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Dutta S, Chandra A. A Multiple Proton Transfer Mechanism for the Charging Step of the Aminoacylation Reaction at the Active Site of Aspartyl tRNA Synthetase. J Chem Inf Model 2023; 63:1819-1832. [PMID: 36893463 DOI: 10.1021/acs.jcim.2c01332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Aspartyl-tRNA synthetase catalyzes the attachment of aspartic acid to its cognate tRNA by the aminoacylation reaction during the initiation of the protein biosynthesis process. In the second step of the aminoacylation reaction, known as the charging step, the aspartate moiety is transferred from aspartyl-adenylate to the 3'-OH of A76 of tRNA through a proton transfer process. We have investigated different pathways for the charging step through three separate QM/MM simulations combined with the enhanced sampling method of well-sliced metadynamics and found out the most feasible pathway for the reaction at the active site of the enzyme. In the charging reaction, both the phosphate group and the ammonium group after deprotonation can potentially act as a base for proton transfer in the substrate-assisted mechanism. We have considered three possible mechanisms involving different pathways of proton transfer, and only one of them is determined to be enzymatically feasible. The free energy landscape along reaction coordinates where the phosphate group acts as the general base showed that, in the absence of water, the barrier height is 52.6 kcal/mol. The free energy barrier is reduced to 39.7 kcal/mol when the active site water molecules are also treated quantum mechanically, thus allowing a water mediated proton transfer. The charging reaction involving the ammonium group of the aspartyl adenylate is found to follow a path where first a proton from the ammonium group moves to a water in the vicinity forming a hydronium ion (H3O+) and NH2 group. The hydronium ion subsequently passes the proton to the Asp233 residue, thus minimizing the chance of back proton transfer from hydronium to the NH2 group. The neutral NH2 group subsequently takes the proton from the O3' of A76 with a free energy barrier of 10.7 kcal/mol. In the next step, the deprotonated O3' makes a nucleophilic attack to the carbonyl carbon forming a tetrahedral transition state with a free energy barrier of 24.8 kcal/mol. Thus, the present work shows that the charging step proceeds through a multiple proton transfer mechanism where the amino group formed after deprotonation acts as the base to capture a proton from O3' of A76 rather than the phosphate group. The current study also shows the important role played by Asp233 in the proton transfer process.
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Affiliation(s)
- Saheb Dutta
- Department of Chemistry, Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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Ohtsuka H, Kobayashi M, Shimasaki T, Sato T, Akanuma G, Kitaura Y, Otsubo Y, Yamashita A, Aiba H. Magnesium depletion extends fission yeast lifespan via general amino acid control activation. Microbiologyopen 2021; 10:e1176. [PMID: 33970532 PMCID: PMC8088111 DOI: 10.1002/mbo3.1176] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 12/31/2022] Open
Abstract
Nutrients including glucose, nitrogen, sulfur, zinc, and iron are involved in the regulation of chronological lifespan (CLS) of yeast, which serves as a model of the lifespan of differentiated cells of higher organisms. Herein, we show that magnesium (Mg2+) depletion extends CLS of the fission yeast Schizosaccharomyces pombe through a mechanism involving the Ecl1 gene family. We discovered that ecl1+ expression, which extends CLS, responds to Mg2+ depletion. Therefore, we investigated the underlying intracellular responses. In amino acid auxotrophic strains, Mg2+ depletion robustly induces ecl1+ expression through the activation of the general amino acid control (GAAC) pathway—the equivalent of the amino acid response of mammals. Polysome analysis indicated that the expression of Ecl1 family genes was required for regulating ribosome amount when cells were starved, suggesting that Ecl1 family gene products control the abundance of ribosomes, which contributes to longevity through the activation of the evolutionarily conserved GAAC pathway. The present study extends our understanding of the cellular response to Mg2+ depletion and its influence on the mechanism controlling longevity.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Mikuto Kobayashi
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Teppei Sato
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Genki Akanuma
- Department of Life Science, College of Sciences, Rikkyo University, Tokyo, Japan.,Department of Life Science, Graduate School of Science, Gakushuin University, Tokyo, Japan
| | - Yasuyuki Kitaura
- Laboratory of Nutritional Biochemistry, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yoko Otsubo
- Laboratory of Cell Responses, National Institute for Basic Biology, Okazaki, Japan.,National Institute for Fusion Science, Toki, Japan.,Center for Novel Science Initiatives, National Institutes of Natural Sciences, Okazaki, Japan
| | - Akira Yamashita
- Laboratory of Cell Responses, National Institute for Basic Biology, Okazaki, Japan.,Center for Novel Science Initiatives, National Institutes of Natural Sciences, Okazaki, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies, Okazaki, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
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3
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Saha A, Nandi N. Role of the transfer ribonucleic acid (tRNA) bound magnesium ions in the charging step of aminoacylation reaction in the glutamyl tRNA synthetase and the seryl tRNA synthetase bound with cognate tRNA. J Biomol Struct Dyn 2021; 40:8538-8559. [PMID: 33896406 DOI: 10.1080/07391102.2021.1914732] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Aminoacylation reaction is the first step of protein biosynthesis. Transfer RNA (tRNA) is charged with an amino acid in this reaction and the reaction is catalyzed by aminoacyl tRNA synthetase enzyme (aaRS). In the present work, we use classical molecular dynamics simulation to show that the tRNA bound Mg2+ ions significantly influence the charging step of class I TtGluRS: Glu-AMP: tRNAGlu and class II dimeric TtSerRS: Ser-AMP: tRNASer. The CCA end of the acceptor terminal is disordered in the absence of coordinated Mg2+ ions and the CCA end can freely explore beyond the specific conformational space of the tRNA in its precharging state. A balance between the conformational disorder of the tRNA and the restriction imposed on the CCA terminal via coordination with the Mg2+ ions is needed for the placement of the CCA terminal in a precharging state organization. This result provides a molecular-level explanation of the experimental observation that the presence of Mg2+ ions is a necessary condition for a successful aminoacylation reaction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amrita Saha
- Department of Chemistry, University of Kalyani, Kalyani, Nadia, West Bengal, India
| | - Nilashis Nandi
- Department of Chemistry, University of Kalyani, Kalyani, Nadia, West Bengal, India
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4
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Panigrahi GC, Qureshi R, Jakkula P, Kumar KA, Khan N, Qureshi IA. Leishmanial aspartyl-tRNA synthetase: Biochemical, biophysical and structural insights. Int J Biol Macromol 2020; 165:2869-2885. [PMID: 33736288 DOI: 10.1016/j.ijbiomac.2020.10.140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/04/2020] [Accepted: 10/16/2020] [Indexed: 11/18/2022]
Abstract
Aminoacyl tRNA synthetases (aaRSs) are integral components of protein biosynthesis along with several non-canonical cellular processes. Inhibition studies of aaRSs presented these enzymes as promising drug targets in many pathogens, however aspartyl tRNA synthetase has not been studied in trypanosomatids despite its essentiality. Hence, full-length ORF of Leishmania donovani aspartyl tRNA synthetase (LdaspRS) was cloned and purified to homogeneity followed by molecular mass determination. The aminoacylation assay established that the purified protein performs its function optimally at physiological pH and temperature. The kinetic parameters of LdaspRS revealed the affinity of l-aspartate towards the enzyme to be very much lower than the cofactor. Our study also highlights the moonlighting function of LdaspRS to stimulate the pro-inflammatory cytokines and nitric oxide generation by host macrophage. Furthermore, CD and intrinsic tryptophan fluorescence measurements showed the changes in structural conformation at varying pH, denaturants and ligands. The modelled LdaspRS structure presented all the specific characteristics of class II aaRSs, while in silico study suggested binding of pyrimidine-derived inhibitors in its cofactor binding site with high affinity followed by validation using MD simulation. Altogether, this study could provide a platform for exploring LdaspRS to develop potential therapeutics against leishmaniasis.
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Affiliation(s)
- Girish Ch Panigrahi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Rahila Qureshi
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Pranay Jakkula
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - K Amith Kumar
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Nooruddin Khan
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Insaf Ahmed Qureshi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India.
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5
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Tan K, Zhou M, Jedrzejczak RP, Wu R, Higuera RA, Borek D, Babnigg G, Joachimiak A. Structures of teixobactin-producing nonribosomal peptide synthetase condensation and adenylation domains. Curr Res Struct Biol 2020; 2:14-24. [PMID: 34235466 PMCID: PMC8244413 DOI: 10.1016/j.crstbi.2020.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 01/09/2020] [Accepted: 01/13/2020] [Indexed: 11/28/2022] Open
Abstract
The recently discovered antibiotic teixobactin is produced by uncultured soil bacteria. The antibiotic inhibits cell wall synthesis of Gram-positive bacteria by binding to precursors of cell wall building blocks, and therefore it is thought to be less vulnerable to development of resistance. Teixobactin is synthesized by two nonribosomal peptide synthetases (NRPSs), encoded by txo1 and txo2 genes. Like other NRPSs, the Txo1 and Txo2 synthetases are large, multifunctional, and comprised of several modules. Each module is responsible for catalysis of a distinct step of teixobactin synthesis and contains specific functional units, commonly including a condensation (C) domain, an adenylation (A) domain, and a peptidyl carrier protein (PCP) domain. Here we report the structures of the C-A bidomains of the two L-Ser condensing modules, from Txo1 and Txo2, respectively. In the structure of the C domain of the L-Ser subunit of Txo1, a large conformational change is observed, featuring an outward swing of its N-terminal α-helix. This repositioning, if functionally validated, provides the necessary conformational change for the condensation reaction in C domain, and likely represents a regulatory mechanism. In an Acore subdomain, a well-coordinated Mg2+ cation is observed, which is required in the adenylation reaction. The Mg2+-binding site is defined by a largely conserved amino acid sequence motif and is coordinated by the α-phosphate group of AMP (or ATP) when present, providing some structural evidence for the role of the metal cation in the catalysis of A domain.
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Key Words
- A domain, Adenylation domain
- Acore subdomain, Large N-terminal subdomain of A domain
- Adenylation domain
- Asub subdomain, Small C-terminal subdomain of A domain
- C domain, Condensation domain
- CCterm subdomain, C-terminal subdomain of C domain
- CNterm subdomain, N-terminal subdomain of C domain
- COMA domain, Acceptor communication-mediating domain
- COMD domain, Donor communication-mediating domain
- Condensation domain
- Conformational change
- MES, 2- morpholinoethane sulfonic acid
- Mg2+-binding
- NRPS, Nonribosomal peptide synthetase
- Nonribosomal peptide synthetase
- PCP domain, Peptidyl carrier domain
- RMSD, Root-mean-square deviation
- SAD, Single wavelength diffraction
- SSM, Secondary-structure matching
- Teixobactin
- Txo1
- Txo2
- α-helix regulation
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Affiliation(s)
- Kemin Tan
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA
- Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave. Lemont, IL 60439, USA
| | - Min Zhou
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA
- Biosciences, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Robert P. Jedrzejczak
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA
- Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave. Lemont, IL 60439, USA
| | - Ruiying Wu
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA
- Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave. Lemont, IL 60439, USA
| | - Raul A. Higuera
- BUILDing SCHOLARS, The University of Texas at El Paso, 500 W. University Ave, El Paso, TX 79968, USA
| | - Dominika Borek
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gyorgy Babnigg
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA
- Biosciences, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA
- Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave. Lemont, IL 60439, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60367, USA
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Hewitt SH, Ali R, Mailhot R, Antonen CR, Dodson CA, Butler SJ. A simple, robust, universal assay for real-time enzyme monitoring by signalling changes in nucleoside phosphate anion concentration using a europium(iii)-based anion receptor. Chem Sci 2019; 10:5373-5381. [PMID: 31191895 PMCID: PMC6540902 DOI: 10.1039/c9sc01552c] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 04/24/2019] [Indexed: 12/28/2022] Open
Abstract
Enzymes that consume and produce nucleoside polyphosphate (NPP) anions represent major targets in drug discovery. For example, protein kinases are one of the largest classes of drug targets in the fight against cancer. The accurate determination of enzyme kinetics and mechanisms is a critical aspect of drug discovery research. To increase confidence in the selection of lead drug compounds it is crucial that pharmaceutical researchers have robust, affordable assays to measure enzyme activity accurately. We present a simple, sensitive microplate assay for real-time monitoring of a range of pharmaceutically important enzyme reactions that generate NPP anions, including kinases and glycosyltransferases. Our assay utilises a single, stable europium(iii) complex that binds reversibly to NPP anions, signalling the dynamic changes in NPP product/substrate ratio during an enzyme reaction using time-resolved luminescence. This supramolecular approach to enzyme monitoring overcomes significant limitations in existing assays, obviating the need for expensive antibodies or equipment, chemically labelled substrates or products and isolation or purification steps. Our label and antibody-free method enables rapid and quantitative analysis of enzyme activities and inhibition, offering a potentially powerful tool for use in drug discovery, suitable for high-throughput screening of inhibitors and accurate measurements of enzyme kinetic parameters.
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Affiliation(s)
- Sarah H Hewitt
- Department of Chemistry , Loughborough University , Epinal Way , Loughborough , LE11 3TU , UK .
| | - Rozee Ali
- Department of Chemistry , Loughborough University , Epinal Way , Loughborough , LE11 3TU , UK .
| | - Romain Mailhot
- Department of Chemistry , Loughborough University , Epinal Way , Loughborough , LE11 3TU , UK .
| | - Chloe R Antonen
- Department of Chemistry , Loughborough University , Epinal Way , Loughborough , LE11 3TU , UK .
| | - Charlotte A Dodson
- Department of Pharmacy & Pharmacology , University of Bath , Claverton Down , Bath , BA2 7AY , UK
| | - Stephen J Butler
- Department of Chemistry , Loughborough University , Epinal Way , Loughborough , LE11 3TU , UK .
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Clark L, Leatherby D, Krilich E, Ropelewski AJ, Perozich J. In silico analysis of class I adenylate-forming enzymes reveals family and group-specific conservations. PLoS One 2018; 13:e0203218. [PMID: 30180199 PMCID: PMC6122825 DOI: 10.1371/journal.pone.0203218] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/16/2018] [Indexed: 12/24/2022] Open
Abstract
Luciferases, aryl- and fatty-acyl CoA synthetases, and non-ribosomal peptide synthetase proteins belong to the class I adenylate-forming enzyme superfamily. The reaction catalyzed by the adenylate-forming enzymes is categorized by a two-step process of adenylation and thioesterification. Although all of these proteins perform a similar two-step process, each family may perform the process to yield completely different results. For example, luciferase proteins perform adenylation and oxidation to produce the green fluorescent light found in fireflies, while fatty-acyl CoA synthetases perform adenylation and thioesterification with coenzyme A to assist in metabolic processes involving fatty acids. This study aligned a total of 374 sequences belonging to the adenylate-forming superfamily. Analysis of the sequences revealed five fully conserved residues throughout all sequences, as well as 78 more residues conserved in at least 60% of sequences aligned. Conserved positions are involved in magnesium and AMP binding and maintaining enzyme structure. Also, ten conserved sequence motifs that included most of the conserved residues were identified. A phylogenetic tree was used to assign sequences into nine different groups. Finally, group entropy analysis identified novel conservations unique to each enzyme group. Common group-specific positions identified in multiple groups include positions critical to coordinating AMP and the CoA-bound product, a position that governs active site shape, and positions that help to maintain enzyme structure through hydrogen bonds and hydrophobic interactions. These positions could serve as excellent targets for future research.
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Affiliation(s)
- Louis Clark
- Department of Biology, Franciscan University of Steubenville, Steubenville, OH, United States of America
| | - Danielle Leatherby
- Department of Biology, Franciscan University of Steubenville, Steubenville, OH, United States of America
| | - Elizabeth Krilich
- Department of Biology, Franciscan University of Steubenville, Steubenville, OH, United States of America
| | - Alexander J Ropelewski
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - John Perozich
- Department of Biology, Franciscan University of Steubenville, Steubenville, OH, United States of America
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Hewitt SH, Parris J, Mailhot R, Butler SJ. A continuous luminescence assay for monitoring kinase activity: signalling the ADP/ATP ratio using a discrete europium complex. Chem Commun (Camb) 2018; 53:12626-12629. [PMID: 29131206 DOI: 10.1039/c7cc05887j] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We report the application of a stable cationic europium complex [Eu.1]+ in a continuous-read luminescence assay for kinase activity. [Eu.1]+ binds reversibly to ATP and ADP in water, at neutral pH, in the presence of Mg2+ ions, providing distinctive luminescence responses that permits the kinase-catalysed conversion of ATP to ADP to be monitored in real-time.
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Affiliation(s)
- Sarah H Hewitt
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, UK.
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Liu X, Ngo HT, Ge Z, Butler SJ, Jolliffe KA. Tuning colourimetric indicator displacement assays for naked-eye sensing of pyrophosphate in aqueous media. Chem Sci 2013. [DOI: 10.1039/c3sc22233k] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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Butler SJ, Jolliffe KA. Selective Pyrophosphate Recognition by Cyclic Peptide Receptors in Physiological Saline. Chem Asian J 2012; 7:2621-8. [DOI: 10.1002/asia.201200627] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Indexed: 11/06/2022]
Affiliation(s)
- Stephen J. Butler
- School of Chemistry (Building F11), The University of Sydney, NSW, 2006, Australia, Fax: (+61) 2‐9351‐3329
| | - Katrina A. Jolliffe
- School of Chemistry (Building F11), The University of Sydney, NSW, 2006, Australia, Fax: (+61) 2‐9351‐3329
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12
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Wang H, Xu W, Zhang H, Li D, Yang Z, Xie X, Li T, Liu X. EcoRI-modified gold nanoparticles for dual-mode colorimetric detection of magnesium and pyrophosphate ions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:1987-1992. [PMID: 21671433 DOI: 10.1002/smll.201100470] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 04/11/2011] [Indexed: 05/30/2023]
Affiliation(s)
- Hongbo Wang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
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Schmelz S, Naismith JH. Adenylate-forming enzymes. Curr Opin Struct Biol 2010; 19:666-71. [PMID: 19836944 DOI: 10.1016/j.sbi.2009.09.004] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Revised: 08/26/2009] [Accepted: 09/15/2009] [Indexed: 01/06/2023]
Abstract
Thioesters, amides, and esters are common chemical building blocks in a wide array of natural products. The formation of these bonds can be catalyzed in a variety of ways. For chemists, the use of an activating group is a common strategy and adenylate enzymes are exemplars of this approach. Adenylating enzymes activate the otherwise unreactive carboxylic acid by transforming the normal hydroxyl leaving group into adenosine monophosphate. Recently there have been a number of studies of such enzymes and in this review we suggest a new classification scheme. The review highlights the diversity in enzyme fold, active site architecture, and metal coordination that has evolved to catalyze this particular reaction.
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Affiliation(s)
- Stefan Schmelz
- Scottish Structural Proteomics Facility and Biomedical Science Research Complex, The University of St Andrews, Scotland KY16 9ST, UK
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