification of PurK 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].

In the area of enzyme engineering, domain exchange studies between the structurally homologous E. coli PurK and PurT revealed that domain-swapped hybrids could catalyze partial reactions, but further modifications were necessary for catalysis of the full reaction. These studies were consistent with the proposal of domain swapping as a mechanism for protein evolution [Li09a].

Review: [Zhang08c]

Locations: cytosol

Map Position: [550,750 <- 551,817]

Molecular Weight of Polypeptide: 39.461 kD (from nucleotide sequence), 39.0 kD (experimental) [Meyer92 ]

Molecular Weight of Multimer: 79.0 kD (experimental) [Meyer92]

Unification Links: ASAP:ABE-0001794 , CGSC:17995 , EchoBASE:EB0789 , EcoGene:EG10796 , EcoliWiki:b0522 , ModBase:P09029 , OU-Microarray:b0522 , PortEco:purK , PR:PRO_000023641 , Pride:P09029 , Protein Model Portal:P09029 , RefSeq:NP_415055 , RegulonDB:EG10796 , SMR:P09029 , String:511145.b0522 , UniProt:P09029

Relationship Links: InterPro:IN-FAMILY:IPR003135 , InterPro:IN-FAMILY:IPR005875 , InterPro:IN-FAMILY:IPR011054 , InterPro:IN-FAMILY:IPR011761 , InterPro:IN-FAMILY:IPR013816 , InterPro:IN-FAMILY:IPR016185 , PDB:Structure:1B6R , PDB:Structure:1B6S , PDB:Structure:3ETH , PDB:Structure:3ETJ , Pfam:IN-FAMILY:PF02222 , Prosite:IN-FAMILY:PS50975

Gene-Reaction 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:0004638 - phosphoribosylaminoimidazole carboxylase activity Inferred from experiment Inferred by computational analysis [GOA01a, Mueller94a]
GO:0005524 - ATP binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Mueller94a, Thoden08]
GO:0034028 - 5-(carboxyamino)imidazole ribonucleotide synthase activity Inferred from experiment Inferred by computational analysis [GOA01, Mueller94a]
GO:0042803 - protein homodimerization activity Inferred from experiment [Meyer92]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0016874 - ligase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm

MultiFun Terms: metabolism biosynthesis of building blocks nucleotides purine biosynthesis

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


Enzymatic reaction of: N5-carboxyaminoimidazole ribonucleotide synthetase

Synonyms: N5-carboxyaminoimidazole ribonucleotide synthase, N5-CAIR synthase, N5-CAIR synthetase, 5-(carboxyamino)imidazole ribonucleotide synthetase, 5-(carboxyamino)imidazole ribonucleotide synthase, N5-AIR carboxylase

EC Number: 6.3.4.18

5-amino-1-(5-phospho-β-D-ribosyl)imidazole + ATP + hydrogen carbonate <=> N5-carboxyaminoimidazole ribonucleotide + ADP + phosphate + 2 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 physiologically 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

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

Summary:
PurK catalyzed production of N5-carboxyaminoimidazole ribonucleotide, ADP, and phosphate from 5-amino-1-(5-phospho-D-ribosyl)imidazole, bicarbonate and ATP was monitored using a pyruvate kinase/lactate dehydrogenase coupled assay in which NADH consumption was followed spectrophotometrically [Mueller94a].

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
5-amino-1-(5-phospho-β-D-ribosyl)imidazole
66.0
[Li09a, BRENDA14]
ATP
48.0
5.9
[Li09a, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 64 -> 65
[Tiedeman89, UniProt10]
Alternate sequence: PD; UniProt: (in Ref. 1; CAA31421);
Amino-Acid-Sites-That-Bind 80
[UniProt10]
UniProt: ATP;
Conserved-Region 84 -> 267
[UniProt09]
UniProt: ATP-grasp;
Amino-Acid-Sites-That-Bind 120
[UniProt10]
UniProt: ATP;
Amino-Acid-Sites-That-Bind 131
[UniProt10]
UniProt: ATP;
Nucleotide-Phosphate-Binding-Region 153 -> 156
[UniProt10]
UniProt: ATP;
Amino-Acid-Sites-That-Bind 161
[UniProt10]
UniProt: ATP;
Nucleotide-Phosphate-Binding-Region 237 -> 238
[UniProt10]
UniProt: ATP;

History:
10/20/97 Gene b0522 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10796; confirmed by SwissProt match.


References

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

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

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

Li09a: Li H, Fast W, Benkovic SJ (2009). "Structural and functional modularity of proteins in the de novo purine biosynthetic pathway." Protein Sci 18(5);881-92. PMID: 19384989

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

Mueller94a: 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

Thoden08: Thoden JB, Holden HM, Firestine SM (2008). "Structural analysis of the active site geometry of N5-carboxyaminoimidazole ribonucleotide synthetase from Escherichia coli." Biochemistry 47(50);13346-53. PMID: 19053251

Thoden99b: Thoden JB, Kappock TJ, Stubbe J, Holden HM (1999). "Three-dimensional structure of N5-carboxyaminoimidazole ribonucleotide synthetase: a member of the ATP grasp protein superfamily." Biochemistry 1999;38(47);15480-92. PMID: 10569930

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.

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

Zhang08c: Zhang Y, Morar M, Ealick SE (2008). "Structural biology of the purine biosynthetic pathway." Cell Mol Life Sci 65(23);3699-724. PMID: 18712276


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 Sat Nov 22, 2014, BIOCYC13A.