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Patel KD, Oliver RA, Lichstrahl MS, Li R, Townsend CA, Gulick AM. The structure of the monobactam-producing thioesterase domain of SulM forms a unique complex with the upstream carrier protein domain. bioRxiv 2024:2024.04.06.588331. [PMID: 38617275 PMCID: PMC11014566 DOI: 10.1101/2024.04.06.588331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Nonribosomal peptide synthetases (NRPSs) are responsible for the production of important biologically active peptides. The large, multidomain NRPSs operate through an assembly line strategy in which the growing peptide is tethered to carrier domains that deliver the intermediates to neighboring catalytic domains. While most NRPS domains catalyze standard chemistry of amino acid activation, peptide bond formation and product release, some canonical NRPS catalytic domains promote unexpected chemistry. The paradigm monobactam antibiotic sulfazecin is produced through the activity of a terminal thioesterase domain that catalyzes an unusual β-lactam forming reaction in which the nitrogen of the C-terminal N-sulfo-2,3-diaminopropionate residue attacks its thioester tether to release the β-lactam product. We have determined the structure of the thioesterase domain as both a free-standing domain and a didomain complex with the upstream holo peptidyl-carrier domain. The structure illustrates a constrained active site that orients the substrate properly for β-lactam formation. In this regard, the structure is similar to the β-lactone forming thioesterase domain responsible for the production of obafluorin. Analysis of the structure identifies features that are responsible for this four-membered ring closure and enable bioinformatic analysis to identify additional, uncharacterized β-lactam-forming biosynthetic gene clusters by genome mining.
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Affiliation(s)
- Ketan D. Patel
- Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, 14203, USA
| | - Ryan A. Oliver
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218 USA
| | - Michael S. Lichstrahl
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218 USA
| | - Rongfeng Li
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218 USA
| | - Craig A. Townsend
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218 USA
| | - Andrew M. Gulick
- Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, 14203, USA
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2
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Patel KD, Gulick AM. Structural and functional insights into δ-poly-L-ornithine polymer biosynthesis from Acinetobacter baumannii. Commun Biol 2023; 6:982. [PMID: 37752201 PMCID: PMC10522769 DOI: 10.1038/s42003-023-05362-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
Cationic homo-polyamino acid (CHPA) peptides containing isopeptide bonds of diamino acids have been identified from Actinomycetes strains. However, none has been reported from other bacteria. Here, we report a δ-poly-L-ornithine synthetase from Acinetobacter baumannii, which we name PosA. Surprisingly, structural analysis of the adenylation domain and biochemical assay shows L-ornithine as the substrate for PosA. The product from the enzymatic reaction was purified and identified as poly-L-ornithine composed of 7-12 amino acid units. Chemical labeling of the polymer confirmed the isopeptide linkage of δ-poly-L-ornithine. We examine the biological activity of chemically synthesized 12-mer δ-poly-L-ornithine, illustrating that the polymer may act as an anti-fungal agent. Structures of the isolated adenylation domain from PosA are presented with several diamino acids and biochemical assays identify important substrate binding residues. Structurally-guided genome-mining led to the identification of homologs with different substrate binding residues that could activate additional substrates. A homolog from Bdellovibrionales sp. shows modest activity with L-arginine but not with any diamino acids observed to be substrates for previously examined CHPA synthetases. Our study indicates the possibility that additional CHPAs may be produced by various microbes, supporting the further exploration of uncharacterized natural products.
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Affiliation(s)
- Ketan D Patel
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, SUNY, Buffalo, NY, 14203, USA
| | - Andrew M Gulick
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, SUNY, Buffalo, NY, 14203, USA.
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3
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Patel KD, MacDonald MR, Ahmed SF, Singh J, Gulick AM. Structural advances toward understanding the catalytic activity and conformational dynamics of modular nonribosomal peptide synthetases. Nat Prod Rep 2023; 40:1550-1582. [PMID: 37114973 PMCID: PMC10510592 DOI: 10.1039/d3np00003f] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Indexed: 04/29/2023]
Abstract
Covering: up to fall 2022.Nonribosomal peptide synthetases (NRPSs) are a family of modular, multidomain enzymes that catalyze the biosynthesis of important peptide natural products, including antibiotics, siderophores, and molecules with other biological activity. The NRPS architecture involves an assembly line strategy that tethers amino acid building blocks and the growing peptides to integrated carrier protein domains that migrate between different catalytic domains for peptide bond formation and other chemical modifications. Examination of the structures of individual domains and larger multidomain proteins has identified conserved conformational states within a single module that are adopted by NRPS modules to carry out a coordinated biosynthetic strategy that is shared by diverse systems. In contrast, interactions between modules are much more dynamic and do not yet suggest conserved conformational states between modules. Here we describe the structures of NRPS protein domains and modules and discuss the implications for future natural product discovery.
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Affiliation(s)
- Ketan D Patel
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Monica R MacDonald
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Syed Fardin Ahmed
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Jitendra Singh
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Andrew M Gulick
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
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4
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Patel KD, Ahmed SF, MacDonald MR, Gulick AM. Structural Studies of Modular Nonribosomal Peptide Synthetases. Methods Mol Biol 2023; 2670:17-46. [PMID: 37184698 DOI: 10.1007/978-1-0716-3214-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The non-ribosomal peptide synthetases (NRPSs) are a family of modular enzymes involved in the production of peptide natural products. Not restricted by the constraints of ribosomal peptide and protein production, the NRPSs are able to incorporate unusual amino acids and other suitable building blocks into the final product. The NRPSs operate with an assembly line strategy in which peptide intermediates are covalently tethered to a peptidyl carrier protein and transported to different catalytic domains for the multiple steps in the biosynthesis. Often the carrier and catalytic domains are joined into a single large multidomain protein. This chapter serves to introduce the NRPS enzymes, using the nocardicin NRPS system as an example that highlights many common features to NRPS biochemistry. We then describe recent advances in the structural biology of NRPSs focusing on large multidomain structures that have been determined.
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Affiliation(s)
- Ketan D Patel
- Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Syed Fardin Ahmed
- Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Monica R MacDonald
- Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Andrew M Gulick
- Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, USA.
- Department of Structural Biology, Jacobs School of Medicine & Biomedical Sciences, Buffalo, NY, USA.
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5
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Yang J, Banas VS, Patel KD, Rivera GSM, Mydy LS, Gulick AM, Wencewicz TA. An acyl-adenylate mimic reveals the structural basis for substrate recognition by the iterative siderophore synthetase DesD. J Biol Chem 2022; 298:102166. [PMID: 35750210 PMCID: PMC9356276 DOI: 10.1016/j.jbc.2022.102166] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/13/2022] [Accepted: 06/16/2022] [Indexed: 11/18/2022] Open
Abstract
Siderophores are conditionally essential metabolites used by microbes for environmental iron sequestration. Most Streptomyces strains produce hydroxamate-based desferrioxamine (DFO) siderophores composed of repeating units of N1-hydroxy-cadaverine (or N1-hydroxy-putrescine) and succinate. The DFO biosynthetic operon, desABCD, is highly conserved in Streptomyces; however, expression of desABCD alone does not account for the vast structural diversity within this natural product class. Here, we report the in vitro reconstitution and biochemical characterization of four DesD orthologs from Streptomyces strains that produce unique DFO siderophores. Under in vitro conditions, all four DesD orthologs displayed similar saturation steady-state kinetics (Vmax = 0.9–2.5 μM⋅min−1) and produced the macrocyclic trimer DFOE as the favored product, suggesting a conserved role for DesD in the biosynthesis of DFO siderophores. We further synthesized a structural mimic of N1-hydroxy-N1-succinyl-cadaverine (HSC)-acyl-adenylate, the HSC-acyl sulfamoyl adenosine analog (HSC-AMS), and obtained crystal structures of DesD in the ATP-bound, AMP/PPi-bound, and HSC-AMS/Pi-bound forms. We found HSC-AMS inhibited DesD orthologs (IC50 values = 48–53 μM) leading to accumulation of linear trimeric DFOG and di-HSC at the expense of macrocyclic DFOE. Addition of exogenous PPi enhanced DesD inhibition by HSC-AMS, presumably via stabilization of the DesD–HSC-AMS complex, similar to the proposed mode of adenylate stabilization where PPi remains buried in the active site. In conclusion, our data suggest that acyl-AMS derivatives may have utility as chemical probes and bisubstrate inhibitors to reveal valuable mechanistic and structural insight for this unique family of adenylating enzymes.
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Affiliation(s)
- Jinping Yang
- Department of Chemistry, Washington University in St Louis, St Louis, Missouri, USA
| | - Victoria S Banas
- Department of Chemistry, Washington University in St Louis, St Louis, Missouri, USA
| | - Ketan D Patel
- Department of Structural Biology, Jacobs School of Medicine & Biomedical Sciences at the University at Buffalo, Buffalo, New York, USA
| | - Gerry S M Rivera
- Department of Chemistry, Washington University in St Louis, St Louis, Missouri, USA
| | - Lisa S Mydy
- Department of Structural Biology, Jacobs School of Medicine & Biomedical Sciences at the University at Buffalo, Buffalo, New York, USA
| | - Andrew M Gulick
- Department of Structural Biology, Jacobs School of Medicine & Biomedical Sciences at the University at Buffalo, Buffalo, New York, USA.
| | - Timothy A Wencewicz
- Department of Chemistry, Washington University in St Louis, St Louis, Missouri, USA.
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6
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Patel KD, Gulick AM. Anti-Zika candidates from a marine fungus with a remarkable biosynthetic repertoire. J Biol Chem 2021; 297:101047. [PMID: 34358564 PMCID: PMC8384895 DOI: 10.1016/j.jbc.2021.101047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
The study of natural products provides exciting opportunities for the discovery of novel biologically active molecules and biosynthetic pathways. Recently, Yuan and colleagues described 30 cyclic depsipeptides that are biosynthesized by proteins encoded by three distinct gene clusters in the marine fungus, Beauveria felina. Genetic and biochemical studies confirmed the involvement of nonribosomal peptide synthetases in the production of multiple compounds, some of which inhibit Zika virus replication.
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Affiliation(s)
- Ketan D Patel
- Department of Structural Biology, Jacobs School of Medicine and Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | - Andrew M Gulick
- Department of Structural Biology, Jacobs School of Medicine and Biological Sciences, University at Buffalo, Buffalo, New York, USA.
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7
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Swayambhu G, Bruno M, Gulick AM, Pfeifer BA. Siderophore natural products as pharmaceutical agents. Curr Opin Biotechnol 2021; 69:242-251. [PMID: 33640597 DOI: 10.1016/j.copbio.2021.01.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/09/2021] [Accepted: 01/25/2021] [Indexed: 11/27/2022]
Abstract
Siderophore natural products are characterized by an ability to tightly chelate metals. The origins of such compounds are often pathogenic microbes utilizing siderophores as virulence factors during host infection. The mechanism for siderophore formation typically involves the activity of nonribosomal peptide synthetases producing compounds across functional group classifications that include catecholate, phenolate, hydroxamate, and mixed categories. Though siderophore production has been a hallmark of pathogenicity, the evolutionarily-optimized binding abilities of siderophores suggest the possibility of re-directing the compounds towards alternative beneficial applications. In this mini-review, we will first describe siderophore formation origins before discussing alternative applications as pharmaceutical products. In so doing, we will cover examples and applications that include reducing metal overload, targeted antibiotic delivery, cancer treatment, vaccine development, and diagnostics. Included in this analysis will be a discussion on the native production hosts of siderophores and prospects for improvement in compound access through the adoption of heterologous biosynthesis.
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Affiliation(s)
- Girish Swayambhu
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, United States
| | - Michael Bruno
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, United States
| | - Andrew M Gulick
- Department of Structural Biology, University at Buffalo, The State University of New York, Buffalo, NY, United States
| | - Blaine A Pfeifer
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, United States.
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8
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Mhashal AR, Romero-Rivera A, Mydy LS, Cristobal JR, Gulick AM, Richard JP, Kamerlin SCL. Modeling the Role of a Flexible Loop and Active Site Side Chains in Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase. ACS Catal 2020; 10:11253-11267. [PMID: 33042609 PMCID: PMC7536716 DOI: 10.1021/acscatal.0c02757] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/31/2020] [Indexed: 11/30/2022]
Abstract
![]()
Glycerol-3-phosphate
dehydrogenase is a biomedically important
enzyme that plays a crucial role in lipid biosynthesis. It is activated
by a ligand-gated conformational change that is necessary for the
enzyme to reach a catalytically competent conformation capable of
efficient transition-state stabilization. While the human form (hlGPDH) has been the subject of extensive structural and
biochemical studies, corresponding computational studies to support
and extend experimental observations have been lacking. We perform
here detailed empirical valence bond and Hamiltonian replica exchange
molecular dynamics simulations of wild-type hlGPDH
and its variants, as well as providing a crystal structure of the
binary hlGPDH·NAD R269A variant where the enzyme
is present in the open conformation. We estimated the activation free
energies for the hydride transfer reaction in wild-type and substituted hlGPDH and investigated the effect of mutations on catalysis
from a detailed structural study. In particular, the K120A and R269A
variants increase both the volume and solvent exposure of the active
site, with concomitant loss of catalytic activity. In addition, the
R269 side chain interacts with both the Q295 side chain on the catalytic
loop, and the substrate phosphodianion. Our structural data and simulations
illustrate the critical role of this side chain in facilitating the
closure of hlGPDH into a catalytically competent
conformation, through modulating the flexibility of a key catalytic
loop (292-LNGQKL-297). This, in turn, rationalizes a tremendous 41,000
fold decrease experimentally in the turnover number, kcat, upon truncating this residue, as loop closure is
essential for both correct positioning of key catalytic residues in
the active site, as well as sequestering the active site from the
solvent. Taken together, our data highlight the importance of this
ligand-gated conformational change in catalysis, a feature that can
be exploited both for protein engineering and for the design of allosteric
inhibitors targeting this biomedically important enzyme.
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Affiliation(s)
- Anil R. Mhashal
- Department of Chemistry—BMC, Uppsala University, Box 576, Uppsala SE-751 23, Sweden
| | - Adrian Romero-Rivera
- Department of Chemistry—BMC, Uppsala University, Box 576, Uppsala SE-751 23, Sweden
| | - Lisa S. Mydy
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203-1121, United States
| | - Judith R. Cristobal
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Andrew M. Gulick
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203-1121, United States
| | - John P. Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Shina C. L. Kamerlin
- Department of Chemistry—BMC, Uppsala University, Box 576, Uppsala SE-751 23, Sweden
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9
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Shi C, Miller BR, Alexander EM, Gulick AM, Aldrich CC. Design, Synthesis, and Biophysical Evaluation of Mechanism-Based Probes for Condensation Domains of Nonribosomal Peptide Synthetases. ACS Chem Biol 2020; 15:1813-1819. [PMID: 32568518 DOI: 10.1021/acschembio.0c00411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are remarkable modular enzymes that synthesize peptide natural products. The condensation (C) domain catalyzes the key amide bond-forming reaction, but structural characterization with bound donor and acceptor substrates has proven elusive. We describe the chemoenzymatic synthesis of condensation domain probes C1 and C2 designed to cross-link the donor and acceptor substrates within the condensation domain active site. These pantetheine probes contain nonhydrolyzable ketone and α,α-difluoroketone isosteres of the native thioester linkage. Using the bimodular NRPS responsible for synthesis of the siderophore enterobactin as a model system, probe C2 was shown by surface plasmon resonance (SPR) to stabilize an intermolecular interaction between the peptidyl carrier protein (PCP) and C domains in EntB and EntF, respectively, with a dissociation constant of 1-2 nM, whereas the unmodified holo-EntB showed no interaction with EntF. The described condensation domain chemical probes provide powerful tools to study dynamic multifunctional NRPS systems.
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Affiliation(s)
- Ce Shi
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Bradley R. Miller
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, United States
| | - Evan M. Alexander
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Andrew M. Gulick
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, United States
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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10
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Alexander EM, Kreitler DF, Guidolin V, Hurben AK, Drake E, Villalta PW, Balbo S, Gulick AM, Aldrich CC. Biosynthesis, Mechanism of Action, and Inhibition of the Enterotoxin Tilimycin Produced by the Opportunistic Pathogen Klebsiella oxytoca. ACS Infect Dis 2020; 6:1976-1997. [PMID: 32485104 PMCID: PMC7354218 DOI: 10.1021/acsinfecdis.0c00326] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Tilimycin is an enterotoxin produced by the opportunistic pathogen Klebsiella oxytoca that causes antibiotic-associated hemorrhagic colitis (AAHC). This pyrrolobenzodiazepine (PBD) natural product is synthesized by a bimodular nonribosomal peptide synthetase (NRPS) pathway composed of three proteins: NpsA, ThdA, and NpsB. We describe the functional and structural characterization of the fully reconstituted NRPS system and report the steady-state kinetic analysis of all natural substrates and cofactors as well as the structural characterization of both NpsA and ThdA. The mechanism of action of tilimycin was confirmed using DNA adductomics techniques through the detection of putative N-2 guanine alkylation after tilimycin exposure to eukaryotic cells, providing the first structural characterization of a PBD-DNA adduct formed in cells. Finally, we report the rational design of small-molecule inhibitors that block tilimycin biosynthesis in whole cell K. oxytoca (IC50 = 29 ± 4 μM) through the inhibition of NpsA (KD = 29 ± 4 nM).
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Affiliation(s)
- Evan M. Alexander
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Dale F. Kreitler
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences University at Buffalo, Buffalo, New York 14203, USA
| | - Valeria Guidolin
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Alexander K. Hurben
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Eric Drake
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences University at Buffalo, Buffalo, New York 14203, USA
| | - Peter W. Villalta
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Silvia Balbo
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Andrew M. Gulick
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences University at Buffalo, Buffalo, New York 14203, USA
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
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11
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Mydy LS, Bailey DC, Patel KD, Rice MR, Gulick AM. The Siderophore Synthetase IucA of the Aerobactin Biosynthetic Pathway Uses an Ordered Mechanism. Biochemistry 2020; 59:2143-2153. [PMID: 32432457 DOI: 10.1021/acs.biochem.0c00250] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biosynthesis of the hydroxamate siderophore aerobactin requires the activity of four proteins encoded within the iuc operon. Recently, we biochemically reconstituted the biosynthetic pathway and structurally characterized IucA and IucC, two enzymes that sequentially couple N6-acetyl-N6-hydroxylysine to the primary carboxylates of citrate. IucA and IucC are members of a family of non-ribosomal peptide synthetase-independent siderophore (NIS) synthetases that are involved in the production of other siderophores, including desferrioxamine, achromobactin, and petrobactin. While structures of several members of this family were solved previously, there is limited mechanistic insight into the reaction catalyzed by NIS synthetases. Therefore, we performed a terreactant steady-state kinetic analysis and herein provide evidence for an ordered mechanism in which the chemistry is preceded by the formation of the quaternary complex. We further probed two regions of the active site with site-directed mutagenesis and identified several residues, including a conserved motif that is present on a dynamic loop, that are important for substrate binding and catalysis.
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Affiliation(s)
- Lisa S Mydy
- Department of Structural Biology, University at Buffalo, The State University of New York, Buffalo, New York 14203, United States
| | - Daniel C Bailey
- Department of Structural Biology, University at Buffalo, The State University of New York, Buffalo, New York 14203, United States
| | - Ketan D Patel
- Department of Structural Biology, University at Buffalo, The State University of New York, Buffalo, New York 14203, United States
| | - Matthew R Rice
- Department of Structural Biology, University at Buffalo, The State University of New York, Buffalo, New York 14203, United States
| | - Andrew M Gulick
- Department of Structural Biology, University at Buffalo, The State University of New York, Buffalo, New York 14203, United States
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12
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Branchini BR, Fontaine DM, Southworth TL, Huta BP, Racela A, Patel KD, Gulick AM. Mutagenesis and Structural Studies Reveal the Basis for the Activity and Stability Properties That Distinguish the Photinus Luciferases scintillans and pyralis. Biochemistry 2019; 58:4293-4303. [PMID: 31560532 DOI: 10.1021/acs.biochem.9b00719] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The dazzling yellow-green light emission of the common North American firefly Photinus pyralis and other bioluminescent organisms has provided a wide variety of prominent research applications like reporter gene assays and in vivo imaging methods. While the P. pyralis enzyme has been extensively studied, only recently has a second Photinus luciferase been cloned from the species scintillans. Even though the enzymes share very high sequence identity (89.8%), the color of the light they emit, their specific activity and their stability to heat, pH, and chemical denaturation are quite different with the scintillans luciferase being generally more resistant. Through the construction and evaluation of the properties of chimeric domain swapped, single point, and various combined variants, we have determined that only six amino acid changes are necessary to confer all of the properties of the scintillans enzyme to wild-type P. pyralis luciferase. Altered stability properties were attributed to four of the amino acid changes (T214N/S276T/H332N/E354N), and single mutations each predominantly changed emission color (Y255F) and specific activity (A222C). Results of a crystallographic study of the P. pyralis enzyme containing the six changes (Pps6) provide some insight into the structural basis for some of the documented property differences.
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Affiliation(s)
- Bruce R Branchini
- Department of Chemistry , Connecticut College , New London , Connecticut 06320 , United States
| | - Danielle M Fontaine
- Department of Chemistry , Connecticut College , New London , Connecticut 06320 , United States
| | - Tara L Southworth
- Department of Chemistry , Connecticut College , New London , Connecticut 06320 , United States
| | - Brian P Huta
- Department of Chemistry , Connecticut College , New London , Connecticut 06320 , United States
| | - Allison Racela
- Department of Chemistry , Connecticut College , New London , Connecticut 06320 , United States
| | - Ketan D Patel
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences , University at Buffalo , Buffalo , New York 14203 , United States
| | - Andrew M Gulick
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences , University at Buffalo , Buffalo , New York 14203 , United States
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13
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Gulick AM, Aldrich CC. Trapping interactions between catalytic domains and carrier proteins of modular biosynthetic enzymes with chemical probes. Nat Prod Rep 2019; 35:1156-1184. [PMID: 30046790 DOI: 10.1039/c8np00044a] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to early 2018 The Nonribosomal Peptide Synthetases (NRPSs) and Polyketide Synthases (PKSs) are families of modular enzymes that produce a tremendous diversity of natural products, with antibacterial, antifungal, immunosuppressive, and anticancer activities. Both enzymes utilize a fascinating modular architecture in which the synthetic intermediates are covalently attached to a peptidyl- or acyl-carrier protein that is delivered to catalytic domains for natural product elongation, modification, and termination. An investigation of the structural mechanism therefore requires trapping the often transient interactions between the carrier and catalytic domains. Many novel chemical probes have been produced to enable the structural and functional investigation of multidomain NRPS and PKS structures. This review will describe the design and implementation of the chemical tools that have proven to be useful in biochemical and biophysical studies of these natural product biosynthetic enzymes.
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Affiliation(s)
- Andrew M Gulick
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 955 Main St, Buffalo, NY 14203, USA.
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14
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Abstract
Hypervirulent Klebsiella pneumoniae (hvKp) is an underrecognized pathotype of K. pneumoniae since the majority of cases have occurred in East Asia. However, hvKp is a public health threat due to its ability to infect healthy individuals, ongoing dissemination, and acquisition of resistance determinants. hvKp-directed antivirulence therapy is appealing since it has the potential to minimize resistance selection. The discovery that aerobactin is a critical hvKp-specific virulence factor has made its biosynthetic enzymes attractive targets for the development of small molecule inhibitors. However, identification of additional high value targets is needed to enable a robust countermeasure program for this evolving superbug.
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Affiliation(s)
- Thomas A. Russo
- The Veterans Administration Western New York Healthcare System, 3495 Bailey Avenue, Buffalo, New York 14215, United States
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15
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Mydy LS, Cristobal JR, Katigbak RD, Bauer P, Reyes AC, Kamerlin SCL, Richard JP, Gulick AM. Human Glycerol 3-Phosphate Dehydrogenase: X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies. Biochemistry 2019; 58:1061-1073. [PMID: 30640445 DOI: 10.1021/acs.biochem.8b01103] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human liver glycerol 3-phosphate dehydrogenase ( hlGPDH) catalyzes the reduction of dihydroxyacetone phosphate (DHAP) to form glycerol 3-phosphate, using the binding energy associated with the nonreacting phosphodianion of the substrate to properly orient the enzyme-substrate complex within the active site. Herein, we report the crystal structures for unliganded, binary E·NAD, and ternary E·NAD·DHAP complexes of wild type hlGPDH, illustrating a new position of DHAP, and probe the kinetics of multiple mutant enzymes with natural and truncated substrates. Mutation of Lys120, which is positioned to donate a proton to the carbonyl of DHAP, results in similar increases in the activation barrier to hlGPDH-catlyzed reduction of DHAP and to phosphite dianion-activated reduction of glycolaldehyde, illustrating that these transition states show similar interactions with the cationic K120 side chain. The K120A mutation results in a 5.3 kcal/mol transition state destabilization, and 3.0 kcal/mol of the lost transition state stabilization is rescued by 1.0 M ethylammonium cation. The 6.5 kcal/mol increase in the activation barrier observed for the D260G mutant hlGPDH-catalyzed reaction represents a 3.5 kcal/mol weakening of transition state stabilization by the K120A side chain and a 3.0 kcal/mol weakening of the interactions with other residues. The interactions, at the enzyme active site, between the K120 side chain and the Q295 and R269 side chains were likewise examined by double-mutant analyses. These results provide strong evidence that the enzyme rate acceleration is due mainly or exclusively to transition state stabilization by electrostatic interactions with polar amino acid side chains.
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Affiliation(s)
- Lisa S Mydy
- Department of Structural Biology , University at Buffalo, SUNY , Buffalo , New York 14203 , United States
| | - Judith R Cristobal
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Roberto D Katigbak
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Paul Bauer
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 24 Uppsala , Sweden
| | - Archie C Reyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 24 Uppsala , Sweden
| | - John P Richard
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Andrew M Gulick
- Department of Structural Biology , University at Buffalo, SUNY , Buffalo , New York 14203 , United States
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16
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Bailey DC, Bohac TJ, Shapiro JA, Giblin DE, Wencewicz TA, Gulick AM. Crystal Structure of the Siderophore Binding Protein BauB Bound to an Unusual 2:1 Complex Between Acinetobactin and Ferric Iron. Biochemistry 2018; 57:6653-6661. [PMID: 30406986 DOI: 10.1021/acs.biochem.8b00986] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The critical role that iron plays in many biochemical processes has led to an elaborate battle between bacterial pathogens and their hosts to acquire and withhold this critical nutrient. Exploitation of iron nutritional immunity is being increasingly appreciated as a potential antivirulence therapeutic strategy, especially against problematic multidrug resistant Gram-negative pathogens such as Acinetobacter baumannii. To facilitate iron uptake and promote growth, A. baumannii produces a nonribosomally synthesized peptide siderophore called acinetobactin. Acinetobactin is unusual in that it is first biosynthesized in an oxazoline form called preacinetobactin that spontaneously isomerizes to the final isoxazolidinone acinetobactin. Interestingly, both isomers can bind iron and both support growth of A. baumannii. To address how the two isomers chelate their ferric cargo and how the complexes are used by A. baumannii, structural studies were carried out with the ferric acinetobactin complex and its periplasmic siderophore binding protein BauB. Herein, we present the crystal structure of BauB bound to a bis-tridentate (Fe3+L2) siderophore complex. Additionally, we present binding studies that show multiple variants of acinetobactin bind BauB with no apparent change in affinity. These results are consistent with the structural model that depicts few direct polar interactions between BauB and the acinetobactin backbone. This structural and functional characterization of acinetobactin and its requisite binding protein BauB provides insight that could be exploited to target this critical iron acquisition system and provide a novel approach to treat infections caused by this important multidrug resistant pathogen.
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Affiliation(s)
- Daniel C Bailey
- Department of Structural Biology , Jacobs School of Medicine & Biomedical Sciences at the University at Buffalo , 955 Main Street , Buffalo , New York 14203 , United States
| | - Tabbetha J Bohac
- Department of Chemistry , Washington University in St. Louis , One Brookings Drive , St. Louis , Missouri 63130 , United States
| | - Justin A Shapiro
- Department of Chemistry , Washington University in St. Louis , One Brookings Drive , St. Louis , Missouri 63130 , United States
| | - Daryl E Giblin
- Department of Chemistry , Washington University in St. Louis , One Brookings Drive , St. Louis , Missouri 63130 , United States
| | - Timothy A Wencewicz
- Department of Chemistry , Washington University in St. Louis , One Brookings Drive , St. Louis , Missouri 63130 , United States
| | - Andrew M Gulick
- Department of Structural Biology , Jacobs School of Medicine & Biomedical Sciences at the University at Buffalo , 955 Main Street , Buffalo , New York 14203 , United States
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17
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Bailey DC, Buckley BP, Chernov MV, Gulick AM. Development of a High-Throughput Biochemical Assay to Screen for Inhibitors of Aerobactin Synthetase IucA. SLAS Discov 2018; 23:1070-1082. [PMID: 29991301 DOI: 10.1177/2472555218787140] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Acquiring sufficient quantities of iron to support survival is often a critical limitation for pathogenic bacteria. To meet this demand, bacteria have evolved unique strategies to scavenge iron and circumvent the nutritional immunity exerted by their hosts. One common strategy, which is often a key virulence factor for bacterial pathogens, involves the synthesis, secretion, and reuptake of iron chelators known as siderophores. In vitro and in vivo studies have demonstrated that the siderophore aerobactin is critical for virulence in the hypervirulent pathotype of Klebsiella pneumoniae (hvKP). Given the high rate of multidrug resistance in K. pneumoniae, and in light of the ever-increasing demand for novel Gram-negative therapeutic targets, we identified aerobactin production as a promising antivirulence target in hvKP. Herein, we describe the development of a high-throughput biochemical assay for identifying inhibitors of the aerobactin synthetase IucA. The assay was employed to screen ~110,000 compounds across several commercially available small-molecule libraries. IucA inhibitors with activity at micromolar concentrations were identified in our screening campaigns and confirmed using secondary orthogonal assays. However, the most potent compounds also exhibited some properties commonly observed with promiscuous/nonspecific inhibitors, including incubation time and target enzyme concentration dependence, as well as the potential to antagonize unrelated enzymes.
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Affiliation(s)
- Daniel C Bailey
- 1 Department of Structural Biology, Jacobs School of Medicine & Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA.,2 The Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
| | - Brian P Buckley
- 3 Small Molecule Screening Shared Resource, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Mikhail V Chernov
- 3 Small Molecule Screening Shared Resource, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Andrew M Gulick
- 1 Department of Structural Biology, Jacobs School of Medicine & Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA.,2 The Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
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18
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Abstract
We report the unprecedented reaction between a nitroalkane and an active-site cysteine residue to yield a thiohydroximate adduct. Structural and kinetic evidence suggests the nitro group is activated by conversion to its nitronic acid tautomer within the active site. The nitro group, therefore, shows promise as a masked electrophile in the design of covalent inhibitors targeting binding pockets with appropriately placed cysteine and general acid residues.
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Affiliation(s)
- Sneha Ray
- Department of Chemistry, University at Buffalo, Buffalo, New York 14260-3000, United States
| | - Dale F. Kreitler
- Hauptman-Woodward Institute and Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203-1102, United States
| | - Andrew M. Gulick
- Hauptman-Woodward Institute and Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203-1102, United States
| | - Andrew S. Murkin
- Department of Chemistry, University at Buffalo, Buffalo, New York 14260-3000, United States
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19
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Bailey DC, Alexander E, Rice MR, Drake EJ, Mydy LS, Aldrich CC, Gulick AM. Structural and functional delineation of aerobactin biosynthesis in hypervirulent Klebsiella pneumoniae. J Biol Chem 2018; 293:7841-7852. [PMID: 29618511 DOI: 10.1074/jbc.ra118.002798] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 03/30/2018] [Indexed: 12/17/2022] Open
Abstract
Aerobactin, a citryl-hydroxamate siderophore, is produced by a number of pathogenic Gram-negative bacteria to aid in iron assimilation. Interest in this well-known siderophore was reignited by recent investigations suggesting that it plays a key role in mediating the enhanced virulence of a hypervirulent pathotype of Klebsiella pneumoniae (hvKP). In contrast to classical opportunistic strains of K. pneumoniae, hvKP causes serious life-threatening infections in previously healthy individuals in the community. Multiple contemporary reports have confirmed fears that the convergence of multidrug-resistant and hvKP pathotypes has led to the evolution of a highly transmissible, drug-resistant, and virulent "super bug." Despite hvKP harboring four distinct siderophore operons, knocking out production of only aerobactin led to a significant attenuation of virulence. Herein, we continue our structural and functional studies on the biosynthesis of this crucial virulence factor. In vivo heterologous production and in vitro reconstitution of aerobactin biosynthesis from hvKP was carried out, demonstrating the specificity, stereoselectivity, and kinetic throughput of the complete pathway. Additionally, we present a steady-state kinetic analysis and the X-ray crystal structure of the second aerobactin synthetase IucC, as well as describe a surface entropy reduction strategy that was employed for structure determination. Finally, we show solution X-ray scattering data that support a unique dimeric quaternary structure for IucC. These new insights into aerobactin assembly will help inform potential antivirulence strategies and advance our understanding of siderophore biosynthesis.
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Affiliation(s)
- Daniel C Bailey
- From the Department of Structural Biology, The Jacobs School of Medicine & Biomedical Sciences, State University of New York, Buffalo, New York 14203.,the Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203, and
| | - Evan Alexander
- the Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Matthew R Rice
- the Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203, and
| | - Eric J Drake
- From the Department of Structural Biology, The Jacobs School of Medicine & Biomedical Sciences, State University of New York, Buffalo, New York 14203.,the Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203, and
| | - Lisa S Mydy
- From the Department of Structural Biology, The Jacobs School of Medicine & Biomedical Sciences, State University of New York, Buffalo, New York 14203.,the Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203, and
| | - Courtney C Aldrich
- the Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Andrew M Gulick
- From the Department of Structural Biology, The Jacobs School of Medicine & Biomedical Sciences, State University of New York, Buffalo, New York 14203, .,the Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203, and
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20
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Abstract
Covering: up to 2017.Natural products are important secondary metabolites produced by bacterial and fungal species that play important roles in cellular growth and signaling, nutrient acquisition, intra- and interspecies communication, and virulence. A subset of natural products is produced by nonribosomal peptide synthetases (NRPSs), a family of large, modular enzymes that function in an assembly line fashion. Because of the pharmaceutical activity of many NRPS products, much effort has gone into the exploration of their biosynthetic pathways and the diverse products they make. Many interesting NRPS pathways have been identified and characterized from both terrestrial and marine bacterial sources. Recently, several NRPS pathways in human commensal bacterial species have been identified that produce molecules with antibiotic activity, suggesting another source of interesting NRPS pathways may be the commensal and pathogenic bacteria that live on the human body. The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) have been identified as a significant cause of human bacterial infections that are frequently multidrug resistant. The emerging resistance profile of these organisms has prompted calls from multiple international agencies to identify novel antibacterial targets and develop new approaches to treat infections from ESKAPE pathogens. Each of these species contains several NRPS biosynthetic gene clusters. While some have been well characterized and produce known natural products with important biological roles in microbial physiology, others have yet to be investigated. This review catalogs the NRPS pathways of ESKAPE pathogens. The exploration of novel NRPS products may lead to a better understanding of the chemical communication used by human pathogens and potentially to the discovery of novel therapeutic approaches.
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Affiliation(s)
- Andrew M Gulick
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.
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21
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Clevenger KD, Mascarenhas R, Catlin D, Wu R, Kelleher NL, Drake EJ, Gulick AM, Liu D, Fast W. Substrate Trapping in the Siderophore Tailoring Enzyme PvdQ. ACS Chem Biol 2017; 12:643-647. [PMID: 28186406 DOI: 10.1021/acschembio.7b00031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Siderophore biosynthesis by Pseudomonas aeruginosa enhances virulence and represents an attractive drug target. PvdQ functions in the type-1 pyoverdine biosynthetic pathway by removing a myristoyl anchor from a pyoverdine precursor, allowing eventual release from the periplasm. A circularly permuted version of PvdQ bypasses the self-processing step of this Ntn-hydrolase and retains the activity, selectivity, and structure of wild-type PvdQ, as revealed by a 1.8 Å resolution X-ray crystal structure. A 2.55 Å resolution structure of the inactive S1A/N269D-cpPvdQ mutant in complex with the pyoverdine precursor PVDIq reveals a specific binding pocket for the d-Tyr of this modified peptide substrate. To our knowledge, this structure is the first of a pyoverdine precursor peptide bound to a biosynthetic enzyme. Details of the observed binding interactions have implications for control of pyoverdine biosynthesis and inform future drug design efforts.
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Affiliation(s)
- Kenneth D. Clevenger
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Romila Mascarenhas
- Department
of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Daniel Catlin
- Department
of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Rui Wu
- Department
of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Neil L. Kelleher
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Eric J. Drake
- Hauptman-Woodward
Medical Research Institute and Department of Structural Biology, SUNY University at Buffalo, Buffalo, New York 14203, United States
| | - Andrew M. Gulick
- Hauptman-Woodward
Medical Research Institute and Department of Structural Biology, SUNY University at Buffalo, Buffalo, New York 14203, United States
| | - Dali Liu
- Department
of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
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22
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Branchini BR, Southworth TL, Fontaine DM, Murtiashaw MH, McGurk A, Talukder MH, Qureshi R, Yetil D, Sundlov JA, Gulick AM. Cloning of the Orange Light-Producing Luciferase from Photinus scintillans-A New Proposal on how Bioluminescence Color is Determined. Photochem Photobiol 2017; 93:479-485. [PMID: 27861940 DOI: 10.1111/php.12671] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/04/2016] [Indexed: 11/29/2022]
Abstract
Unlike the enchanting yellow-green flashes of light produced on warm summer evenings by Photinus pyralis, the most common firefly species in North America, the orange lights of Photinus scintillans are infrequently observed. These Photinus species, and likely all bioluminescent beetles, use the same substrates beetle luciferin, ATP and oxygen to produce light. It is the structure of the particular luciferase enzyme that is the key to determining the color of the emitted light. We report here the molecular cloning of the P. scintillans luc gene and the expression and characterization of the corresponding novel recombinant luciferase enzyme. A comparison of the amino acid sequence with that of the highly similar P. pyralis enzyme and subsequent mutagenesis studies revealed that the single conservative amino acid change tyrosine to phenylalanine at position 255 accounted for the entire emission color difference. Additional mutagenesis and crystallographic studies were performed on a H-bond network, which includes the position 255 residue and five other stringently conserved beetle luciferase residues, that is proximal to the substrate/emitter binding site. The results are interpreted in the context of a speculative proposal that this network is key to the understanding of bioluminescence color determination.
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Affiliation(s)
| | | | | | | | - Alex McGurk
- Department of Chemistry, Connecticut College, New London, CT
| | | | - Rakhshi Qureshi
- Department of Chemistry, Connecticut College, New London, CT
| | - Deniz Yetil
- Department of Chemistry, Connecticut College, New London, CT
| | - Jesse A Sundlov
- Hauptman-Woodward Institute, Buffalo, NY.,Department of Structural Biology, University of Buffalo, Buffalo, NY
| | - Andrew M Gulick
- Hauptman-Woodward Institute, Buffalo, NY.,Department of Structural Biology, University of Buffalo, Buffalo, NY
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23
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Gulick AM. Structural insight into the necessary conformational changes of modular nonribosomal peptide synthetases. Curr Opin Chem Biol 2016; 35:89-96. [PMID: 27676239 DOI: 10.1016/j.cbpa.2016.09.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/06/2016] [Accepted: 09/12/2016] [Indexed: 01/09/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) catalyze the assembly line biosynthesis of peptide natural products that play important roles in microbial signaling and communication. These multidomain enzymes use an integrated carrier protein that delivers the growing peptide to the catalytic domains, requiring coordinated conformational changes that allow the proper sequence of synthetic steps. Recent structural studies of NRPSs have described important conformational states and illustrate the critical role of a small subdomain within the adenylation domains. This subdomain alternates between catalytic conformations and also serves as a linker domain, providing further conformational flexibility to enable the carrier to project from the core of NRPS. These studies are described along with remaining questions in the study of the structural dynamics of NRPSs.
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Affiliation(s)
- Andrew M Gulick
- Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA; Department of Structural Biology, University at Buffalo, Buffalo, NY, USA.
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24
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Miller BR, Drake EJ, Shi C, Aldrich CC, Gulick AM. Structures of a Nonribosomal Peptide Synthetase Module Bound to MbtH-like Proteins Support a Highly Dynamic Domain Architecture. J Biol Chem 2016; 291:22559-22571. [PMID: 27597544 DOI: 10.1074/jbc.m116.746297] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/26/2016] [Indexed: 11/06/2022] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) produce a wide variety of peptide natural products. During synthesis, the multidomain NRPSs act as an assembly line, passing the growing product from one module to the next. Each module generally consists of an integrated peptidyl carrier protein, an amino acid-loading adenylation domain, and a condensation domain that catalyzes peptide bond formation. Some adenylation domains interact with small partner proteins called MbtH-like proteins (MLPs) that enhance solubility or activity. A structure of an MLP bound to an adenylation domain has been previously reported using a truncated adenylation domain, precluding any insight that might be derived from understanding the influence of the MLP on the intact adenylation domain or on the dynamics of the entire NRPS module. Here, we present the structures of the full-length NRPS EntF bound to the MLPs from Escherichia coli and Pseudomonas aeruginosa These new structures, along with biochemical and bioinformatics support, further elaborate the residues that define the MLP-adenylation domain interface. Additionally, the structures highlight the dynamic behavior of NRPS modules, including the module core formed by the adenylation and condensation domains as well as the orientation of the mobile thioesterase domain.
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Affiliation(s)
- Bradley R Miller
- From the Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203.,the Department of Structural Biology, University at Buffalo, Buffalo, New York 14203, and
| | - Eric J Drake
- From the Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203.,the Department of Structural Biology, University at Buffalo, Buffalo, New York 14203, and
| | - Ce Shi
- the Center for Drug Design and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Courtney C Aldrich
- the Center for Drug Design and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Andrew M Gulick
- From the Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203, .,the Department of Structural Biology, University at Buffalo, Buffalo, New York 14203, and
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25
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Abstract
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The shikimate pathway of bacteria,
fungi, and plants generates
chorismate, which is drawn into biosynthetic pathways that form aromatic
amino acids and other important metabolites, including folates, menaquinone,
and siderophores. Many of the pathways initiated at this branch point
transform chorismate using an MST enzyme. The MST enzymes (menaquinone, siderophore, and tryptophan biosynthetic enzymes) are structurally homologous and magnesium-dependent,
and all perform similar chemical permutations to chorismate by nucleophilic
addition (hydroxyl or amine) at the 2-position of the ring, inducing
displacement of the 4-hydroxyl. The isomerase enzymes release isochorismate
or aminodeoxychorismate as the product, while the synthase enzymes
also have lyase activity that displaces pyruvate to form either salicylate
or anthranilate. This has led to the hypothesis that the isomerase
and lyase activities performed by the MST enzymes are functionally
conserved. Here we have developed tailored pre-steady-state approaches
to establish the kinetic mechanisms of the isochorismate and salicylate
synthase enzymes of siderophore biosynthesis. Our data are centered
on the role of magnesium ions, which inhibit the isochorismate synthase
enzymes but not the salicylate synthase enzymes. Prior structural
data have suggested that binding of the metal ion occludes access
or egress of substrates. Our kinetic data indicate that for the production
of isochorismate, a high magnesium ion concentration suppresses the
rate of release of product, accounting for the observed inhibition
and establishing the basis of the ordered-addition kinetic mechanism.
Moreover, we show that isochorismate is channeled through the synthase
reaction as an intermediate that is retained in the active site by
the magnesium ion. Indeed, the lyase-active enzyme has 3 orders of
magnitude higher affinity for the isochorismate complex relative to
the chorismate complex. Apparent negative-feedback inhibition by ferrous
ions is documented at nanomolar concentrations, which is a potentially
physiologically relevant mode of regulation for siderophore biosynthesis
in vivo.
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Affiliation(s)
- Kathleen M Meneely
- Department of Molecular Biosciences, University of Kansas , Lawrence, Kansas 66045, United States
| | - Jesse A Sundlov
- Hauptman-Woodward Medical Research Institute , 700 Ellicott Street, Buffalo, New York 14203, United States
| | - Andrew M Gulick
- Hauptman-Woodward Medical Research Institute , 700 Ellicott Street, Buffalo, New York 14203, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee , Milwaukee, Wisconsin 53201, United States
| | - Audrey L Lamb
- Department of Molecular Biosciences, University of Kansas , Lawrence, Kansas 66045, United States
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26
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Bailey DC, Drake EJ, Grant TD, Gulick AM. Structural and Functional Characterization of Aerobactin Synthetase IucA from a Hypervirulent Pathotype of Klebsiella pneumoniae. Biochemistry 2016; 55:3559-70. [PMID: 27253399 PMCID: PMC4928626 DOI: 10.1021/acs.biochem.6b00409] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Iron is a vital mineral nutrient required by virtually all life forms to prosper; pathogenic bacteria are no exception. Despite the abundance of iron within the human host, highly regulated iron physiology can result in exceedingly low levels of iron bioavailable to prospective invading bacteria. To combat this scarcity of iron, many pathogenic bacteria have acquired specific and efficient iron acquisition systems, which allow them to thrive in iron-deficient host environments. One of the more prominent bacterial iron acquisition systems involves the synthesis, secretion, and reuptake of small-molecule iron chelators known as siderophores. Aerobactin, a citrate-hydroxamate siderophore originally isolated nearly 50 years ago, is produced by a number of pathogenic Gram-negative bacteria. Aerobactin has recently been demonstrated to play a pivotal role in mediating the enhanced virulence of a particularly invasive pathotype of Klebsiella pneumoniae (hvKP). Toward further understanding of this key virulence factor, we report the structural and functional characterization of aerobactin synthetase IucA from a strain of hvKP. The X-ray crystal structures of unliganded and ATP-bound forms of IucA were solved, forming the foundation of our structural analysis. Small angle X-ray scattering (SAXS) data suggest that, unlike its closest structurally characterized homologues, IucA adopts a tetrameric assembly in solution. Finally, we employed activity assays to investigate the substrate specificity and determine the apparent steady-state kinetic parameters of IucA.
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Affiliation(s)
- Daniel C Bailey
- The Hauptman-Woodward Medical Research Institute , Buffalo, New York, United States
| | - Eric J Drake
- The Hauptman-Woodward Medical Research Institute , Buffalo, New York, United States
| | - Thomas D Grant
- The Hauptman-Woodward Medical Research Institute , Buffalo, New York, United States
| | - Andrew M Gulick
- The Hauptman-Woodward Medical Research Institute , Buffalo, New York, United States
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27
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Richard JP, Amyes TL, Malabanan MM, Zhai X, Kim KJ, Reinhardt CJ, Wierenga RK, Drake EJ, Gulick AM. Structure-Function Studies of Hydrophobic Residues That Clamp a Basic Glutamate Side Chain during Catalysis by Triosephosphate Isomerase. Biochemistry 2016; 55:3036-47. [PMID: 27149328 PMCID: PMC4934371 DOI: 10.1021/acs.biochem.6b00311] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Kinetic
parameters are reported for the reactions of whole substrates
(kcat/Km,
M–1 s–1) (R)-glyceraldehyde
3-phosphate (GAP) and
dihydroxyacetone phosphate (DHAP) and for the substrate pieces [(kcat/Km)E·HPi/Kd, M–2 s–1] glycolaldehyde (GA) and phosphite dianion
(HPi) catalyzed by the I172A/L232A mutant of triosephosphate
isomerase
from Trypanosoma brucei brucei (TbbTIM). A comparison with the corresponding parameters for wild-type,
I172A, and L232A TbbTIM-catalyzed reactions shows
that the effect of I172A and L232A mutations on ΔG⧧ for the wild-type TbbTIM-catalyzed
reactions of the substrate pieces is nearly the same
as the effect of the same mutations on TbbTIM previously
mutated at the second side chain. This provides strong evidence that
mutation of the first hydrophobic side chain does not affect the functioning
of the second side chain in catalysis of the reactions of the substrate
pieces. By contrast, the effects of I172A and L232A mutations on ΔG⧧ for wild-type TbbTIM-catalyzed
reactions of the whole substrate are different from
the effect of the same mutations on TbbTIM previously
mutated at the second side chain. This is due to the change in the
rate-determining step that determines the barrier to the isomerization
reaction. X-ray crystal structures are reported for I172A, L232A,
and I172A/L232A TIMs and for the complexes of these mutants to the
intermediate analogue phosphoglycolate (PGA). The structures of the
PGA complexes with wild-type and mutant enzymes are nearly superimposable,
except that the space opened by replacement of the hydrophobic side
chain is occupied by a water molecule that lies ∼3.5 Å
from the basic side chain of Glu167. The new water at I172A mutant TbbTIM provides a simple rationalization for the increase
in the activation barrier ΔG⧧ observed for mutant enzyme-catalyzed
reactions of the whole substrate and substrate pieces. By contrast,
the new water at the L232A mutant does not predict the decrease in
ΔG⧧ observed for the mutant
enzyme-catalyzed
reactions of the substrate piece GA.
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Affiliation(s)
- John P Richard
- Department of Chemistry, University at Buffalo, State University of New York , Buffalo, New York 14260, United States
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, State University of New York , Buffalo, New York 14260, United States
| | - M Merced Malabanan
- Department of Chemistry, University at Buffalo, State University of New York , Buffalo, New York 14260, United States
| | - Xiang Zhai
- Department of Chemistry, University at Buffalo, State University of New York , Buffalo, New York 14260, United States
| | - Kalvin J Kim
- Department of Chemistry, University at Buffalo, State University of New York , Buffalo, New York 14260, United States
| | - Christopher J Reinhardt
- Department of Chemistry, University at Buffalo, State University of New York , Buffalo, New York 14260, United States
| | - Rik K Wierenga
- Department of Biochemistry and Biocenter, University of Oulu , P.O. Box 3000, FIN-90014 Oulu, Finland
| | - Eric J Drake
- Hauptman-Woodward Institute , 700 Ellicott Street, Buffalo, New York 14203, United States.,Department of Structural Biology, University at Buffalo, State University of New York , Buffalo, New York 14203, United States
| | - Andrew M Gulick
- Hauptman-Woodward Institute , 700 Ellicott Street, Buffalo, New York 14203, United States.,Department of Structural Biology, University at Buffalo, State University of New York , Buffalo, New York 14203, United States
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28
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Drake EJ, Gulick AM. 1.2 Å resolution crystal structure of the periplasmic aminotransferase PvdN from Pseudomonas aeruginosa. Acta Crystallogr F Struct Biol Commun 2016; 72:403-8. [PMID: 27139833 DOI: 10.1107/s2053230x16006257] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/14/2016] [Indexed: 02/03/2023]
Abstract
The Gram-negative pathogen Pseudomonas aeruginosa uses a nonribosomal peptide synthetase (NRPS) biosynthetic cluster for the production of a peptide siderophore. In addition to four multimodular NRPS proteins, the biosynthetic pathway also requires several additional enzymes involved in the production of nonproteinogenic amino acids and maturation of the peptide product. Among the proteins that are required for the final steps in pyoverdine synthesis is PvdN, a pyridoxal phosphate-dependent enzyme that catalyzes an uncharacterized step in pyoverdine production. This study reports the high-resolution structure of PvdN bound to a PLP cofactor solved by multi-wavelength anomalous dispersion (MAD). The PvdN model shows high structural homology to type I aspartate aminotransferases and also contains positive density that suggests an uncharacterized external aldimine.
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Affiliation(s)
- Eric J Drake
- Hauptman-Woodward Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Andrew M Gulick
- Hauptman-Woodward Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
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29
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Branchini BR, Behney CE, Southworth TL, Fontaine DM, Gulick AM, Vinyard DJ, Brudvig GW. Experimental Support for a Single Electron-Transfer Oxidation Mechanism in Firefly Bioluminescence. J Am Chem Soc 2015; 137:7592-5. [PMID: 26057379 DOI: 10.1021/jacs.5b03820] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Firefly luciferase produces light by converting substrate beetle luciferin into the corresponding adenylate that it subsequently oxidizes to oxyluciferin, the emitter of bioluminescence. We have confirmed the generally held notions that the oxidation step is initiated by formation of a carbanion intermediate and that a hydroperoxide (anion) is involved. Additionally, structural evidence is presented that accounts for the delivery of oxygen to the substrate reaction site. Herein, we report key convincing spectroscopic evidence of the participation of superoxide anion in a related chemical model reaction that supports a single electron-transfer pathway for the critical oxidative process. This mechanism may be a common feature of bioluminescence processes in which light is produced by an enzyme in the absence of cofactors.
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Affiliation(s)
- Bruce R Branchini
- †Department of Chemistry, Connecticut College, New London, Connecticut 06320, United States
| | - Curran E Behney
- †Department of Chemistry, Connecticut College, New London, Connecticut 06320, United States
| | - Tara L Southworth
- †Department of Chemistry, Connecticut College, New London, Connecticut 06320, United States
| | - Danielle M Fontaine
- †Department of Chemistry, Connecticut College, New London, Connecticut 06320, United States
| | - Andrew M Gulick
- §Hauptman-Woodward Institute, Buffalo, New York 14203, United States.,∥Department of Structural Biology, University of Buffalo, Buffalo, New York 14203, United States
| | - David J Vinyard
- ‡Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Gary W Brudvig
- ‡Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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30
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Zhu J, Lippa GM, Gulick AM, Tipton PA. Examining Reaction Specificity in PvcB, a Source of Diversity in Isonitrile-Containing Natural Products. Biochemistry 2015; 54:2659-69. [PMID: 25866990 DOI: 10.1021/acs.biochem.5b00255] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many bacteria produce isonitrile-containing natural products that are derived from aromatic amino acids. The synthetic clusters that control biosynthesis most commonly encode two enzymes, designated PvcA and PvcB, as well as additional enzymes that direct synthesis of the natural product. The PvcA enzyme installs the isonitrile moiety at the amino group of either tyrosine or tryptophan, as dictated by the particular pathway. The common pathway intermediate produced by PvcA is directed toward different ultimate products by PvcB, a member of the family of Fe(2+), α-ketoglutarate-dependent oxygenases. To continue our investigation of the structural and functional properties of the isonitrile biosynthetic pathways, we present here a study of the PvcB homologues from three organisms. Two pathways, derived from Pseudomonas aeruginosa and Xenorhabdus nematophila, produce known products. A third PvcB homologue from Erwinia amylovora is part of an uncharacterized pathway. Our results demonstrate the diversity of reactions catalyzed. Although all PvcB enzymes catalyze the hydroxylation of the tyrosine isonitrile substrate, the elimination of the hydroxyl in Pseudomonas and Erwinia is driven by deprotonation at Cα, resulting in the initial production of an unsaturated tyrosine isonitrile product that then cyclizes to a coumarin derivative. PvcB from Xenorhabdus, in contrast, catalyzes the same oxygenation, but loss of the hydroxyl group is accompanied by decarboxylation of the intermediate. Steady-state kinetic analysis of the three reactions and a docking model for the binding of the tyrosine isonitrile substrate in the PvcB active site highlight subtle differences between the PvcB homologues.
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Affiliation(s)
- Jing Zhu
- †Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Geoffrey M Lippa
- ‡Hauptman-Woodward Medical Research Foundation, Buffalo, New York 14203, United States
| | - Andrew M Gulick
- ‡Hauptman-Woodward Medical Research Foundation, Buffalo, New York 14203, United States.,§Department of Structural Biology, University at Buffalo, Buffalo, New York 14203, United States
| | - Peter A Tipton
- †Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
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31
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Kholodar S, Allen CL, Gulick AM, Murkin AS. The role of phosphate in a multistep enzymatic reaction: reactions of the substrate and intermediate in pieces. J Am Chem Soc 2015; 137:2748-56. [PMID: 25642788 PMCID: PMC4507815 DOI: 10.1021/ja512911f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Indexed: 01/17/2023]
Abstract
Several mechanistically unrelated enzymes utilize the binding energy of their substrate's nonreacting phosphoryl group to accelerate catalysis. Evidence for the involvement of the phosphodianion in transition state formation has come from reactions of the substrate in pieces, in which reaction of a truncated substrate lacking its phosphorylmethyl group is activated by inorganic phosphite. What has remained unknown until now is how the phosphodianion group influences the reaction energetics at different points along the reaction coordinate. 1-Deoxy-D-xylulose-5-phosphate (DXP) reductoisomerase (DXR), which catalyzes the isomerization of DXP to 2-C-methyl-D-erythrose 4-phosphate (MEsP) and subsequent NADPH-dependent reduction, presents a unique opportunity to address this concern. Previously, we have reported the effect of covalently linked phosphate on the energetics of DXP turnover. Through the use of chemically synthesized MEsP and its phosphate-truncated analogue, 2-C-methyl-D-glyceraldehyde, the current study revealed a loss of 6.1 kcal/mol of kinetic barrier stabilization upon truncation, of which 4.4 kcal/mol was regained in the presence of phosphite dianion. The activating effect of phosphite was accompanied by apparent tightening of its interactions within the active site at the intermediate stage of the reaction, suggesting a role of the phosphodianion in disfavoring intermediate release and in modulation of the on-enzyme isomerization equilibrium. The results of kinetic isotope effect and structural studies indicate rate limitation by physical steps when the covalent linkage is severed. These striking differences in the energetics of the natural reaction and the reactions in pieces provide a deeper insight into the contribution of enzyme-phosphodianion interactions to the reaction coordinate.
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Affiliation(s)
- Svetlana
A. Kholodar
- Department
of Chemistry, University at Buffalo, Buffalo, New York 14260-3000, United States
| | - C. Leigh Allen
- Hauptman-Woodward
Institute and Department of Structural Biology, University at Buffalo, Buffalo, New York 14203-1102, United States
| | - Andrew M. Gulick
- Hauptman-Woodward
Institute and Department of Structural Biology, University at Buffalo, Buffalo, New York 14203-1102, United States
| | - Andrew S. Murkin
- Department
of Chemistry, University at Buffalo, Buffalo, New York 14260-3000, United States
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32
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Mitchell CA, Tucker AC, Escalante-Semerena JC, Gulick AM. The structure of S. lividans acetoacetyl-CoA synthetase shows a novel interaction between the C-terminal extension and the N-terminal domain. Proteins 2015; 83:575-81. [PMID: 25488501 DOI: 10.1002/prot.24738] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 11/14/2014] [Accepted: 11/26/2014] [Indexed: 12/31/2022]
Abstract
The adenosine monoposphate-forming acyl-CoA synthetase enzymes catalyze a two-step reaction that involves the initial formation of an acyl adenylate that reacts in a second partial reaction to form a thioester between the acyl substrate and CoA. These enzymes utilize a Domain Alternation catalytic mechanism, whereby a ∼ 110 residue C-terminal domain rotates by 140° to form distinct catalytic conformations for the two partial reactions. The structure of an acetoacetyl-CoA synthetase (AacS) is presented that illustrates a novel aspect of this C-terminal domain. Specifically, several acetyl- and acetoacetyl-CoA synthetases contain a 30-residue extension on the C-terminus compared to other members of this family. Whereas residues from this extension are disordered in prior structures, the AacS structure shows that residues from this extension may interact with key catalytic residues from the N-terminal domain.
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Affiliation(s)
- Carter A Mitchell
- Hauptman-Woodward Institute, Buffalo, New York, 14203; Department of Structural Biology, University at Buffalo, Buffalo, New York, 14203
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33
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Wurst JM, Drake EJ, Theriault JR, Jewett IT, VerPlank L, Perez JR, Dandapani S, Palmer M, Moskowitz SM, Schreiber SL, Munoz B, Gulick AM. Identification of inhibitors of PvdQ, an enzyme involved in the synthesis of the siderophore pyoverdine. ACS Chem Biol 2014; 9:1536-44. [PMID: 24824984 PMCID: PMC4215858 DOI: 10.1021/cb5001586] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
Pseudomonas aeruginosa produces the peptide siderophore
pyoverdine, which is used to acquire essential Fe3+ ions
from the environment. PvdQ, an Ntn hydrolase, is required for the
biosynthesis of pyoverdine. PvdQ knockout strains
are not infectious in model systems, suggesting that disruption of
siderophore production via PvdQ inhibition could be exploited as a
target for novel antibacterial agents, by preventing cells from acquiring
iron in the low iron environments of most biological settings. We
have previously described a high-throughput screen to identify inhibitors
of PvdQ that identified inhibitors with IC50 values of
∼100 μM. Here, we describe the discovery of ML318, a
biaryl nitrile inhibitor of PvdQ acylase. ML318 inhibits PvdQ in vitro (IC50 = 20 nM) by binding in the acyl-binding
site, as confirmed by the X-ray crystal structure of PvdQ bound to
ML318. Additionally, the PvdQ inhibitor is active in a whole cell
assay, preventing pyoverdine production and limiting the growth of P. aeruginosa under iron-limiting conditions.
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Affiliation(s)
| | - Eric J. Drake
- Hauptman−Woodward Medical Research Institute, New
York 14203, United States
- Department
of Structural Biology, University at Buffalo, Buffalo, New York 14203, United States
| | | | - Ivan T. Jewett
- The Broad Institute, Cambridge, Massachusetts 02142, United States
| | - Lynn VerPlank
- The Broad Institute, Cambridge, Massachusetts 02142, United States
| | - Jose R. Perez
- The Broad Institute, Cambridge, Massachusetts 02142, United States
| | | | - Michelle Palmer
- The Broad Institute, Cambridge, Massachusetts 02142, United States
| | - Samuel M. Moskowitz
- Department
of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department
of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | | | - Benito Munoz
- The Broad Institute, Cambridge, Massachusetts 02142, United States
| | - Andrew M. Gulick
- Hauptman−Woodward Medical Research Institute, New
York 14203, United States
- Department
of Structural Biology, University at Buffalo, Buffalo, New York 14203, United States
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34
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Miller BR, Sundlov JA, Drake EJ, Makin TA, Gulick AM. Analysis of the linker region joining the adenylation and carrier protein domains of the modular nonribosomal peptide synthetases. Proteins 2014; 82:2691-702. [PMID: 24975514 DOI: 10.1002/prot.24635] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 06/06/2014] [Accepted: 06/18/2014] [Indexed: 12/29/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are multimodular proteins capable of producing important peptide natural products. Using an assembly line process, the amino acid substrate and peptide intermediates are passed between the active sites of different catalytic domains of the NRPS while bound covalently to a peptidyl carrier protein (PCP) domain. Examination of the linker sequences that join the NRPS adenylation and PCP domains identified several conserved proline residues that are not found in standalone adenylation domains. We examined the roles of these proline residues and neighboring conserved sequences through mutagenesis and biochemical analysis of the reaction catalyzed by the adenylation domain and the fully reconstituted NRPS pathway. In particular, we identified a conserved LPxP motif at the start of the adenylation-PCP linker. The LPxP motif interacts with a region on the adenylation domain to stabilize a critical catalytic lysine residue belonging to the A10 motif that immediately precedes the linker. Further, this interaction with the C-terminal subdomain of the adenylation domain may coordinate movement of the PCP with the conformational change of the adenylation domain. Through this work, we extend the conserved A10 motif of the adenylation domain and identify residues that enable proper adenylation domain function.
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Affiliation(s)
- Bradley R Miller
- Hauptman-Woodward Medical Research Institute and Department of Structural Biology, University at Buffalo, Buffalo, New York, 14203
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35
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Allen CL, Gulick AM. Structural and bioinformatic characterization of an Acinetobacter baumannii type II carrier protein. ACTA ACUST UNITED AC 2014; 70:1718-25. [PMID: 24914982 DOI: 10.1107/s1399004714008311] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 04/12/2014] [Indexed: 02/02/2023]
Abstract
Microorganisms produce a variety of natural products via secondary metabolic biosynthetic pathways. Two of these types of synthetic systems, the nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), use large modular enzymes containing multiple catalytic domains in a single protein. These multidomain enzymes use an integrated carrier protein domain to transport the growing, covalently bound natural product to the neighboring catalytic domains for each step in the synthesis. Interestingly, some PKS and NRPS clusters contain free-standing domains that interact intermolecularly with other proteins. Being expressed outside the architecture of a multi-domain protein, these so-called type II proteins present challenges to understand the precise role they play. Additional structures of individual and multi-domain components of the NRPS enzymes will therefore provide a better understanding of the features that govern the domain interactions in these interesting enzyme systems. The high-resolution crystal structure of a free-standing carrier protein from Acinetobacter baumannii that belongs to a larger NRPS-containing operon, encoded by the ABBFA_003406-ABBFA_003399 genes of A. baumannii strain AB307-0294, that has been implicated in A. baumannii motility, quorum sensing and biofilm formation, is presented here. Comparison with the closest structural homologs of other carrier proteins identifies the requirements for a conserved glycine residue and additional important sequence and structural requirements within the regions that interact with partner proteins.
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Affiliation(s)
- C Leigh Allen
- Hauptman-Woodward Medical Research Institute and Department of Structural Biology, University at Buffalo, Buffalo, NY 14203, USA
| | - Andrew M Gulick
- Hauptman-Woodward Medical Research Institute and Department of Structural Biology, University at Buffalo, Buffalo, NY 14203, USA
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36
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Kholodar SA, Tombline G, Liu J, Tan Z, Allen CL, Gulick AM, Murkin AS. Alteration of the flexible loop in 1-deoxy-D-xylulose-5-phosphate reductoisomerase boosts enthalpy-driven inhibition by fosmidomycin. Biochemistry 2014; 53:3423-31. [PMID: 24825256 PMCID: PMC4045324 DOI: 10.1021/bi5004074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
1-Deoxy-d-xylulose-5-phosphate reductoisomerase (DXR),
which catalyzes the first committed step in the 2-C-methyl-d-erythritol 4-phosphate pathway of isoprenoid biosynthesis
used by Mycobacterium tuberculosis and other infectious
microorganisms, is absent in humans and therefore an attractive drug
target. Fosmidomycin is a nanomolar inhibitor of DXR, but despite
great efforts, few analogues with comparable potency have been developed.
DXR contains a strictly conserved residue, Trp203, within a flexible
loop that closes over and interacts with the bound inhibitor. We report
that while mutation to Ala or Gly abolishes activity, mutation to
Phe and Tyr only modestly impacts kcat and Km. Moreover, pre-steady-state kinetics
and primary deuterium kinetic isotope effects indicate that while
turnover is largely limited by product release for the wild-type enzyme,
chemistry is significantly more rate-limiting for W203F and W203Y.
Surprisingly, these mutants are more sensitive to inhibition by fosmidomycin,
resulting in Km/Ki ratios up to 19-fold higher than that of wild-type DXR. In
agreement, isothermal titration calorimetry revealed that fosmidomycin
binds up to 11-fold more tightly to these mutants. Most strikingly,
mutation strongly tips the entropy–enthalpy balance of total
binding energy from 50% to 75% and 91% enthalpy in W203F and W203Y,
respectively. X-ray crystal structures suggest that these enthalpy
differences may be linked to differences in hydrogen bond interactions
involving a water network connecting fosmidomycin’s phosphonate
group to the protein. These results confirm the importance of the
flexible loop, in particular Trp203, in ligand binding and suggest
that improved inhibitor affinity may be obtained against the wild-type
protein by introducing interactions with this loop and/or the surrounding
structured water network.
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Affiliation(s)
- Svetlana A Kholodar
- Department of Chemistry, University at Buffalo , Buffalo, New York 14260-3000, United States
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37
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Sundlov JA, Gulick AM. Structure determination of the functional domain interaction of a chimeric nonribosomal peptide synthetase from a challenging crystal with noncrystallographic translational symmetry. Acta Crystallogr D Biol Crystallogr 2013; 69:1482-92. [PMID: 23897471 DOI: 10.1107/s0907444913009372] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 04/07/2013] [Indexed: 12/21/2022]
Abstract
The nonribosomal peptide synthetases (NRPSs) are a family of modular proteins that contain multiple catalytic domains joined in a single protein. Together, these domains work to produce chemically diverse peptides, including compounds with antibiotic activity or that play a role in iron acquisition. Understanding the structural mechanisms that govern the domain interactions has been a long-standing goal. During NRPS synthesis, amino-acid substrates are loaded onto integrated carrier protein domains through the activity of NRPS adenylation domains. The structures of two adenylation domain-carrier protein domain complexes have recently been determined in an effort that required the use of a mechanism-based inhibitor to trap the domain interaction. Here, the continued analysis of these proteins is presented, including a higher resolution structure of an engineered di-domain protein containing the EntE adenylation domain fused with the carrier protein domain of its partner EntB. The protein crystallized in a novel space group in which molecular replacement and refinement were challenged by noncrystallographic pseudo-translational symmetry. The structure determination and how the molecular packing impacted the diffraction intensities are reported. Importantly, the structure illustrates that in this new crystal form the functional interface between the adenylation domain and the carrier protein domain remains the same as that observed previously. At a resolution that allows inclusion of water molecules, additional interactions are observed between the two protein domains and between the protein and its ligands. In particular, a highly solvated region that surrounds the carrier protein cofactor is described.
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Affiliation(s)
- Jesse A Sundlov
- Hauptman-Woodward Medical Research Institute and Department of Structural Biology, University at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA
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38
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Demonte D, Drake EJ, Lim KH, Gulick AM, Park S. Structure-based engineering of streptavidin monomer with a reduced biotin dissociation rate. Proteins 2013; 81:1621-33. [PMID: 23670729 DOI: 10.1002/prot.24320] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 04/18/2013] [Accepted: 04/22/2013] [Indexed: 11/07/2022]
Abstract
We recently reported the engineering of monomeric streptavidin, mSA, corresponding to one subunit of wild type (wt) streptavidin tetramer. The monomer was designed by homology modeling, in which the streptavidin and rhizavidin sequences were combined to engineer a high affinity binding pocket containing residues from a single subunit only. Although mSA is stable and binds biotin with nanomolar affinity, its fast off rate (koff ) creates practical challenges during applications. We obtained a 1.9 Å crystal structure of mSA bound to biotin to understand their interaction in detail, and used the structure to introduce targeted mutations to improve its binding kinetics. To this end, we compared mSA to shwanavidin, which contains a hydrophobic lid containing F43 in the binding pocket and binds biotin tightly. However, the T48F mutation in mSA, which introduces a comparable hydrophobic lid, only resulted in a modest 20-40% improvement in the measured koff . On the other hand, introducing the S25H mutation near the bicyclic ring of bound biotin increased the dissociation half life (t½ ) from 11 to 83 min at 20°C. Molecular dynamics (MD) simulations suggest that H25 stabilizes the binding loop L3,4 by interacting with A47, and protects key intermolecular hydrogen bonds by limiting solvent entry into the binding pocket. Concurrent T48F or T48W mutation clashes with H25 and partially abrogates the beneficial effects of H25. Taken together, this study suggests that stabilization of the binding loop and solvation of the binding pocket are important determinants of the dissociation kinetics in mSA.
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Affiliation(s)
- Daniel Demonte
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, New York, 14260
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39
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Neres J, Engelhart CA, Drake EJ, Wilson DJ, Fu P, Boshoff HI, Barry CE, Gulick AM, Aldrich CC. Non-nucleoside inhibitors of BasE, an adenylating enzyme in the siderophore biosynthetic pathway of the opportunistic pathogen Acinetobacter baumannii. J Med Chem 2013; 56:2385-405. [PMID: 23437866 DOI: 10.1021/jm301709s] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Siderophores are small-molecule iron chelators produced by bacteria and other microorganisms for survival under iron limiting conditions such as found in a mammalian host. Siderophore biosynthesis is essential for the virulence of many important Gram-negative pathogens including Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Escherichia coli. We performed high-throughput screening against BasE, which is involved in siderophore biosynthesis in A. baumannii, and identified 6-phenyl-1-(pyridin-4-ylmethyl)-1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid 15. Herein we report the synthesis, biochemical, and microbiological evaluation of a systematic series of analogues of the HTS hit 15. Analogue 67 is the most potent analogue with a KD of 2 nM against BasE. Structural characterization of the inhibitors with BasE reveals that they bind in a unique orientation in the active site, occupying all three substrate binding sites, and thus can be considered as multisubstrate inhibitors. These results provide a foundation for future studies aimed at increasing both enzyme potency and antibacterial activity.
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Affiliation(s)
- João Neres
- Center for Drug Design, Academic Health Center, University of Minnesota , Minneapolis, Minnesota 55455, USA
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40
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Wilson DJ, Shi C, Teitelbaum AM, Gulick AM, Aldrich CC. Characterization of AusA: a dimodular nonribosomal peptide synthetase responsible for the production of aureusimine pyrazinones. Biochemistry 2013; 52:926-37. [PMID: 23302043 PMCID: PMC3577359 DOI: 10.1021/bi301330q] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aureusimines have been identified as potential virulence factors in Staphylococcus aureus. These pyrazinone secondary metabolites are produced by a nonribosomal peptide synthetase (NRPS) annotated as AusA. We report the overproduction of AusA as a 277 kDa soluble protein with A(1)-T(1)-C-A(2)-T(2)-R bimodular architecture. The substrate specificity of each adenylation (A) domain was initially probed using an ATP-pyrophosphate exchange assay with A-domain selective bisubstrate inhibitors to chemically knock out each companion A-domain. The activity of AusA was then reconstituted in vitro and shown to produce all naturally occurring aureusimines and non-natural pyrazinone products with k(cat) values ranging from 0.4 to 1.3 min(-1). Steady-state kinetic parameters were determined for all substrates and cofactors, providing the first comprehensive steady-state characterization of a NRPS employing a product formation assay. The K(M) values for the amino acids were up to 60-fold lower with the product formation assay than with the ATP-pyrophosphate exchange assay, most commonly used to assess A-domain substrate specificity. The C-terminal reductase (R) domain catalyzes reductive release of the dipeptidyl intermediate, leading to formation of an amino aldehyde that cyclizes to a dihydropyrazinone. We show oxidation to the final pyrazinone heterocycle is spontaneous. The activity and specificity of the R-domain was independently investigated using a NADPH consumption assay. AusA is a minimal autonomous two-module NRPS that represents an excellent model system for further kinetic and structural characterization.
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Affiliation(s)
- Daniel J. Wilson
- Center for Drug Design, University of Minnesota, Minneapolis, Minnesota 55455
| | - Ce Shi
- Center for Drug Design, University of Minnesota, Minneapolis, Minnesota 55455
| | - Aaron M. Teitelbaum
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, MN 55455
| | - Andrew M. Gulick
- Hauptman-Woodward Institute and Department of Structural Biology, University at Buffalo, Buffalo, NY, 14203 USA
| | - Courtney C. Aldrich
- Center for Drug Design, University of Minnesota, Minneapolis, Minnesota 55455
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Tessier MB, Grant OC, Heimburg-Molinaro J, Smith D, Jadey S, Gulick AM, Glushka J, Deutscher SL, Rittenhouse-Olson K, Woods RJ. Computational screening of the human TF-glycome provides a structural definition for the specificity of anti-tumor antibody JAA-F11. PLoS One 2013; 8:e54874. [PMID: 23365681 PMCID: PMC3554700 DOI: 10.1371/journal.pone.0054874] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 12/17/2012] [Indexed: 11/19/2022] Open
Abstract
Recombinant antibodies are of profound clinical significance; yet, anti-carbohydrate antibodies are prone to undesirable cross-reactivity with structurally related-glycans. Here we introduce a new technology called Computational Carbohydrate Grafting (CCG), which enables a virtual library of glycans to be assessed for protein binding specificity, and employ it to define the scope and structural origin of the binding specificity of antibody JAA-F11 for glycans containing the Thomsen-Friedenreich (TF) human tumor antigen. A virtual library of the entire human glycome (GLibrary-3D) was constructed, from which 1,182 TF-containing human glycans were identified and assessed for their ability to fit into the antibody combining site. The glycans were categorized into putative binders, or non-binders, on the basis of steric clashes with the antibody surface. The analysis employed a structure of the immune complex, generated by docking the TF-disaccharide (Galβ1-3GalNAcα) into a crystal structure of the JAA-F11 antigen binding fragment, which was shown to be consistent with saturation transfer difference (STD) NMR data. The specificities predicted by CCG were fully consistent with data from experimental glycan array screening, and confirmed that the antibody is selective for the TF-antigen and certain extended core-2 type mucins. Additionally, the CCG analysis identified a limited number of related putative binding motifs, and provided a structural basis for interpreting the specificity. CCG can be utilized to facilitate clinical applications through the determination of the three-dimensional interaction of glycans with proteins, thus augmenting drug and vaccine development techniques that seek to optimize the specificity and affinity of neutralizing proteins, which target glycans associated with diseases including cancer and HIV.
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Affiliation(s)
- Matthew B. Tessier
- Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia, United States of America
| | - Oliver C. Grant
- School of Chemistry, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Jamie Heimburg-Molinaro
- Department of Biotechnical and Clinical Laboratory Sciences, State University of New York, Buffalo, New York, United States of America
| | - David Smith
- Department of Biochemistry, Emory University, Atlanta, Georgia, United States of America
| | - Snehal Jadey
- Department of Biotechnical and Clinical Laboratory Sciences, State University of New York, Buffalo, New York, United States of America
| | - Andrew M. Gulick
- Hauptman-Woodward Institute, Department of Structural Biology, State University of New York, Buffalo, New York, United States of America
| | - John Glushka
- Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia, United States of America
| | - Susan L. Deutscher
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Kate Rittenhouse-Olson
- Department of Biotechnical and Clinical Laboratory Sciences, State University of New York, Buffalo, New York, United States of America
- * E-mail: (KRO); (RJW)
| | - Robert J. Woods
- Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia, United States of America
- School of Chemistry, National University of Ireland, Galway, University Road, Galway, Ireland
- * E-mail: (KRO); (RJW)
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Muppidi A, Doi K, Edwardraja S, Drake EJ, Gulick AM, Wang HG, Lin Q. Rational design of proteolytically stable, cell-permeable peptide-based selective Mcl-1 inhibitors. J Am Chem Soc 2012; 134:14734-7. [PMID: 22920569 DOI: 10.1021/ja306864v] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Direct chemical modifications provide a simple and effective means to "translate" bioactive helical peptides into potential therapeutics targeting intracellular protein-protein interactions. We previously showed that distance-matching bisaryl cross-linkers can reinforce peptide helices containing two cysteines at the i and i+7 positions and confer cell permeability to the cross-linked peptides. Here we report the first crystal structure of a biphenyl-cross-linked Noxa peptide in complex with its target Mcl-1 at 2.0 Å resolution. Guided by this structure, we remodeled the surface of this cross-linked peptide through side-chain substitution and N-methylation and obtained a pair of cross-linked peptides with substantially increased helicity, cell permeability, proteolytic stability, and cell-killing activity in Mcl-1-overexpressing U937 cells.
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Affiliation(s)
- Avinash Muppidi
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, USA
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43
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Sundlov JA, Fontaine DM, Southworth TL, Branchini BR, Gulick AM. Crystal structure of firefly luciferase in a second catalytic conformation supports a domain alternation mechanism. Biochemistry 2012; 51:6493-5. [PMID: 22852753 DOI: 10.1021/bi300934s] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Beetle luciferases catalyze a two-step reaction that includes the initial adenylation of the luciferin substrate, followed by an oxidative decarboxylation that ultimately produces light. Evidence for homologous acyl-CoA synthetases supports a domain alternation catalytic mechanism in which these enzymes' C-terminal domain rotates by ~140° to adopt two conformations that are used to catalyze the two partial reactions. While many structures exist of acyl-CoA synthetases in both conformations, to date only biochemical evidence supports domain alternation with luciferase. We have determined the structure of a cross-linked luciferase enzyme that is trapped in the second conformation. This new structure supports the role of the second catalytic conformation and provides insights into the biochemical mechanism of the luciferase oxidative step.
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Affiliation(s)
- Jesse A Sundlov
- Hauptman-Woodward Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
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Sundlov JA, Shi C, Wilson DJ, Aldrich CC, Gulick AM. Structural and functional investigation of the intermolecular interaction between NRPS adenylation and carrier protein domains. ACTA ACUST UNITED AC 2012; 19:188-98. [PMID: 22365602 DOI: 10.1016/j.chembiol.2011.11.013] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 11/17/2011] [Accepted: 11/22/2011] [Indexed: 10/28/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are modular proteins that produce peptide antibiotics and siderophores. These enzymes act as catalytic assembly lines where substrates, covalently bound to integrated carrier domains, are delivered to adjacent catalytic domains. The carrier domains are initially loaded by adenylation domains, which use two distinct conformations to catalyze sequentially the adenylation of the substrate and the thioesterification of the pantetheine cofactor. We have used a mechanism-based inhibitor to determine the crystal structure of an engineered adenylation-carrier domain protein illustrating the intermolecular interaction between the adenylation and carrier domains. This structure enabled directed mutations to improve the interaction between nonnative partner proteins. Comparison with prior NRPS adenylation domain structures provides insights into the assembly line dynamics of these modular enzymes.
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Affiliation(s)
- Jesse A Sundlov
- Hauptman-Woodward Institute and Department of Structural Biology, University at Buffalo, Buffalo, NY 14203 USA
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45
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Mitchell CA, Shi C, Aldrich CC, Gulick AM. Structure of PA1221, a nonribosomal peptide synthetase containing adenylation and peptidyl carrier protein domains. Biochemistry 2012; 51:3252-63. [PMID: 22452656 DOI: 10.1021/bi300112e] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many bacteria use large modular enzymes for the synthesis of polyketide and peptide natural products. These multidomain enzymes contain integrated carrier domains that deliver bound substrates to multiple catalytic domains, requiring coordination of these chemical steps. Nonribosomal peptide synthetases (NRPSs) load amino acids onto carrier domains through the activity of an upstream adenylation domain. Our lab recently determined the structure of an engineered two-domain NRPS containing fused adenylation and carrier domains. This structure adopted a domain-swapped dimer that illustrated the interface between these two domains. To continue our investigation, we now examine PA1221, a natural two-domain protein from Pseudomonas aeruginosa. We have determined the amino acid specificity of this new enzyme and used domain specific mutations to demonstrate that loading the downstream carrier domain within a single protein molecule occurs more quickly than loading of a nonfused carrier domain intermolecularly. Finally, we have determined crystal structures of both apo- and holo-PA1221 proteins, the latter using a valine-adenosine vinylsulfonamide inhibitor that traps the adenylation domain-carrier domain interaction. The protein adopts an interface similar to that seen with the prior adenylation domain-carrier protein construct. A comparison of these structures with previous structures of multidomain NRPSs suggests that a large conformational change within the NRPS adenylation domains guides the carrier domain into the active site for thioester formation.
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Affiliation(s)
- Carter A Mitchell
- Hauptman-Woodward Institute and Department of Structural Biology, University at Buffalo, Buffalo, New York 14203, United States
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Drake EJ, Gulick AM. Structural characterization and high-throughput screening of inhibitors of PvdQ, an NTN hydrolase involved in pyoverdine synthesis. ACS Chem Biol 2011; 6:1277-86. [PMID: 21892836 DOI: 10.1021/cb2002973] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The human pathogen Pseudomonas aeruginosa produces a variety of virulence factors including pyoverdine, a nonribosomally produced peptide siderophore. The maturation pathway of the pyoverdine peptide is complex and provides a unique target for inhibition. Within the pyoverdine biosynthetic cluster is a periplasmic hydrolase, PvdQ, that is required for pyoverdine production. However, the precise role of PvdQ in the maturation pathway has not been biochemically characterized. We demonstrate herein that the initial module of the nonribosomal peptide synthetase PvdL adds a myristate moiety to the pyoverdine precursor. We extracted this acylated precursor, called PVDIq, from a pvdQ mutant strain and show that the PvdQ enzyme removes the fatty acid catalyzing one of the final steps in pyoverdine maturation. Incubation of PVDIq with crystals of PvdQ allowed us to capture the acylated enzyme and confirm through structural studies the chemical composition of the incorporated acyl chain. Finally, because inhibition of siderophore synthesis has been identified as a potential antibiotic strategy, we developed a high-throughput screening assay and tested a small chemical library for compounds that inhibit PvdQ activity. Two compounds that block PvdQ have been identified, and their binding within the fatty acid binding pocket was structurally characterized.
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Affiliation(s)
- Eric J. Drake
- Hauptman-Woodward Medical Research Institute and Department of Structural Biology, State University of New York at Buffalo, 700 Ellicott Street, Buffalo, New York 14203-1102, United States
| | - Andrew M. Gulick
- Hauptman-Woodward Medical Research Institute and Department of Structural Biology, State University of New York at Buffalo, 700 Ellicott Street, Buffalo, New York 14203-1102, United States
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47
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Drake EJ, Duckworth BP, Neres J, Aldrich CC, Gulick AM. Biochemical and structural characterization of bisubstrate inhibitors of BasE, the self-standing nonribosomal peptide synthetase adenylate-forming enzyme of acinetobactin synthesis. Biochemistry 2010; 49:9292-305. [PMID: 20853905 DOI: 10.1021/bi101226n] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The human pathogen Acinetobacter baumannii produces a siderophore called acinetobactin that is derived from one molecule each of threonine, histidine, and 2,3-dihydroxybenzoic acid (DHB). The activity of several nonribosomal peptide synthetase (NRPS) enzymes is used to combine the building blocks into the final molecule. The acinetobactin synthesis pathway initiates with a self-standing adenylation enzyme, BasE, that activates the DHB molecule and covalently transfers it to the pantetheine cofactor of an aryl-carrier protein of BasF, a strategy that is shared with many siderophore-producing NRPS clusters. In this reaction, DHB reacts with ATP to form the aryl adenylate and pyrophosphate. In a second partial reaction, the DHB is transferred to the carrier protein. Inhibitors of BasE and related enzymes have been identified that prevent growth of bacteria on iron-limiting media. Recently, a new inhibitor of BasE has been identified via high-throughput screening using a fluorescence polarization displacement assay. We present here biochemical and structural studies to examine the binding mode of this inhibitor. The kinetics of the wild-type BasE enzyme is shown, and inhibition studies demonstrate that the new compound exhibits competitive inhibition against both ATP and 2,3-dihydroxybenzoate. Structural examination of BasE bound to this inhibitor illustrates a novel binding mode in which the phenyl moiety partially fills the enzyme pantetheine binding tunnel. Structures of rationally designed bisubstrate inhibitors are also presented.
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Affiliation(s)
- Eric J Drake
- Hauptman-Woodward Institute and Department of Structural Biology, University at Buffalo, Buffalo, NY 14203-1102, USA
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48
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Abstract
Bacteria utilize multiple strategies to circumvent antibiotics, producing broad specificity exporters or enzymes that catalyze the modification of either antibiotics or their targets. A report in this issue of Structure provides the structural and catalytic mechanisms of LinB, an adenylyltransferase of E. faecium that confers resistance to the lincosamide antibiotic clindamycin.
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Affiliation(s)
- Jesse A Sundlov
- Department of Structural Biology, Hauptman-Woodward Medical Research Institute, State University of New York at Buffalo, Buffalo, NY, USA
| | - Andrew M Gulick
- Department of Structural Biology, Hauptman-Woodward Medical Research Institute, State University of New York at Buffalo, Buffalo, NY, USA.
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49
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Shah MB, Ingram-Smith C, Cooper LL, Qu J, Meng Y, Smith KS, Gulick AM. The 2.1 A crystal structure of an acyl-CoA synthetase from Methanosarcina acetivorans reveals an alternate acyl-binding pocket for small branched acyl substrates. Proteins 2010; 77:685-98. [PMID: 19544569 DOI: 10.1002/prot.22482] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The acyl-AMP forming family of adenylating enzymes catalyze two-step reactions to activate a carboxylate with the chemical energy derived from ATP hydrolysis. X-ray crystal structures have been determined for multiple members of this family and, together with biochemical studies, provide insights into the active site and catalytic mechanisms used by these enzymes. These studies have shown that the enzymes use a domain rotation of 140 degrees to reconfigure a single active site to catalyze the two partial reactions. We present here the crystal structure of a new medium chain acyl-CoA synthetase from Methanosarcina acetivorans. The binding pocket for the three substrates is analyzed, with many conserved residues present in the AMP binding pocket. The CoA binding pocket is compared to the pockets of both acetyl-CoA synthetase and 4-chlorobenzoate:CoA ligase. Most interestingly, the acyl-binding pocket of the new structure is compared with other acyl- and aryl-CoA synthetases. A comparison of the acyl-binding pocket of the acyl-CoA synthetase from M. acetivorans with other structures identifies a shallow pocket that is used to bind the medium chain carboxylates. These insights emphasize the high sequence and structural diversity among this family in the area of the acyl-binding pocket.
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Affiliation(s)
- Manish B Shah
- Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203-1102, USA
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50
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Gulick AM. Conformational dynamics in the Acyl-CoA synthetases, adenylation domains of non-ribosomal peptide synthetases, and firefly luciferase. ACS Chem Biol 2009; 4:811-27. [PMID: 19610673 DOI: 10.1021/cb900156h] [Citation(s) in RCA: 314] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ANL superfamily of adenylating enzymes contains acyl- and aryl-CoA synthetases, firefly luciferase, and the adenylation domains of the modular non-ribosomal peptide synthetases (NRPSs). Members of this family catalyze two partial reactions: the initial adenylation of a carboxylate to form an acyl-AMP intermediate, followed by a second partial reaction, most commonly the formation of a thioester. Recent biochemical and structural evidence has been presented that supports the use by this enzyme family of a remarkable catalytic strategy for the two catalytic steps. The enzymes use a 140 degrees domain rotation to present opposing faces of the dynamic C-terminal domain to the active site for the different partial reactions. Support for this domain alternation strategy is presented along with an explanation of the advantage of this catalytic strategy for the reaction catalyzed by the ANL enzymes. Finally, the ramifications of this domain rotation in the catalytic cycle of the modular NRPS enzymes are discussed.
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Affiliation(s)
- Andrew M. Gulick
- Hauptman-Woodward Medical Research Institute and Department of Structural Biology, State University of New York at Buffalo, 700 Ellicott St., Buffalo, New York 14203-1102
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