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Nasir MH, Jabeen E, Qureshi R, Ansari FL, Shaukat A, Nasir U, Ahmed A. Investigation of redox mechanism and DNA binding of novel 2-(x-nitrophenyl)-5-nitrobenzimidazole (x = 2, 3 and 4). Biophys Chem 2019; 258:106316. [PMID: 31986436 DOI: 10.1016/j.bpc.2019.106316] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/11/2019] [Accepted: 12/13/2019] [Indexed: 02/08/2023]
Abstract
The present study describes the investigation of the binding modes of potential anti-cancerous nitrophenyl derivatives of 2-(x-nitrophenyl)-5-nitrobenzimidazole with calf thymus DNA. The -2-(x-nitrophenyl)-5-nitrobenzimidazoles under investigation differ only in position x of nitro group in nitrophenyl substituent relative to benzimidazole moiety leading to 1-NPNB (x = 2), 2-NPNB (x = 3) and 3-NPNB (x = 4). The DFT calculations predicted that derivatives were electrochemically reducible which was then confirmed by cyclic voltammetry. In cyclic voltammetry, the second reversible peak was dependent on first irreversible reduction. This revealed that electrochemical irreversible process was governed by some other process which was then followed by reversible second electron transfer. Thus, ECE (electron transfer leading to coupled chemical reaction followed by another electron transfer process) mechanism was attributed for electrochemical reduction. Experimental results based on UV-Vis spectroscopy vaguely showed intercalation of 1-NPNB, 2-NPNB and 3-NPNB into DNA which was assisted by cyclic voltammetry. However, thermal melting and florescence spectroscopy unambiguously established intercalation for all three compounds. Molecular docking analysis ascertained in pocket stacking of 5-nitrobenzimidazole moiety in 1-NPNB and 2-NPNB while nitro phenyl substitution in 3-NPNB stacks between DNA base pair during intercalation which was in agreement with DFT computed molecular geometry. Therefore, the relative positions of nitro group and 5-nitrobenzimidazole moieties in 2-(x-nitrophenyl)- 5-nitrobenzimidazole influenced the DNA binding pattern of compounds during intercalation. The cytotoxicity of these compounds was comparable to standard drug doxorubicin against both cancerous (MCF-7) and normal (MCF-10A) breast cells which depicts their anti-cancerous potential.
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Affiliation(s)
- Mehwish H Nasir
- Department of Chemistry, Quaid-i-Azam University, 45320 Islamabad, Pakistan
| | - Erum Jabeen
- Department of Chemistry, Faculty of Sciences, Allama Iqbal Open University, 44000 Islamabad, Pakistan.
| | - Rumana Qureshi
- Department of Chemistry, Quaid-i-Azam University, 45320 Islamabad, Pakistan
| | - Farzana L Ansari
- Department of Chemistry, Quaid-i-Azam University, 45320 Islamabad, Pakistan
| | - Awais Shaukat
- Department of Chemistry, Quaid-i-Azam University, 45320 Islamabad, Pakistan
| | - Usman Nasir
- Department of Electrical Engineering, COMSAT Institute of IT, Islamabad, Pakistan.
| | - Aftab Ahmed
- Department of Science Education, Faculty of Education, Iqbal Open University, Islamabad, Pakistan
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Streeter CC, Lin Q, Firestine SM. Isatins Inhibit N 5-CAIR Synthetase by a Substrate Depletion Mechanism. Biochemistry 2019; 58:2260-2268. [PMID: 30964980 DOI: 10.1021/acs.biochem.8b00939] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The continued rise of antibiotic-resistant infections coupled with the limited pipeline of new antimicrobials highlights the pressing need for the development of new antibacterial agents. One potential pathway for new agents is de novo purine biosynthesis as studies have shown that bacteria and lower eukaryotes synthesize purines differently than humans. Microorganisms utilize two enzymes, N5-CAIR synthetase and N5-CAIR mutase, to convert 5-aminoimidazole ribonucleotide (AIR) into 4-carboxy-5-aminoimidazole ribonucleotide (CAIR) through the intermediate N5-carboxy-5-aminoimidazole ribonucleotide (N5-CAIR). In contrast, vertebrates directly convert AIR to CAIR via the enzyme AIR carboxylase. A high-throughput screen against N5-CAIR synthetase identified a group of compounds with a 2,3-indolinedione (isatin) core that inhibited the enzyme. While initial studies suggested that isatins inhibited the enzyme by a noncompetitive mechanism, here we show that isatins inhibit N5-CAIR synthetase by a substrate depletion mechanism. Unexpectedly, we found that isatin reacts rapidly and reversibly with the substrate AIR. The rate of the reaction is dependent upon the substituents on the phenyl moiety of isatin, with 5- and 7-bromoisatin being faster than 4-bromoisatin. These studies suggest that care should be taken when exploring isatin compounds because the biological activity could be a result of their reactivity.
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Affiliation(s)
- Cale C Streeter
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences , Wayne State University , Detroit , Michigan 48201 , United States
| | - Qian Lin
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences , Wayne State University , Detroit , Michigan 48201 , United States
| | - Steven M Firestine
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences , Wayne State University , Detroit , Michigan 48201 , United States
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Synthesis, characterization, crystal structure and DNA-binding studies of two zinc(II) complexes with the V-shaped bis(benzimidazole)-thiapropane and its derivative ligand. Inorganica Chim Acta 2012. [DOI: 10.1016/j.ica.2011.12.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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4
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A V-shaped ligand 1,3-bis(1-methylbenzimidazol-2-yl)-2-oxapropane and its Cu(II) complex: Synthesis, crystal structure, antioxidation and DNA-binding properties. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2011; 105:190-7. [DOI: 10.1016/j.jphotobiol.2011.09.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 09/01/2011] [Accepted: 09/05/2011] [Indexed: 01/22/2023]
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Le Nours J, Bulloch EMM, Zhang Z, Greenwood DR, Middleditch MJ, Dickson JMJ, Baker EN. Structural analyses of a purine biosynthetic enzyme from Mycobacterium tuberculosis reveal a novel bound nucleotide. J Biol Chem 2011; 286:40706-16. [PMID: 21956117 DOI: 10.1074/jbc.m111.291138] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Enzymes of the de novo purine biosynthetic pathway have been identified as essential for the growth and survival of Mycobacterium tuberculosis and thus have potential for the development of anti-tuberculosis drugs. The final two steps of this pathway are carried out by the bifunctional enzyme 5-aminoimidazole-4-carboxamide ribonucleotide transformylase/inosine monophosphate cyclohydrolase (ATIC), also known as PurH. This enzyme has already been the target of anti-cancer drug development. We have determined the crystal structures of the M. tuberculosis ATIC (Rv0957) both with and without the substrate 5-aminoimidazole-4-carboxamide ribonucleotide, at resolutions of 2.5 and 2.2 Å, respectively. As for other ATIC enzymes, the protein is folded into two domains, the N-terminal domain (residues 1-212) containing the cyclohydrolase active site and the C-terminal domain (residues 222-523) containing the formyltransferase active site. An adventitiously bound nucleotide was found in the cyclohydrolase active site in both structures and was identified by NMR and mass spectral analysis as a novel 5-formyl derivative of an earlier intermediate in the biosynthetic pathway 4-carboxy-5-aminoimidazole ribonucleotide. This result and other studies suggest that this novel nucleotide is a cyclohydrolase inhibitor. The dimer formed by M. tuberculosis ATIC is different from those seen for human and avian ATICs, but it has a similar ∼50-Å separation of the two active sites of the bifunctional enzyme. Evidence in M. tuberculosis ATIC for reactivity of half-the-sites in the cyclohydrolase domains can be attributed to ligand-induced movements that propagate across the dimer interface and may be a common feature of ATIC enzymes.
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Affiliation(s)
- Jérôme Le Nours
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
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Iaroshenko VO, Ostrovskyi D, Petrosyan A, Mkrtchyan S, Villinger A, Langer P. Synthesis of Fluorinated Purine and 1-Deazapurine Glycosides as Potential Inhibitors of Adenosine Deaminase. J Org Chem 2011; 76:2899-903. [DOI: 10.1021/jo102579g] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Viktor O. Iaroshenko
- Institut für Chemie der Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany
- National Taras Shevchenko University, Volodymyrska st 62., Kyiv-33, 01033, Ukraine
| | - Dmytro Ostrovskyi
- Institut für Chemie der Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany
- National Taras Shevchenko University, Volodymyrska st 62., Kyiv-33, 01033, Ukraine
| | - Andranik Petrosyan
- Institut für Chemie der Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany
| | - Satenik Mkrtchyan
- Institut für Chemie der Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany
| | - Alexander Villinger
- Institut für Chemie der Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany
| | - Peter Langer
- Institut für Chemie der Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany
- Leibniz Institut für Katalyse e.V. an der Universität Rostock, Albert-Einstein-Strasse 29a, D-18059 Rostock, Germany
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Samota MK, Seth G. Synthesis, characterization, and antimicrobial activity of palladium(II) and platinum(II) complexes with 2-substituted benzoxazole ligands. HETEROATOM CHEMISTRY 2010. [DOI: 10.1002/hc.20578] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Charafeddine A, Chapuis H, Strazewski P. Facile and Rapid Access to Inosine Puromycin Analogues through the Use of Adenylate Deaminase. Org Lett 2007; 9:2787-90. [PMID: 17592852 DOI: 10.1021/ol070818q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To study the ribosomal peptidyl transfer, puromycin analogues are of interest in which adenine has been replaced by hypoxanthine. We synthesized inosine puromycin analogues from 3'-azidodeoxyadenosine derivatives using adenylate deaminase for the quantitative transformation of the N-heterocycle. The amino acid coupling was carried out under Staudinger-Vilarrasa conditions in 94% yield starting from the protected and in 82% using the unprotected azide, thus, in the presence of two hydroxyls and a lactam function.
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Affiliation(s)
- Adib Charafeddine
- Laboratoire de Synthèse de Biomolécules, UMR 5246, ICBMS, Bâtiment Eugène Chevreul 5ième Etage, Université Claude Bernard Lyon 1, Villeurbanne Cedex, France
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9
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Vyskocilová P, Hornik P, Friedecký D, Frycák P, Lemr K, Adam T. Synthesis and mass spectrometric fragmentation characteristics of imidazole ribosides-analogs of intermediates of purine de novo synthetic pathway. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2007; 25:1237-40. [PMID: 17065098 DOI: 10.1080/15257770600894691] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Two inherited deficiencies have been described in purine de novo synthesis pathway. Both the defects are diagnosed by detecting ribosides--dephosphorylated substrates of the enzymes--in patient's urine. We describe here a synthesis and mass spectrometric fragmentation of ribosides potentially of diagnostic importance for defects in the second part of the pathway. All the species, except 5-amino-4-imidazolesuccinocarboxamideriboside can be synthesized from the commercially available 5-amino-4-imidazolecarboxamideriboside by chemical methods. Fragmentation spectra of the compounds were obtained by the ion trap mass spectrometry. During fragmentation an opening of the imidazole ring was not observed for any of the compounds but loss of its substituents in the form of small molecules (NH3, CO2, CO) is the major route of fragmentation. The ribose moiety cleaves off molecule(s) of water, undergoes a cross-ring cleavage or breaks away as a whole.
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Affiliation(s)
- P Vyskocilová
- Department of Clinical Biochemistry, Laboratory for Inherited Metabolic Disorders, Medical Hospital, Olomouc, Czech Republic
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Ginder ND, Binkowski DJ, Fromm HJ, Honzatko RB. Nucleotide complexes of Escherichia coli phosphoribosylaminoimidazole succinocarboxamide synthetase. J Biol Chem 2006; 281:20680-20688. [PMID: 16687397 DOI: 10.1074/jbc.m602109200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phosphoribosylaminoimidazole-succinocarboxamide synthetase (SAICAR synthetase) converts 4-carboxy-5-aminoimidazole ribonucleotide (CAIR) to 4-(N-succinylcarboxamide)-5-aminoimidazole ribonucleotide (SAICAR). The enzyme is a target of natural products that impair cell growth. Reported here are the crystal structures of the ADP and the ADP.CAIR complexes of SAICAR synthetase from Escherichia coli, the latter being the first instance of a CAIR-ligated SAICAR synthetase. ADP and CAIR bind to the active site in association with three Mg(2+), two of which coordinate the same oxygen atom of the 4-carboxyl group of CAIR; whereas, the third coordinates the alpha- and beta-phosphoryl groups of ADP. The ADP.CAIR complex is the basis for a transition state model of a phosphoryl transfer reaction involving CAIR and ATP, but also supports an alternative chemical pathway in which the nucleophilic attack of l-aspartate precedes the phosphoryl transfer reaction. The polypeptide fold for residues 204-221 of the E. coli structure differs significantly from those of the ligand-free SAICAR synthetase from Thermatoga maritima and the adenine nucleotide complexes of the synthetase from Saccharomyces cerevisiae. Conformational differences between the E. coli, T. maritima, and yeast synthetases suggest the possibility of selective inhibition of de novo purine nucleotide biosynthesis in microbial organisms.
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Affiliation(s)
- Nathaniel D Ginder
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
| | - Daniel J Binkowski
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
| | - Herbert J Fromm
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
| | - Richard B Honzatko
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011.
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11
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Agh-Atabay NM, Dulger B, Gucin F. Structural characterization and antimicrobial activity of 1,3-bis(2-benzimidazyl)-2-thiapropane ligand and its Pd(II) and Zn(II) halide complexes. Eur J Med Chem 2005; 40:1096-102. [PMID: 15992966 DOI: 10.1016/j.ejmech.2005.05.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2004] [Revised: 03/24/2005] [Accepted: 05/09/2005] [Indexed: 12/01/2022]
Abstract
1,3-Bis(2-benzimidazyl)-2-thiapropane(L) forms 5-coordinate square pyramidal and 4-coordinate tetrahedral, monometallic complexes with PdCl(2) and ZnX(2) (X=Cl, Br, I), respectively. In the palladium complex, the ligand acts as a chelating tridentate, through two of the nitrogen atoms in the imidazole ring and the sulfur atom of the bridging group together with two chloride ions forming a rare five coordinate complex. In the zinc halide complexes, the ligand acts as chelating bidentate, via two of the nitrogen atoms combined with two halide ions giving common tetrahedral complexes. The ligand and its complexes are characterized by analytical data and spectroscopic methods such as FT-Raman, FT-IR (mid-IR, far-IR), (1)H and (13)C NMR. Their antimicrobial activities are evaluated by the minimal inhibitory concentration (MIC) against 10 bacteria, each with multiple, fresh clinical isolates (10-15), and the results are compared with those of ampicillin, ciprofloxacin, cefazolin, ofloxacin, and piperacillin antibacterial agents. The compound's antifungal activities are reported on Candida albicans, Candida utilis, and Cryptococcus neoformans yeasts, each with multiple isolates (10), and the results are referenced with amphotericin-B, fluconazole and flucytosine antifungal agents. In most cases, the compounds show broad-spectrum (Gram(+) and Gram(-)) activities that are either, more active, or equipotent to, the antibiotic and antifungal agents in the comparison tests.
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Affiliation(s)
- Naz M Agh-Atabay
- Department of Chemistry, Faculty of Arts and Science, Fatih University, 34500 Buyukcekmece, Istanbul, Turkey.
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Ciuffreda P, Buzzi B, Alessandrini L, Santaniello E. Activity of Adenosine Deaminase (ADA) and Adenylate Deaminase (AMPDA) Towards 6-Chloropurine Nucleosides Modified in the Ribose Moiety. European J Org Chem 2004. [DOI: 10.1002/ejoc.200400380] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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13
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Wall M, Shim JH, Benkovic SJ. Human AICAR transformylase: role of the 4-carboxamide of AICAR in binding and catalysis. Biochemistry 2000; 39:11303-11. [PMID: 10985775 DOI: 10.1021/bi0007268] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have prepared 4-substituted analogues of 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) to investigate the specificity and mechanism of AICAR transformylase (AICAR Tfase). Of the nine analogues of AICAR studied, only one analogue, 5-aminoimidazole-4-thiocarboxamide ribonucleotide, was a substrate, and it was converted to 6-mercaptopurine ribonucleotide. The other analogues either did not bind or were competitive inhibitors, the most potent being 5-amino-4-nitroimidazole ribonucleotide with a K(i) of 0.7 +/- 0.5 microM. The results show that the 4-carboxamide of AICAR is essential for catalysis, and it is proposed to assist in mediating proton transfer, catalyzing the reaction by trapping of the addition compound. AICAR analogues where the nitrogen of the 4-carboxamide was derivatized with a methyl or an allylic group did not bind AICAR Tfase, as determined by pre-steady-state burst kinetics; however, these compounds were potent inhibitors of IMP cyclohydrolase (IMP CHase), a second activity of the bifunctional mammalian enzyme (K(i) = 0.05 +/- 0.02 microM for 4-N-allyl-AlCAR). It is proposed that the conformation of the carboxamide moiety required for binding to AICAR Tfase is different than the conformation required for binding to IMP CHase, which is supported by inhibition studies of purine ribonucleotides. It is shown that 5-formyl-AICAR (FAICAR) is a product inhibitor of AICAR Tfase with K(i) of 0.4 +/- 0.1 microM. We have determined the equilibrium constant of the transformylase reaction to be 0.024 +/- 0.001, showing that the reaction strongly favors AICAR and the 10-formyl-folate cofactor. The coupling of the AICAR Tfase and IMP CHase activities on a single polypeptide allows the overall conversion of AICAR to IMP to be favorable by coupling the unfavorable formation of FAICAR with the highly favorable cyclization reaction. The current kinetic studies have also indicated that the release of FAICAR is the rate-limiting step, under steady-state conditions, in the bifunctional enzyme and channeling is not observed between AICAR Tfase and IMP CHase.
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Affiliation(s)
- M Wall
- Department of Chemistry, 415 Wartik Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Meyer E, Kappock TJ, Osuji C, Stubbe J. 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; 38:3012-8. [PMID: 10074353 DOI: 10.1021/bi9827159] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Formation of 4-carboxy-5-aminoimidazole ribonucleotide (CAIR) in the purine pathway in most prokaryotes requires ATP, HCO3-, aminoimidazole ribonucleotide (AIR), and the gene products PurK and PurE. PurK catalyzes the conversion of AIR to N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) in a reaction that requires both ATP and HCO3-. PurE catalyzes the unusual rearrangement of N5-CAIR to CAIR. To investigate the mechanism of this rearrangement, [4,7-13C]-N5-CAIR and [7-14C]-N5-CAIR were synthesized and separately incubated with PurE in the presence of ATP, aspartate, and 4-(N-succinocarboxamide)-5-aminoimidazole ribonucleotide (SAICAR) synthetase (PurC). The SAICAR produced was isolated and analyzed by NMR spectroscopy or scintillation counting, respectively. The PurC trapping of CAIR as SAICAR was required because of the reversibility of the PurE reaction. Results from both experiments reveal that the carboxylate group of the carbamate of N5-CAIR is transferred directly to generate CAIR without equilibration with CO2/HCO3- in solution. The mechanistic implications of these results relative to the PurE-only (CO2- and AIR-requiring) AIR carboxylases are discussed.
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Affiliation(s)
- E Meyer
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139, USA
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