1
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Saha D, Nath Jha A. Computational multi-target approach to target essential enzymes of Leishmania donovani using comparative molecular dynamic simulations and MMPBSA analysis. PHYTOCHEMICAL ANALYSIS : PCA 2023; 34:842-854. [PMID: 36760044 DOI: 10.1002/pca.3213] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/13/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Visceral leishmaniasis (VL) is caused by Leishmania donovani. The purine and pyrimidine pathways are essential for L. donovani. Simultaneously inhibiting multiple targets could be an effective strategy to eliminate the pathogen and treat VL. OBJECTIVE We aimed to target the essential enzymes of L. donovani and inhibit them using a multi-target approach. MATERIALS AND METHODS A systematic analytical method was followed, in which first reported inhibitors of two essential enzymes (adenine phosphoribosyl-transferase [APRT] and dihydroorotate dehydrogenase [DHODH]) were collected and then ADMET and PASS analyses were conducted using the Lipinski rule and Veber's rule. Additionally, molecular docking between screened ligands and proteins were performed. The stability of complexes was analyzed using molecular dynamics (MD) simulations and MMPBSA analysis. RESULTS Initially, 6,220 unique molecules were collected from the PubChem database, and then the Lipinski rule and Veber's rule were used for screening. In total, 203 compounds passed the ADMET test; their antileishmanial properties were tested by PASS analysis. As a result, 15 ligands were identified. Molecular docking simulations between APRT or DHODH and these 15 ligands were performed. Four molecules were found to be plant-derived compounds. Lig_2 and Lig_3 had good docking scores with both proteins. MD simulations were performed to determine the dynamic behavior and binding patterns of complexes. Both MD simulations and MMPBSA analysis showed Lig_3 is a promising antileishmanial inhibitor of both targets. CONCLUSION Promising plant-derived compounds that might be used to combat VL were obtained through a multi-target approach.
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Affiliation(s)
- Debanjan Saha
- Computational Biophysics Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | - Anupam Nath Jha
- Computational Biophysics Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
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2
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Glockzin K, Meneely KM, Hughes R, Maatouk SW, Piña GE, Suthagar K, Clinch K, Buckler JN, Lamb AL, Tyler PC, Meek TD, Katzfuss A. Kinetic and Structural Characterization of Trypanosoma cruzi Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferases and Repurposing of Transition-State Analogue Inhibitors. Biochemistry 2023. [PMID: 37418678 DOI: 10.1021/acs.biochem.3c00116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
Over 70 million people are currently at risk of developing Chagas Disease (CD) infection, with more than 8 million people already infected worldwide. Current treatments are limited and innovative therapies are required. Trypanosoma cruzi, the etiological agent of CD, is a purine auxotroph that relies on phosphoribosyltransferases to salvage purine bases from their hosts for the formation of purine nucleoside monophosphates. Hypoxanthine-guanine-xanthine phosphoribosyltransferases (HGXPRTs) catalyze the salvage of 6-oxopurines and are promising targets for the treatment of CD. HGXPRTs catalyze the formation of inosine, guanosine, and xanthosine monophosphates from 5-phospho-d-ribose 1-pyrophosphate and the nucleobases hypoxanthine, guanine, and xanthine, respectively. T. cruzi possesses four HG(X)PRT isoforms. We previously reported the kinetic characterization and inhibition of two isoforms, TcHGPRTs, demonstrating their catalytic equivalence. Here, we characterize the two remaining isoforms, revealing nearly identical HGXPRT activities in vitro and identifying for the first time T. cruzi enzymes with XPRT activity, clarifying their previous annotation. TcHGXPRT follows an ordered kinetic mechanism with a postchemistry event as the rate-limiting step(s) of catalysis. Its crystallographic structures reveal implications for catalysis and substrate specificity. A set of transition-state analogue inhibitors (TSAIs) initially developed to target the malarial orthologue were re-evaluated, with the most potent compound binding to TcHGXPRT with nanomolar affinity, validating the repurposing of TSAIs to expedite the discovery of lead compounds against orthologous enzymes. We identified mechanistic and structural features that can be exploited in the optimization of inhibitors effective against TcHGPRT and TcHGXPRT concomitantly, which is an important feature when targeting essential enzymes with overlapping activities.
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Affiliation(s)
- Kayla Glockzin
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, Texas 77843-2128, United States
| | - Kathleen M Meneely
- Department of Chemistry, University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, United States
| | - Ryan Hughes
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, Texas 77843-2128, United States
| | - Sean W Maatouk
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, Texas 77843-2128, United States
| | - Grace E Piña
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, Texas 77843-2128, United States
| | - Kajitha Suthagar
- Ferrier Research Institute, Victoria University of Wellington, Gracefield Research Centre, 69 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand
| | - Keith Clinch
- Ferrier Research Institute, Victoria University of Wellington, Gracefield Research Centre, 69 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand
| | - Joshua N Buckler
- Ferrier Research Institute, Victoria University of Wellington, Gracefield Research Centre, 69 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand
| | - Audrey L Lamb
- Department of Chemistry, University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, United States
| | - Peter C Tyler
- Ferrier Research Institute, Victoria University of Wellington, Gracefield Research Centre, 69 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand
| | - Thomas D Meek
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, Texas 77843-2128, United States
| | - Ardala Katzfuss
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, Texas 77843-2128, United States
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3
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Glockzin K, Kostomiris D, Minnow YVT, Suthagar K, Clinch K, Gai S, Buckler JN, Schramm VL, Tyler PC, Meek TD, Katzfuss A. Kinetic Characterization and Inhibition of Trypanosoma cruzi Hypoxanthine–Guanine Phosphoribosyltransferases. Biochemistry 2022; 61:2088-2105. [PMID: 36193631 PMCID: PMC9536471 DOI: 10.1021/acs.biochem.2c00312] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
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Chagas disease, caused by the parasitic protozoan Trypanosoma cruzi, affects over 8 million people
worldwide. Current antiparasitic treatments for Chagas disease are
ineffective in treating advanced, chronic stages of the disease, and
are noted for their toxicity. Like most parasitic protozoa, T. cruzi is unable to synthesize purines de novo, and relies on the salvage of preformed purines
from the host. Hypoxanthine–guanine phosphoribosyltransferases
(HGPRTs) are enzymes that are critical for the salvage of preformed
purines, catalyzing the formation of inosine monophosphate (IMP) and
guanosine monophosphate (GMP) from the nucleobases hypoxanthine and
guanine, respectively. Due to the central role of HGPRTs in purine
salvage, these enzymes are promising targets for the development of
new treatment methods for Chagas disease. In this study, we characterized
two gene products in the T. cruzi CL
Brener strain that encodes enzymes with functionally identical HGPRT
activities in vitro: TcA (TcCLB.509693.70) and TcC
(TcCLB.506457.30). The TcC isozyme was kinetically characterized to
reveal mechanistic details on catalysis, including identification
of the rate-limiting step(s) of catalysis. Furthermore, we identified
and characterized inhibitors of T. cruzi HGPRTs originally developed as transition-state analogue inhibitors
(TSAIs) of Plasmodium falciparum hypoxanthine–guanine–xanthine
phosphoribosyltransferase (PfHGXPRT), where the most
potent compound bound to T. cruzi HGPRT
with low nanomolar affinity. Our results validated the repurposing
of TSAIs to serve as selective inhibitors for orthologous molecular
targets, where primary and secondary structures as well as putatively
common chemical mechanisms are conserved.
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Affiliation(s)
- Kayla Glockzin
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, Texas 77843-2128, United States
| | - Demetrios Kostomiris
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, Texas 77843-2128, United States
| | - Yacoba V. T. Minnow
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461-1602, United States
| | - Kajitha Suthagar
- Ferrier Research Institute, Victoria University of Wellington, Gracefield Research Centre, 69 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand
| | - Keith Clinch
- Ferrier Research Institute, Victoria University of Wellington, Gracefield Research Centre, 69 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand
| | - Sinan Gai
- Ferrier Research Institute, Victoria University of Wellington, Gracefield Research Centre, 69 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand
| | - Joshua N. Buckler
- Ferrier Research Institute, Victoria University of Wellington, Gracefield Research Centre, 69 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand
| | - Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461-1602, United States
| | - Peter C. Tyler
- Ferrier Research Institute, Victoria University of Wellington, Gracefield Research Centre, 69 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand
| | - Thomas D. Meek
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, Texas 77843-2128, United States
| | - Ardala Katzfuss
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, Texas 77843-2128, United States
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4
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Glockzin K, Meek TD, Katzfuss A. Characterization of adenine phosphoribosyltransferase (APRT) activity in Trypanosoma brucei brucei: Only one of the two isoforms is kinetically active. PLoS Negl Trop Dis 2022; 16:e0009926. [PMID: 35104286 PMCID: PMC8836349 DOI: 10.1371/journal.pntd.0009926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/11/2022] [Accepted: 01/22/2022] [Indexed: 11/17/2022] Open
Abstract
Human African Trypanosomiasis (HAT), also known as sleeping sickness, is a Neglected Tropical Disease endemic to 36 African countries, with approximately 70 million people currently at risk for infection. Current therapeutics are suboptimal due to toxicity, adverse side effects, and emerging resistance. Thus, both effective and affordable treatments are urgently needed. The causative agent of HAT is the protozoan Trypanosoma brucei ssp. Annotation of its genome confirms previous observations that T. brucei is a purine auxotroph. Incapable of de novo purine synthesis, these protozoan parasites rely on purine phosphoribosyltransferases to salvage purines from their hosts for the synthesis of purine monophosphates. Complete and accurate genome annotations in combination with the identification and characterization of the catalytic activity of purine salvage enzymes enables the development of target-specific therapies in addition to providing a deeper understanding of purine metabolism in T. brucei. In trypanosomes, purine phosphoribosyltransferases represent promising drug targets due to their essential and central role in purine salvage. Enzymes involved in adenine and adenosine salvage, such as adenine phosphoribosyltransferases (APRTs, EC 2.4.2.7), are of particular interest for their potential role in the activation of adenine and adenosine-based pro-drugs. Analysis of the T. brucei genome shows two putative aprt genes: APRT1 (Tb927.7.1780) and APRT2 (Tb927.7.1790). Here we report studies of the catalytic activity of each putative APRT, revealing that of the two T. brucei putative APRTs, only APRT1 is kinetically active, thereby signifying a genomic misannotation of Tb927.7.1790 (putative APRT2). Reliable genome annotation is necessary to establish potential drug targets and identify enzymes involved in adenine and adenosine-based pro-drug activation.
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Affiliation(s)
- Kayla Glockzin
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Thomas D. Meek
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
- * E-mail: (TDM); (AK)
| | - Ardala Katzfuss
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
- * E-mail: (TDM); (AK)
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5
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Shen Q, Zhang SJ, Xue YZ, Peng F, Cheng DY, Xue YP, Zheng YG. Biological synthesis of nicotinamide mononucleotide. Biotechnol Lett 2021; 43:2199-2208. [PMID: 34626279 DOI: 10.1007/s10529-021-03191-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 09/23/2021] [Indexed: 01/09/2023]
Abstract
Nicotinamide mononucleotide (NMN) or Nicotinamide-1-ium-1-β-D-ribofuranoside 5'-phosphate is a nucleotide that can be converted into nicotinamide adenine dinucleotide (NAD) in human cells. NMN has recently attracted great attention because of its potential as an anti-aging drug, leading to great efforts for its effective manufacture. The chemical synthesis of NMN is a challenging task since it is an isomeric compound with a complicated structure. The majority of biological synthetic routes for NMN is through the intermediate phosphoribosyl diphosphate (PRPP), which is further converted to NMN by nicotinamide phosphoribosyltransferase (Nampt). There are various routes for the synthesis of PRPP from simple starting materials such as ribose, adenosine, and xylose, but all of these require the expensive phosphate donor adenosine triphosphate (ATP). Thus, an ATP regeneration system can be included, leading to diminished ATP consumption during the catalytic process. The regulations of enzymes that are not directly involved in the synthesis of NMN are also critical for the production of NMN. The aim of this review is to present an overview of the biological production of NMN with respect to the critical enzymes, reaction conditions, and productivity.
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Affiliation(s)
- Qi Shen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Shi-Jia Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Yu-Zhen Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Feng Peng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Dong-Yuan Cheng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China. .,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
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6
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Acyclic nucleoside phosphonates with adenine nucleobase inhibit Trypanosoma brucei adenine phosphoribosyltransferase in vitro. Sci Rep 2021; 11:13317. [PMID: 34172767 PMCID: PMC8233378 DOI: 10.1038/s41598-021-91747-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/28/2021] [Indexed: 02/08/2023] Open
Abstract
All medically important unicellular protozoans cannot synthesize purines de novo and they entirely rely on the purine salvage pathway (PSP) for their nucleotide generation. Therefore, purine derivatives have been considered as a promising source of anti-parasitic compounds since they can act as inhibitors of the PSP enzymes or as toxic products upon their activation inside of the cell. Here, we characterized a Trypanosoma brucei enzyme involved in the salvage of adenine, the adenine phosphoribosyl transferase (APRT). We showed that its two isoforms (APRT1 and APRT2) localize partly in the cytosol and partly in the glycosomes of the bloodstream form (BSF) of the parasite. RNAi silencing of both APRT enzymes showed no major effect on the growth of BSF parasites unless grown in artificial medium with adenine as sole purine source. To add into the portfolio of inhibitors for various PSP enzymes, we designed three types of acyclic nucleotide analogs as potential APRT inhibitors. Out of fifteen inhibitors, four compounds inhibited the activity of the recombinant APRT1 with Ki in single µM values. The ANP phosphoramidate membrane-permeable prodrugs showed pronounced anti-trypanosomal activity in a cell-based assay, despite the fact that APRT enzymes are dispensable for T. brucei growth in vitro. While this suggests that the tested ANP prodrugs exert their toxicity by other means in T. brucei, the newly designed inhibitors can be further improved and explored to identify their actual target(s).
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7
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Ngivprom U, Kluaiphanngam S, Ji W, Siriwibool S, Kamkaew A, Ketudat Cairns JR, Zhang Q, Lai RY. Characterization of NucPNP and NucV involved in the early steps of nucleocidin biosynthesis in Streptomyces calvus. RSC Adv 2021; 11:3510-3515. [PMID: 35424298 PMCID: PMC8694150 DOI: 10.1039/d0ra10878b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 12/18/2022] Open
Abstract
Nucleocidin 1 produced by Streptomyces calvus is one of five characterized natural products containing fluorine. It was discovered in 1956, but its biosynthesis is not yet completely resolved. Recently, the biosynthetic gene cluster of 1 was identified. The nucPNP gene, which was initially annotated as orf206 and encodes a putative purine nucleoside phosphorylase, is essential for nucleocidin production. In this study, we performed in vitro assays and showed NucPNP produced adenine 3 from methylthioadenosine (MTA) 2 and adenosine 4. We also showed the downstream enzyme, NucV annotated as adenine phosphoribosyltransferase (APRT), catalyzes AMP formation from adenine 3 and 5-phospho-α-d-ribose-1-diphosphate (PRPP) 5. However, the catalytic efficiency of NucV was much slower than its homolog ScAPRT involved in the biosynthesis of canonical purine nucleoside in the same strain. These results provide new insights in nucleocidin biosynthesis and could guide future research on organofluorine formation.
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Affiliation(s)
- Utumporn Ngivprom
- School of Chemistry, Institute of Science, Suranaree University of Technology Nakhon Ratchasima 30000 Thailand
| | - Surayut Kluaiphanngam
- School of Chemistry, Institute of Science, Suranaree University of Technology Nakhon Ratchasima 30000 Thailand
| | - Wenjuan Ji
- Department of Chemistry, Fudan University Shanghai 200433 China
| | - Siriwalee Siriwibool
- School of Chemistry, Institute of Science, Suranaree University of Technology Nakhon Ratchasima 30000 Thailand
| | - Anyanee Kamkaew
- School of Chemistry, Institute of Science, Suranaree University of Technology Nakhon Ratchasima 30000 Thailand
| | - James R Ketudat Cairns
- School of Chemistry, Institute of Science, Suranaree University of Technology Nakhon Ratchasima 30000 Thailand .,Center for Biomolecular Structure, Function and Application, Suranaree University of Technology Nakhon Ratchasima 30000 Thailand
| | - Qi Zhang
- Department of Chemistry, Fudan University Shanghai 200433 China
| | - Rung-Yi Lai
- School of Chemistry, Institute of Science, Suranaree University of Technology Nakhon Ratchasima 30000 Thailand .,Center for Biomolecular Structure, Function and Application, Suranaree University of Technology Nakhon Ratchasima 30000 Thailand
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8
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Ito A, Choi JH, Takemura H, Kotajima M, Wu J, Tokuyama S, Hirai H, Asakawa T, Ouchi H, Inai M, Kan T, Kawagishi H. Biosynthesis of the Fairy Chemicals, 2-Azahypoxanthine and Imidazole-4-carboxamide, in the Fairy Ring-Forming Fungus Lepista sordida. JOURNAL OF NATURAL PRODUCTS 2020; 83:2469-2476. [PMID: 32786881 DOI: 10.1021/acs.jnatprod.0c00394] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Fairy rings resulting from a fungus-plant interaction appear worldwide. 2-Azahypoxanthine (AHX) and imidazole-4-carboxamide (ICA) were first isolated from the culture broth of one of the fairy ring-forming fungi, Lepista sordida. Afterward, a common metabolite of AHX in plants, 2-aza-8-oxohypoxanthine (AOH), was found in AHX-treated rice. The biosynthetic pathway of the three compounds that are named as fairy chemicals (FCs) in plants has been partially elucidated; however, that in mushrooms remains unknown. In this study, it was revealed that the carbon skeletons of AHX and ICA were constructed from Gly in L. sordida mycelia and the fungus metabolized 5-aminoimidazole-4-carboxamide (AICA) to both of the compounds. These results indicated that FCs were biosynthesized by a diversion of the purine metabolic pathway in L. sordida mycelia, similar to that in plants. Furthermore, we showed that recombinant adenine phosphoribosyltransferase (APRT) catalyzed reversible interconversion not only between 5-aminoimidazole-4-carboxamide-1-β-d-ribofuranosyl 5'-monophosphate (AICAR) and AICA but also between ICA-ribotide (ICAR) and ICA. Furthermore, the presence of ICAR in L. sordida mycelia was proven for the first time by LC-MS/MS detection, and this study provided the first report that there was a novel metabolic pathway of ICA in which its ribotide was an intermediate in the fungus.
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Affiliation(s)
- Akinobu Ito
- Research Fellow of Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | | | - Hirohide Takemura
- Research Fellow of Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | | | | | | | | | - Tomohiro Asakawa
- Marine Science and Technology, Tokai University, 4-1-1 Kitakaname, Hiratsuka City, Kanagawa 259-1292, Japan
| | - Hitoshi Ouchi
- Department of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Makoto Inai
- Department of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Toshiyuki Kan
- Department of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
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9
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Ozeir M, Huyet J, Burgevin MC, Pinson B, Chesney F, Remy JM, Siddiqi AR, Lupoli R, Pinon G, Saint-Marc C, Gibert JF, Morales R, Ceballos-Picot I, Barouki R, Daignan-Fornier B, Olivier-Bandini A, Augé F, Nioche P. Structural basis for substrate selectivity and nucleophilic substitution mechanisms in human adenine phosphoribosyltransferase catalyzed reaction. J Biol Chem 2019; 294:11980-11991. [PMID: 31160323 DOI: 10.1074/jbc.ra119.009087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Indexed: 11/06/2022] Open
Abstract
The reversible adenine phosphoribosyltransferase enzyme (APRT) is essential for purine homeostasis in prokaryotes and eukaryotes. In humans, APRT (hAPRT) is the only enzyme known to produce AMP in cells from dietary adenine. APRT can also process adenine analogs, which are involved in plant development or neuronal homeostasis. However, the molecular mechanism underlying substrate specificity of APRT and catalysis in both directions of the reaction remains poorly understood. Here we present the crystal structures of hAPRT complexed to three cellular nucleotide analogs (hypoxanthine, IMP, and GMP) that we compare with the phosphate-bound enzyme. We established that binding to hAPRT is substrate shape-specific in the forward reaction, whereas it is base-specific in the reverse reaction. Furthermore, a quantum mechanics/molecular mechanics (QM/MM) analysis suggests that the forward reaction is mainly a nucleophilic substitution of type 2 (SN2) with a mix of SN1-type molecular mechanism. Based on our structural analysis, a magnesium-assisted SN2-type mechanism would be involved in the reverse reaction. These results provide a framework for understanding the molecular mechanism and substrate discrimination in both directions by APRTs. This knowledge can play an instrumental role in the design of inhibitors, such as antiparasitic agents, or adenine-based substrates.
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Affiliation(s)
- Mohammad Ozeir
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR 1124, Centre Interdisciplinaire Chimie Biologie-Paris, Paris, 75006, France; INSERM, UMR 1124, Paris, 75006, France
| | - Jessica Huyet
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR 1124, Centre Interdisciplinaire Chimie Biologie-Paris, Paris, 75006, France; INSERM, UMR 1124, Paris, 75006, France
| | | | - Benoît Pinson
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, Bordeaux cedex, 33077, France
| | - Françoise Chesney
- Sanofi R&D, Translational Science Unit, Chilly-Mazarin, 91385, France
| | - Jean-Marc Remy
- Sanofi R&D, Translational Science Unit, Chilly-Mazarin, 91385, France
| | - Abdul Rauf Siddiqi
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, 45550, Pakistan
| | - Roland Lupoli
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR 1124, Centre Interdisciplinaire Chimie Biologie-Paris, Paris, 75006, France; INSERM, UMR 1124, Paris, 75006, France
| | - Grégory Pinon
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR 1124, Centre Interdisciplinaire Chimie Biologie-Paris, Paris, 75006, France; INSERM, UMR 1124, Paris, 75006, France; Université Paris Descartes, Structural and Molecular Analysis Platform, Paris, 75006, France
| | - Christelle Saint-Marc
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, Bordeaux cedex, 33077, France
| | | | - Renaud Morales
- Sanofi R&D, Translational Science Unit, Chilly-Mazarin, 91385, France
| | - Irène Ceballos-Picot
- Laboratoire de Biochimie Métabolomique et Protéomique, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Faculté de Médecine Paris Descartes, 75006, France
| | - Robert Barouki
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR 1124, Centre Interdisciplinaire Chimie Biologie-Paris, Paris, 75006, France; INSERM, UMR 1124, Paris, 75006, France; Laboratoire de Biochimie Métabolomique et Protéomique, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Faculté de Médecine Paris Descartes, 75006, France
| | - Bertrand Daignan-Fornier
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, Bordeaux cedex, 33077, France
| | | | - Franck Augé
- Sanofi R&D, Translational Science Unit, Chilly-Mazarin, 91385, France.
| | - Pierre Nioche
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR 1124, Centre Interdisciplinaire Chimie Biologie-Paris, Paris, 75006, France; INSERM, UMR 1124, Paris, 75006, France; Université Paris Descartes, Structural and Molecular Analysis Platform, Paris, 75006, France.
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10
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Eltyshev AK, Suntsova PO, Karmatskaia KD, Taniya OS, Slepukhin PA, Benassi E, Belskaya NP. An effective and facile synthesis of new blue fluorophores on the basis of an 8-azapurine core. Org Biomol Chem 2018; 16:9420-9429. [PMID: 30500034 DOI: 10.1039/c8ob02644k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A convenient synthesis of 2-aryl-2,4-dihydro-5H-[1,2,3]triazolo[4,5-d]pyrimidin-5-ones (DTPs) from 3,3-diamino-2-(arylazo)acrylonitriles through a versatile and readily accessible two-step procedure is described. Density functional theory (DFT) calculations were performed to explain the selectivity of the heterocyclization step, which predominantly afforded 6-amino-5-(arylazo)pyrimidin-2(1H)-thiones in chloroform or ethanol, and 2,3-dihydro-1,2,4-triazines in toluene or DMF. Novel 2-aryl-2,4-dihydro-5H-[1,2,3]triazolo[4,5-d]pyrimidin-5-ones were obtained in good yields and showed absorption in the ultraviolet region and good emission in the blue region. The photophysical properties of DTPs were better than those cited in select literature examples of 8-azapurines. Owing to the facile synthesis and good photophysical characteristics in an aqueous medium, the new DTPs should have potential applications as organic fluorophores in fluorescence imaging and materials science.
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11
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Esipov RS, Timofeev VI, Sinitsyna EV, Tuzova ES, Esipova LV, Kostromina MA, Kuranova IP, Miroshnikov AI. Three-Dimensional Structure of Recombinant Adenine Phosphoribosyltransferase from Thermophilic Bacterial Strain Thermus thermophilus HB27. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1068162018050047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Gene dosage effects in yeast support broader roles for the LOG1, HAM1 and DUT1 genes in detoxification of nucleotide analogues. PLoS One 2018; 13:e0196840. [PMID: 29738539 PMCID: PMC5940212 DOI: 10.1371/journal.pone.0196840] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 04/21/2018] [Indexed: 12/22/2022] Open
Abstract
Purine and pyrimidine analogues have important uses in chemotherapies against cancer, and a better understanding of the mechanisms that cause resistance to these drugs is therefore of importance in cancer treatment. In the yeast Saccharomyces cerevisiae, overexpression of the HAM1 gene encoding inosine triphosphate pyrophosphatase confers resistance to both the purine analogue 6-N-hydroxylaminopurine (HAP) and the pyrimidine analogue 5-fluorouracil (5-FU) (Carlsson et al., 2013, PLoS One 8, e52094). To find out more about the mechanisms of resistance to nucleotide analogues, and possible interdependencies between purine and pyrimidine analogue resistance mechanisms, we screened a plasmid library in yeast for genes that confer HAP resistance when overexpressed. We cloned four such genes: ADE4, DUT1, APT2, and ATR1. We further looked for genetic interactions between these genes and genes previously found to confer resistance to 5-FU. We found that HMS1, LOG1 (YJL055W), HAM1, and ATR1 confer resistance to both 5-FU and HAP, whereas ADE4, DUT1 and APT2 are specific for HAP resistance, and CPA1 and CPA2 specific for 5-FU resistance. Possible mechanisms for 5-FU and HAP detoxification are discussed based on the observed genetic interactions. Based on the effect of LOG1 against both 5-FU and HAP toxicity, we propose that the original function of the LOG (LONELY GUY) family of proteins likely was to degrade non-canonical nucleotides, and that their role in cytokinin production is a later development in some organisms.
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13
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Huyet J, Ozeir M, Burgevin MC, Pinson B, Chesney F, Remy JM, Siddiqi AR, Lupoli R, Pinon G, Saint-Marc C, Gibert JF, Morales R, Ceballos-Picot I, Barouki R, Daignan-Fornier B, Olivier-Bandini A, Augé F, Nioche P. Structural Insights into the Forward and Reverse Enzymatic Reactions in Human Adenine Phosphoribosyltransferase. Cell Chem Biol 2018; 25:666-676.e4. [PMID: 29576532 DOI: 10.1016/j.chembiol.2018.02.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 01/05/2018] [Accepted: 02/22/2018] [Indexed: 10/17/2022]
Abstract
Phosphoribosyltransferases catalyze the displacement of a PRPP α-1'-pyrophosphate to a nitrogen-containing nucleobase. How they control the balance of substrates/products binding and activities is poorly understood. Here, we investigated the human adenine phosphoribosyltransferase (hAPRT) that produces AMP in the purine salvage pathway. We show that a single oxygen atom from the Tyr105 side chain is responsible for selecting the active conformation of the 12 amino acid long catalytic loop. Using in vitro, cellular, and in crystallo approaches, we demonstrated that Tyr105 is key for the fine-tuning of the kinetic activity efficiencies of the forward and reverse reactions. Together, our results reveal an evolutionary pressure on the strictly conserved Tyr105 and on the dynamic motion of the flexible loop in phosphoribosyltransferases that is essential for purine biosynthesis in cells. These data also provide the framework for designing novel adenine derivatives that could modulate, through hAPRT, diseases-involved cellular pathways.
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Affiliation(s)
- Jessica Huyet
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France
| | - Mohammad Ozeir
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France
| | | | - Benoît Pinson
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, Bordeaux Cedex 33077, France
| | - Françoise Chesney
- Sanofi R&D, Translational Science Unit, Chilly-Mazarin 91385, France
| | - Jean-Marc Remy
- Sanofi R&D, Translational Science Unit, Chilly-Mazarin 91385, France
| | - Abdul Rauf Siddiqi
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Roland Lupoli
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France; Université Paris Descartes, Structural and Molecular Analysis Platform, Paris 75006, France
| | - Gregory Pinon
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France; Université Paris Descartes, Structural and Molecular Analysis Platform, Paris 75006, France
| | - Christelle Saint-Marc
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, Bordeaux Cedex 33077, France
| | | | - Renaud Morales
- Sanofi R&D, Translational Science Unit, Chilly-Mazarin 91385, France
| | - Irène Ceballos-Picot
- Laboratoire de Biochimie Métabolomique et Protéomique, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Faculté de Médecine Paris Descartes, Paris 75015, France
| | - Robert Barouki
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France; Laboratoire de Biochimie Métabolomique et Protéomique, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Faculté de Médecine Paris Descartes, Paris 75015, France
| | - Bertrand Daignan-Fornier
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, Bordeaux Cedex 33077, France
| | | | - Franck Augé
- Sanofi R&D, Translational Science Unit, Chilly-Mazarin 91385, France.
| | - Pierre Nioche
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France; Université Paris Descartes, Structural and Molecular Analysis Platform, Paris 75006, France.
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14
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Harris LD, Harijan RK, Ducati RG, Evans GB, Hirsch BM, Schramm VL. Synthesis of bis-Phosphate Iminoaltritol Enantiomers and Structural Characterization with Adenine Phosphoribosyltransferase. ACS Chem Biol 2018; 13:152-160. [PMID: 29178779 DOI: 10.1021/acschembio.7b00601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphoribosyl transferases (PRTs) are essential in nucleotide synthesis and salvage, amino acid, and vitamin synthesis. Transition state analysis of several PRTs has demonstrated ribocation-like transition states with a partial positive charge residing on the pentose ring. Core chemistry for synthesis of transition state analogues related to the 5-phospho-α-d-ribosyl 1-pyrophosphate (PRPP) reactant of these enzymes could be developed by stereospecific placement of bis-phosphate groups on an iminoaltritol ring. Cationic character is provided by the imino group and the bis-phosphates anchor both the 1- and 5-phosphate binding sites. We provide a facile synthetic path to these molecules. Cyclic-nitrone redox methodology was applied to the stereocontrolled synthesis of three stereoisomers of a selectively monoprotected diol relevant to the synthesis of transition-state analogue inhibitors. These polyhydroxylated pyrrolidine natural product analogues were bis-phosphorylated to generate analogues of the ribocationic form of 5-phosphoribosyl 1-phosphate. A safe, high yielding synthesis of the key intermediate represents a new route to these transition state mimics. An enantiomeric pair of iminoaltritol bis-phosphates (L-DIAB and D-DIAB) was prepared and shown to display inhibition of Plasmodium falciparum orotate phosphoribosyltransferase and Saccharomyces cerevisiae adenine phosphoribosyltransferase (ScAPRT). Crystallographic inhibitor binding analysis of L- and D-DIAB bound to the catalytic sites of ScAPRT demonstrates accommodation of both enantiomers by altered ring geometry and bis-phosphate catalytic site contacts.
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Affiliation(s)
- Lawrence D. Harris
- The
Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield
Rd, Lower Hutt, 5010, New Zealand
| | - Rajesh K. Harijan
- Department
of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Rodrigo G. Ducati
- Department
of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Gary B. Evans
- The
Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield
Rd, Lower Hutt, 5010, New Zealand
- The
Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Brett M. Hirsch
- Department
of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Vern L. Schramm
- Department
of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
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15
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Sinitsyna EV, Timofeev VI, Tuzova ES, Kostromina MA, Murav’eva TI, Esipov RS, Kuranova IP. Crystallization and preliminary X-ray diffraction study of recombinant adenine phosphoribosyltransferase from the thermophilic bacterium Thermus thermophilus strain HB27. CRYSTALLOGR REP+ 2017. [DOI: 10.1134/s106377451704023x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Abstract
The development and application of a highly versatile suite of tools for mycobacterial genetics, coupled with widespread use of "omics" approaches to elucidate the structure, function, and regulation of mycobacterial proteins, has led to spectacular advances in our understanding of the metabolism and physiology of mycobacteria. In this article, we provide an update on nucleotide metabolism and DNA replication in mycobacteria, highlighting key findings from the past 10 to 15 years. In the first section, we focus on nucleotide metabolism, ranging from the biosynthesis, salvage, and interconversion of purine and pyrimidine ribonucleotides to the formation of deoxyribonucleotides. The second part of the article is devoted to DNA replication, with a focus on replication initiation and elongation, as well as DNA unwinding. We provide an overview of replication fidelity and mutation rates in mycobacteria and summarize evidence suggesting that DNA replication occurs during states of low metabolic activity, and conclude by suggesting directions for future research to address key outstanding questions. Although this article focuses primarily on observations from Mycobacterium tuberculosis, it is interspersed, where appropriate, with insights from, and comparisons with, other mycobacterial species as well as better characterized bacterial models such as Escherichia coli. Finally, a common theme underlying almost all studies of mycobacterial metabolism is the potential to identify and validate functions or pathways that can be exploited for tuberculosis drug discovery. In this context, we have specifically highlighted those processes in mycobacterial DNA replication that might satisfy this critical requirement.
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17
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Wierzchowski J, Antosiewicz JM, Shugar D. 8-Azapurines as isosteric purine fluorescent probes for nucleic acid and enzymatic research. MOLECULAR BIOSYSTEMS 2015; 10:2756-74. [PMID: 25124808 DOI: 10.1039/c4mb00233d] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The 8-azapurines, and their 7-deaza and 9-deaza congeners, represent a unique class of isosteric (isomorphic) analogues of the natural purines, frequently capable of substituting for the latter in many biochemical processes. Particularly interesting is their propensity to exhibit pH-dependent room-temperature fluorescence in aqueous medium, and in non-polar media. We herein review the physico-chemical properties of this class of compounds, with particular emphasis on the fluorescence emission properties of their neutral and/or ionic species, which has led to their widespread use as fluorescent probes in enzymology, including enzymes involved in purine metabolism, agonists/antagonists of adenosine receptors, mechanisms of catalytic RNAs, RNA editing, etc. They are also exceptionally useful fluorescent probes for analytical and clinical applications in crude cell homogenates.
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Affiliation(s)
- Jacek Wierzchowski
- Department of Biophysics, University of Varmia & Masuria, Oczapowskiego 4, 10-719 Olsztyn, Poland.
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18
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Raman J, Fritz TA, Gerken TA, Jamison O, Live D, Liu M, Tabak LA. The catalytic and lectin domains of UDP-GalNAc:polypeptide alpha-N-Acetylgalactosaminyltransferase function in concert to direct glycosylation site selection. J Biol Chem 2008; 283:22942-51. [PMID: 18562306 PMCID: PMC2517002 DOI: 10.1074/jbc.m803387200] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2008] [Revised: 06/17/2008] [Indexed: 11/06/2022] Open
Abstract
UDP-GalNAc:polypeptide alpha-N-Acetylgalactosaminyltransferases (ppGalNAcTs), a family (EC 2.4.1.41) of enzymes that initiate mucin-type O-glycosylation, are structurally composed of a catalytic domain and a lectin domain. Previous studies have suggested that the lectin domain modulates the glycosylation of glycopeptide substrates and may underlie the strict glycopeptide specificity of some isoforms (ppGalNAcT-7 and -10). Using a set of synthetic peptides and glycopeptides based upon the sequence of the mucin, MUC5AC, we have examined the activity and glycosylation site preference of lectin domain deletion and exchange constructs of the peptide/glycopeptide transferase ppGalNAcT-2 (hT2) and the glycopeptide transferase ppGalNAcT-10 (hT10). We demonstrate that the lectin domain of hT2 directs glycosylation site selection for glycopeptide substrates. Pre-steady-state kinetic measurements show that this effect is attributable to two mechanisms, either lectin domain-aided substrate binding or lectin domain-aided product release following glycosylation. We find that glycosylation of peptide substrates by hT10 requires binding of existing GalNAcs on the substrate to either its catalytic or lectin domain, thereby resulting in its apparent strict glycopeptide specificity. These results highlight the existence of two modes of site selection used by these ppGalNAcTs: local sequence recognition by the catalytic domain and the concerted recognition of distal sites of prior glycosylation together with local sequence binding mediated, respectively, by the lectin and catalytic domains. The latter mode may facilitate the glycosylation of serine or threonine residues, which occur in sequence contexts that would not be efficiently glycosylated by the catalytic domain alone. Local sequence recognition by the catalytic domain differs between hT2 and hT10 in that hT10 requires a pre-existing GalNAc residue while hT2 does not.
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Affiliation(s)
- Jayalakshmi Raman
- Section on Biological Chemistry, NIDDK, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, USA
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19
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Nakasugi K, Svenson CJ, Neilan BA. The competence gene, comF, from Synechocystis sp. strain PCC 6803 is involved in natural transformation, phototactic motility and piliation. MICROBIOLOGY-SGM 2007; 152:3623-3631. [PMID: 17159215 DOI: 10.1099/mic.0.29189-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The gene slr0388 was previously annotated to encode a hypothetical protein in Synechocystis sp. strain PCC 6803. When a positively phototactic strain of this cyanobacterium was insertionally inactivated at slr0388, the mutants were not transformable, and appeared to aggregate as a result of increased bundling of type IV pili. Also, these mutants were rendered non-phototactic compared to the wild-type. Quantitative real-time PCR revealed a 3.5-fold increase in pilA1 transcript levels in the mutant over wild-type cells, while there were no changes in the level of pilT1 and comA transcripts. Supernatant from mutant liquid culture contained more PilA1 protein, confirmed by mass spectrometric analysis, compared to the wild-type cells, which corresponded to the increase in pilA1 transcripts. The increase in PilA1 subunits may contribute to the bundling morphology of pili that was observed, which in turn may act to retard DNA uptake by hindering the retraction of pili. This gene is therefore proposed to be designated comF, as it possesses a phosphoribosyltransferase domain, a distinguishing feature of other ComF proteins of naturally transformable heterotrophic bacteria. This report is the second of a competence-related gene from Synechocystis sp. strain PCC 6803, the product of which does not show homology to other well-studied type IV pili proteins.
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MESH Headings
- Amino Acid Sequence
- Bacterial Proteins/genetics
- Bacterial Proteins/physiology
- DNA Transposable Elements
- Fimbriae Proteins/biosynthesis
- Fimbriae, Bacterial/genetics
- Fimbriae, Bacterial/physiology
- Fimbriae, Bacterial/ultrastructure
- Light
- Microscopy, Electron, Scanning
- Microscopy, Electron, Transmission
- Molecular Sequence Data
- Movement
- Mutagenesis, Insertional
- RNA, Bacterial/biosynthesis
- RNA, Messenger/biosynthesis
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Alignment
- Synechocystis/genetics
- Synechocystis/physiology
- Synechocystis/ultrastructure
- Transformation, Bacterial
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Affiliation(s)
- Kenlee Nakasugi
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Charles J Svenson
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Brett A Neilan
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
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20
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Keough DT, Skinner-Adams T, Jones MK, Ng AL, Brereton IM, Guddat LW, de Jersey J. Lead compounds for antimalarial chemotherapy: purine base analogs discriminate between human and P. falciparum 6-oxopurine phosphoribosyltransferases. J Med Chem 2007; 49:7479-86. [PMID: 17149876 DOI: 10.1021/jm061012j] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The malarial parasite Plasmodium falciparum depends on the purine salvage enzyme hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) to convert purine bases from the host to nucleotides needed for DNA and RNA synthesis. An approach to developing antimalarial drugs is to use HGXPRT to convert introduced purine base analogs to nucleotides that are toxic to the parasite. This strategy requires that these compounds be good substrates for the parasite enzyme but poor substrates for the human counterpart, HGPRT. Bases with a chlorine atom in the 6-position or a nitrogen in the 8-position exhibited strong discrimination between P. falciparum HGXPRT and human HGPRT. The k(cat)/K(m) values for the Plasmodium enzyme using 6-chloroguanine and 8-azaguanine as substrates were 50 - 80-fold and 336-fold higher than for the human enzyme, respectively. These and other bases were effective in inhibiting the growth of the parasite in vitro, giving IC(50) values as low as 1 microM.
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Affiliation(s)
- Dianne T Keough
- School of Molecular and Microbial Sciences, The University of Queensland, 4072, Australia
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21
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Barrett C, Alley J, Pulido JC, Spurling H, Li P, Parsons T, Mallender WD, Bembenek ME. Configuration of a scintillation proximity assay for the activity assessment of recombinant human adenine phosphoribosyltransferase. Assay Drug Dev Technol 2007; 4:661-9. [PMID: 17199504 DOI: 10.1089/adt.2006.4.661] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Adenine phosphoribosyltransferase plays a role in purine salvage by catalyzing the direct conversion of adenine to adenosine monophosphate. The involvement of the purine salvage pathway in tumor proliferation and angiogenesis makes adenine phosphoribosyltransferase a potential target for oncology drug discovery. We have expressed and characterized recombinant, N-terminally His-tagged human adenine phosphoribosyltransferase. Two assay formats were assessed for use in a high throughput screen: a spectrophotometric-based enzyme-coupled assay system and a radiometric ionic capture scintillation proximity bead assay format. Ultimately, the scintillation proximity assay format was chosen because of automated screening compatibility limitations of the coupled assay. We describe here the biochemical characterization of adenine phosphoribosyltransferase and the development of a robust, homogeneous, 384-well assay suitable for high throughput screening.
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Affiliation(s)
- Cynthia Barrett
- Discovery Technologies, Millennium Pharmaceuticals, Inc., Cambridge, MA 02139, USA.
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22
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Raman J, Mehrotra S, Anand RP, Balaram H. Unique kinetic mechanism of Plasmodium falciparum adenylosuccinate synthetase. Mol Biochem Parasitol 2005; 138:1-8. [PMID: 15500910 DOI: 10.1016/j.molbiopara.2004.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2004] [Revised: 06/12/2004] [Accepted: 06/23/2004] [Indexed: 10/26/2022]
Abstract
Adenylosuccinate synthetase (AdSS) catalyses the Mg(2+) dependent formation of adenylosuccinate from IMP and aspartate, the reaction being driven by the hydrolysis of GTP to GDP. All characterized AdSS thus far exhibit a random kinetic mechanism. We present here kinetic evidence that unlike all other AdSS, Plasmodium falciparum AdSS (PfAdSS) has ordered substrate binding. Inhibition studies show that binding of GTP requires IMP binding while aspartate binds to the enzyme-IMP-GTP complex. A structural basis for this difference in mechanism is presented. Kinetically, PfAdSS is closer to the mouse acidic isozyme rather than to the mouse basic isozyme. The mouse acidic isozyme is thought to play a role in the purine nucleotide biosynthetic pathway. Regulation of PfAdSS in vivo can therefore, be expected to be similar to the mouse acidic isozyme, in agreement with the role of PfAdSS as the only pathway for the synthesis of adenine nucleotides in the parasite. However, PfAdSS differs from both the mammalian homologs in that fructose-1,6-bisphosphate, a potent inhibitor of the mammalian enzyme, is an activator of PfAdSS. The differences highlighted here are promising in terms of species-specific drug design, targeting this essential enzyme in the parasite.
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Affiliation(s)
- Jayalakshmi Raman
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
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23
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Silva M, Silva CHTP, Iulek J, Oliva G, Thiemann OH. Crystal structure of adenine phosphoribosyltransferase from Leishmania tarentolae: potential implications for APRT catalytic mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2004; 1696:31-9. [PMID: 14726202 DOI: 10.1016/j.bbapap.2003.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The three-dimensional structure of Leishmania tarentolae adenine phosphoribosyltransferase (APRT) in complex with adenosine-5-monophosphate (AMP) and a phosphate ion has been solved. Refinement against X-ray diffraction data extending to 2.2-A resolution led to a final crystallographic R factor of 18.3%. Structural comparisons amongst this APRT enzyme and other 'type I' PRTases whose structures have been determined reveal several important features of the PRTases catalytic mechanism. Based on structural superpositions and molecular interaction potential calculations, it was possible to suggest that the PRPP is the first substrate to bind, while the AMP is the last product to leave the active site, in accordance to recent kinetic studies performed with the Leishmania donovani APRT.
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Affiliation(s)
- M Silva
- Laboratory of Protein Crystallography and Structural Biology, Physics Institute of São Carlos, University of São Paulo-USP, Av. Trabalhador Sãocarlense 400, PO Box 369, 13566-590, São Carlos, SP, Brazil
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Schramm VL, Grubmeyer C. Phosphoribosyltransferase Mechanisms and Roles in Nucleic Acid Metabolism. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2004; 78:261-304. [PMID: 15210333 DOI: 10.1016/s0079-6603(04)78007-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA
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25
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Abstract
Parasites are responsible for a wide variety of infectious diseases in human as well as in domestic and wild animals, causing an enormous health and economical blight. Current containment strategies are not entirely successful and parasitic infections are on the rise. In the absence of availability of antiparasitic vaccines, chemotherapy remains the mainstay for the treatment of most parasitic diseases. However, there is an urgent need for new drugs to prevent or combat some major parasitic infections because of lack of a single effective approach for controlling the parasites (e.g., trypanosomiasis) or because some serious parasitic infections developed resistance to presently available drugs (e.g., malaria). The rational design of a drug is usually based on biochemical and physiological differences between pathogens and host. Some of the most striking differences between parasites and their mammalian host are found in purine metabolism. Purine nucleotides can be synthesized by the de novo and/or the so-called "salvage" pathways. Unlike their mammalian host, most parasites studied lack the pathways for de novo purine biosynthesis and rely on the salvage pathways to meet their purine demands. Moreover, because of the great phylogenic separation between the host and the parasite, there are in some cases sufficient distinctions between corresponding enzymes of the purine salvage from the host and the parasite that can be exploited to design specific inhibitors or "subversive substrates" for the parasitic enzymes. Furthermore, the specificities of purine transport, the first step in purine salvage, diverge significantly between parasites and their mammalian host. This review highlights the unique transporters and enzymes responsible for the salvage of purines in parasites that could constitute excellent potential targets for the design of safe and effective antiparasitic drugs.
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Affiliation(s)
- Mahmoud H el Kouni
- Department of Pharmacology and Toxicology, Center for AIDS Research, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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26
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Shi W, Sarver AE, Wang CC, Tanaka KSE, Almo SC, Schramm VL. Closed site complexes of adenine phosphoribosyltransferase from Giardia lamblia reveal a mechanism of ribosyl migration. J Biol Chem 2002; 277:39981-8. [PMID: 12171925 DOI: 10.1074/jbc.m205596200] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The adenine phosphoribosyltransferase (APRTase) from Giardia lamblia was co-crystallized with 9-deazaadenine and sulfate or with 9-deazaadenine and Mg-phosphoribosylpyrophosphate. The complexes were solved and refined to 1.85 and 1.95 A resolution. Giardia APRTase is a symmetric homodimer with the monomers built around Rossman fold cores, an element common to all known purine phosphoribosyltransferases. The catalytic sites are capped with a small hood domain that is unique to the APRTases. These structures reveal several features relevant to the catalytic function of APRTase: 1) a non-proline cis peptide bond (Glu(61)-Ser(62)) is required to form the pyrophosphate binding site in the APRTase.9dA.MgPRPP complex but is a trans peptide bond in the absence of pyrophosphate group, as observed in the APRTase.9dA.SO4 complex; 2) a catalytic site loop is closed and fully ordered in both complexes, with Glu(100) from the catalytic loop acting as the acid/base for protonation/deprotonation of N-7 of the adenine ring; 3) the pyrophosphoryl charge is neutralized by a single Mg2+ ion and Arg(63), in contrast to the hypoxanthine-guanine phosphoribosyltransferases, which use two Mg2+ ions; and 4) the nearest structural neighbors to APRTases are the orotate phosphoribosyltransferases, suggesting different paths of evolution for adenine relative to other purine PRTases. An overlap comparison of AMP and 9-deazaadenine plus Mg-PRPP at the catalytic sites of APRTases indicated that reaction coordinate motion involves a 2.1-A excursion of the ribosyl anomeric carbon, whereas the adenine ring and the 5-phosphoryl group remained fixed. G. lamblia APRTase therefore provides another example of nucleophilic displacement by electrophile migration.
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Affiliation(s)
- Wuxian Shi
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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27
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Sarver AE, Wang CC. The adenine phosphoribosyltransferase from Giardia lamblia has a unique reaction mechanism and unusual substrate binding properties. J Biol Chem 2002; 277:39973-80. [PMID: 12171924 DOI: 10.1074/jbc.m205595200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Purine phosphoribosyltransferases catalyze the Mg2+ -dependent reaction that transforms a purine base into its corresponding nucleotide. They are present in a wide variety of organisms including plants, mammals, and parasitic protozoa. Giardia lamblia, the causative agent of giardiasis, lacks de novo purine biosynthesis and relies primarily on adenine and guanine phosphoribosyltransferases (APRTase and GPRTase) constituting two independent and essential purine salvage pathways. The APRTase from G. lamblia was cloned and expressed with a 6-His tag at its C terminus and purified to apparent homogeneity. Adenine and alpha-d-5-phosphoribosyl-1-pyrophosphate (PRPP) have K(m) values of 4.2 and 143 microm with a k(cat) of 2.8 s(-1) in the forward reaction, whereas AMP and PP(i) have K(m) values of 87 and 450 microm with a k(cat) of 9.5 x 10(-3) s(-1) in the reverse reaction. Product inhibition studies indicated that the forward reaction follows a random Bi Bi mechanism. Results from the kinetics of equilibrium isotope exchange further verified a random Bi Bi mechanism in the forward reaction. In a mutant enzyme, F25W, with kinetic constants similar to those of the wild type and a tryptophan residue at the adenine binding site, the addition of adenine or AMP to the free mutant enzyme resulted in fluorescence quenching, whereas PRPP caused fluorescence enhancement. The dissociation constants thus estimated are 16.5 microm for adenine, 14.3 microm for AMP, and 83.0 microm for PRPP. PP(i) exerted no detectable effect on the tryptophan fluorescence at all, suggesting a lack of PP(i) binding to the free enzyme. An ordered substrate binding in the reverse reaction with AMP bound first followed by PP(i) is thus postulated.
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Affiliation(s)
- Anne E Sarver
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143-0446, USA
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