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Vetting MW, Errey JC, Blanchard JS. Rv0802c from Mycobacterium tuberculosis: the first structure of a succinyltransferase with the GNAT fold. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:978-85. [PMID: 18997321 PMCID: PMC2581710 DOI: 10.1107/s1744309108031679] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Accepted: 09/30/2008] [Indexed: 05/27/2023]
Abstract
Gene rv0802c from Mycobacterium tuberculosis encodes a 218-amino-acid protein and is annotated as a hypothetical protein with homology to GCN5-related N-acetyltransferases. The structure of Rv0802c was determined in an unliganded form to 2.0 A resolution utilizing single-wavelength anomalous dispersion from a samarium soak that resulted in a single bound Sm(3+):citrate(2) complex. The structure confirms that Rv0802c exhibits the GCN5-related N-acetyltransferase fold and revealed a tetramer composed of a dimer of dimers with approximate 222 symmetry. In addition, a bound acetate ion indicated that Rv0802c may utilize a unique acyl donor for the family. The subsequent determination of the structure of Rv0802c in complex with succinyl-CoA to 2.3 A resolution suggests that Rv0802c is the first known GCN5-related N-acetyltransferase family member to utilize succinyl-CoA as a substrate.
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Affiliation(s)
- Matthew W Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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52
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Gao F, Yan X, Zahr O, Larsen A, Vong K, Auclair K. Synthesis and use of sulfonamide-, sulfoxide-, or sulfone-containing aminoglycoside-CoA bisubstrates as mechanistic probes for aminoglycoside N-6'-acetyltransferase. Bioorg Med Chem Lett 2008; 18:5518-22. [PMID: 18805003 PMCID: PMC3084191 DOI: 10.1016/j.bmcl.2008.09.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Revised: 09/02/2008] [Accepted: 09/03/2008] [Indexed: 10/21/2022]
Abstract
Aminoglycoside-coenzyme A conjugates are challenging synthetic targets because of the wealth of functional groups and high polarity of the starting materials. We previously reported a one-pot synthesis of amide-linked aminoglycoside-CoA bisubstrates. These molecules are nanomolar inhibitors of aminoglycoside N-6'-acetyltransferase Ii (AAC(6')-Ii), an important enzyme involved in bacterial resistance to aminoglycoside antibiotics. We report here the synthesis and biological activity of five new aminoglycoside-CoA bisubstrates containing sulfonamide, sulfoxide, or sulfone groups. Interestingly, the sulfonamide-linked bisubstrate, which was expected to best mimic the tetrahedral intermediate, does not show improved inhibition when compared with amide-linked bisubstrates. On the other hand, most of the sulfone- and sulfoxide-containing bisubstrates prepared are nanomolar inhibitors of AAC(6')-Ii.
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Affiliation(s)
| | | | - Omar Zahr
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada, H3A 2K6
| | - Aaron Larsen
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada, H3A 2K6
| | - Kenward Vong
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada, H3A 2K6
| | - Karine Auclair
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada, H3A 2K6
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53
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Lombès T, Bégis G, Maurice F, Turcaud S, Lecourt T, Dardel F, Micouin L. NMR-guided fragment-based approach for the design of AAC(6')-Ib ligands. Chembiochem 2008; 9:1368-71. [PMID: 18464231 DOI: 10.1002/cbic.200700677] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Thomas Lombès
- Chimie Thérapeutique, UMR 8638, Université Paris Descartes, CNRS, 4 avenue de l'Observatoire, 75006 Paris, France
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54
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Vetting MW, Bareich DC, Yu M, Blanchard JS. Crystal structure of RimI from Salmonella typhimurium LT2, the GNAT responsible for N(alpha)-acetylation of ribosomal protein S18. Protein Sci 2008; 17:1781-90. [PMID: 18596200 DOI: 10.1110/ps.035899.108] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The three ribosomal proteins L7, S5, and S18 are included in the rare subset of prokaryotic proteins that are known to be N(alpha)-acetylated. The GCN5-related N-acetyltransferase (GNAT) protein RimI, responsible for the N(alpha)-acetylation of the ribosomal protein S18, was cloned from Salmonella typhimurium LT2 (RimI(ST)), overexpressed, and purified to homogeneity. Steady-state kinetic parameters for RimI(ST) were determined for AcCoA and a peptide substrate consisting of the first six amino acids of the target protein S18. The crystal structure of RimI(ST) was determined in complex with CoA, AcCoA, and a CoA-S-acetyl-ARYFRR bisubstrate inhibitor. The structures are consistent with a direct nucleophilic addition-elimination mechanism with Glu103 and Tyr115 acting as the catalytic base and acid, respectively. The RimI(ST)-bisubstrate complex suggests that several residues change conformation upon interacting with the N terminus of S18, including Glu103, the proposed active site base, facilitating proton exchange and catalysis.
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Affiliation(s)
- Matthew W Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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55
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Chu X, Wu L, Liu X, Li N, Li D. Detection of broad-spectrum aminoglycoside antibiotics through fluorescence-labeling aminoglycoside acetyltransferase(6′)-Ii. Anal Biochem 2008; 376:144-50. [DOI: 10.1016/j.ab.2008.01.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Revised: 01/19/2008] [Accepted: 01/21/2008] [Indexed: 11/25/2022]
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56
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Davies AM, Tata R, Chauviac FX, Sutton BJ, Brown PR. Structure of a putative acetyltransferase (PA1377) from Pseudomonas aeruginosa. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:338-42. [PMID: 18453699 PMCID: PMC2376411 DOI: 10.1107/s1744309108007665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Accepted: 03/20/2008] [Indexed: 05/26/2023]
Abstract
Gene PA1377 from Pseudomonas aeruginosa encodes a 177-amino-acid conserved hypothetical protein of unknown function. The structure of this protein (termed pitax) has been solved in space group I222 to 2.25 A resolution. Pitax belongs to the GCN5-related N-acetyltransferase family and contains all four sequence motifs conserved among family members. The beta-strand structure in one of these motifs (motif A) is disrupted, which is believed to affect binding of the substrate that accepts the acetyl group from acetyl-CoA.
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Affiliation(s)
- Anna M. Davies
- Randall Division of Cell and Molecular Biophysics, King’s College London, New Hunt’s House, Guy’s Campus, London Bridge, London SE1 1UL, England
| | - Renée Tata
- Randall Division of Cell and Molecular Biophysics, King’s College London, New Hunt’s House, Guy’s Campus, London Bridge, London SE1 1UL, England
| | - François-Xavier Chauviac
- Randall Division of Cell and Molecular Biophysics, King’s College London, New Hunt’s House, Guy’s Campus, London Bridge, London SE1 1UL, England
| | - Brian J. Sutton
- Randall Division of Cell and Molecular Biophysics, King’s College London, New Hunt’s House, Guy’s Campus, London Bridge, London SE1 1UL, England
| | - Paul R. Brown
- Randall Division of Cell and Molecular Biophysics, King’s College London, New Hunt’s House, Guy’s Campus, London Bridge, London SE1 1UL, England
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57
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Jana S, Deb JK. Molecular understanding of aminoglycoside action and resistance. Appl Microbiol Biotechnol 2006; 70:140-50. [PMID: 16391922 DOI: 10.1007/s00253-005-0279-0] [Citation(s) in RCA: 187] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Revised: 11/23/2005] [Accepted: 11/27/2005] [Indexed: 11/26/2022]
Abstract
Aminoglycosides are potent bactericidal antibiotics targeting the bacterial ribosome, where they bind to the A-site and disrupt protein synthesis. They are particularly active against aerobic, Gram-negative bacteria and act synergistically against certain Gram-positive organisms. Aminoglycosides are used in the treatment of severe infections of the abdomen and urinary tract, bacteremia, and endocarditis. They are also used for prophylaxis, especially against endocarditis. Bacterial resistance to aminoglycosides continues to escalate and is widely recognized as a serious health threat. This might be the reason for the interest in understanding the mechanisms of resistance. It is now clear that the resistance occurs by different mechanisms such as prevention of drug entry, active extrusion of drugs, alteration of the drug target (mutational modification of 16S rRNA and mutational modification of ribosomal proteins), and enzymatic inactivation through the expression of enzymes, which covalently modify these antibiotics. Enzymatic inactivation is normally due to acetyltransferases, nucleotidyltransferases, and phosphotransferases. In this review, we focus on the recent concept of molecular understanding of aminoglycoside action and resistance.
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Affiliation(s)
- S Jana
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi
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58
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Gao F, Yan X, Baettig OM, Berghuis AM, Auclair K. Regio- and chemoselective 6'-N-derivatization of aminoglycosides: bisubstrate inhibitors as probes to study aminoglycoside 6'-N-acetyltransferases. Angew Chem Int Ed Engl 2006; 44:6859-62. [PMID: 16206301 DOI: 10.1002/anie.200501399] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Feng Gao
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, H3A 2K6, Canada
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59
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Vetting MW, Yu M, Rendle PM, Blanchard JS. The substrate-induced conformational change of Mycobacterium tuberculosis mycothiol synthase. J Biol Chem 2005; 281:2795-802. [PMID: 16326705 DOI: 10.1074/jbc.m510798200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The structure of the ternary complex of mycothiol synthase from Mycobacterium tuberculosis with bound desacetylmycothiol and CoA was determined to 1.8 A resolution. The structure of the acetyl-CoA-binary complex had shown an active site groove that was several times larger than its substrate. The structure of the ternary complex reveals that mycothiol synthase undergoes a large conformational change in which the two acetyltransferase domains are brought together through shared interactions with the functional groups of desacetylmycothiol, thereby decreasing the size of this large central groove. A comparison of the binary and ternary structures illustrates many of the features that promote catalysis. Desacetylmycothiol is positioned with its primary amine in close proximity and in the proper orientation for direct nucleophilic attack on the si-face of the acetyl group of acetyl-CoA. Glu-234 and Tyr-294 are positioned to act as a general base and general acid to promote acetyl transfer. In addition, this structure provides further evidence that the N-terminal acetyltransferase domain no longer has enzymatic activity and is vestigial in nature.
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Affiliation(s)
- Matthew W Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461-1602, USA
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60
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Gao F, Yan X, Baettig OM, Berghuis AM, Auclair K. Regio- and Chemoselective 6′-N-Derivatization of Aminoglycosides: Bisubstrate Inhibitors as Probes To Study Aminoglycoside 6′-N-Acetyltransferases. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200501399] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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61
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Pourreza A, Witherspoon M, Fox J, Newmark J, Bui D, Tolmasky ME. Mutagenesis analysis of a conserved region involved in acetyl coenzyme A binding in the aminoglycoside 6'-N-acetyltransferase type Ib encoded by plasmid pJHCMW1. Antimicrob Agents Chemother 2005; 49:2979-82. [PMID: 15980378 PMCID: PMC1168681 DOI: 10.1128/aac.49.7.2979-2982.2005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Alanine scanning of motif A in the pJHCMW1-encoded aminoglycoside 6'-N-acetyltransferase type Ib identified amino acids important for the ability of the enzyme to confer wild-type levels of resistance to kanamycin and amikacin. The replacement of two amino acids, D117 or L120, with alanine residues resulted in complete loss of the resistance phenotype.
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Affiliation(s)
- Atousa Pourreza
- Department of Biological Science, School of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, California 92834-6850, USA
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Vetting MW, de Carvalho LPS, Roderick SL, Blanchard JS. A novel dimeric structure of the RimL Nalpha-acetyltransferase from Salmonella typhimurium. J Biol Chem 2005; 280:22108-14. [PMID: 15817456 DOI: 10.1074/jbc.m502401200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RimL is responsible for converting the prokaryotic ribosomal protein from L12 to L7 by acetylation of its N-terminal amino group. We demonstrate that purified RimL is capable of posttranslationally acetylating L12, exhibiting a V(max) of 21 min(-1). We have also determined the apostructure of RimL from Salmonella typhimurium and its complex with coenzyme A, revealing a homodimeric oligomer with structural similarity to other Gcn5-related N-acetyltransferase superfamily members. A large central trough located at the dimer interface provides sufficient room to bind both L12 N-terminal helices. Structural and biochemical analysis indicates that RimL proceeds by single-step transfer rather than a covalent-enzyme intermediate. This is the first structure of a Gcn5-related N-acetyltransferase family member with demonstrated activity toward a protein N(alpha)-amino group and is a first step toward understanding the molecular basis for N(alpha)acetylation and its function in cellular regulation.
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Affiliation(s)
- Matthew W Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461-1602, USA
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63
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Vetting MW, S de Carvalho LP, Yu M, Hegde SS, Magnet S, Roderick SL, Blanchard JS. Structure and functions of the GNAT superfamily of acetyltransferases. Arch Biochem Biophys 2005; 433:212-26. [PMID: 15581578 DOI: 10.1016/j.abb.2004.09.003] [Citation(s) in RCA: 463] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Revised: 09/02/2004] [Indexed: 11/15/2022]
Abstract
The Gcn5-related N-acetyltransferases are an enormous superfamily of enzymes that are universally distributed in nature and that use acyl-CoAs to acylate their cognate substrates. In this review, we will examine those members of this superfamily that have been both structurally and mechanistically characterized. These include aminoglycoside N-acetyltransferases, serotonin N-acetyltransferase, glucosamine-6-phosphate N-acetyltransferase, the histone acetyltransferases, mycothiol synthase, protein N-myristoyltransferase, and the Fem family of amino acyl transferases.
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Affiliation(s)
- Matthew W Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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64
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Vetting MW, Roderick SL, Yu M, Blanchard JS. Crystal structure of mycothiol synthase (Rv0819) from Mycobacterium tuberculosis shows structural homology to the GNAT family of N-acetyltransferases. Protein Sci 2003; 12:1954-9. [PMID: 12930994 PMCID: PMC2323992 DOI: 10.1110/ps.03153703] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Mycothiol is the predominant low-molecular weight thiol produced by actinomycetes, including Mycobacterium tuberculosis. The last reaction in the biosynthetic pathway for mycothiol is catalyzed by mycothiol synthase (MshD), which acetylates the cysteinyl amine of cysteine-glucosamine-inositol (Cys-GlcN-Ins). The crystal structure of MshD was determined in the presence of coenzyme A and acetyl-CoA. MshD consists of two tandem-repeated domains, each exhibiting the Gcn5-related N-acetyltransferase (GNAT) fold. These two domains superimpose with a root-mean-square deviation of 1.7 A over 88 residues, and each was found to bind one molecule of coenzyme, although the binding sites are quite different. The C-terminal domain has a similar active site to many GNAT members in which the acetyl group of the coenzyme is presented to an open active site slot. However, acetyl-CoA bound to the N-terminal domain is buried, and is apparently not positioned to promote acetyl transfer. A modeled substrate complex indicates that Cys-GlcN-Ins would only fill a portion of a negatively charged channel located between the two domains. This is the first structure determined for an enzyme involved in the biosynthesis of mycothiol.
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Affiliation(s)
- Matthew W Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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