401
|
Singh A, Mohammad Arif S, Biak Sang P, Varshney U, Vijayan M. Structural insights into the specificity and catalytic mechanism of mycobacterial nucleotide pool sanitizing enzyme MutT2. J Struct Biol 2018; 204:449-456. [PMID: 30312643 DOI: 10.1016/j.jsb.2018.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/04/2018] [Accepted: 10/07/2018] [Indexed: 12/29/2022]
Abstract
Mis-incorporation of modified nucleotides, such as 5-methyl-dCTP or 8-oxo-dGTP, in DNA can be detrimental to genomic integrity. MutT proteins are sanitization enzymes which function by hydrolyzing such nucleotides and regulating the pool of free nucleotides in the cytoplasm. Mycobacterial genomes have a set of four MutT homologs, namely, MutT1, MutT2, MutT3 and MutT4. Mycobacterial MutT2 hydrolyzes 5 m-dCTP and 8-oxo-dGTP to their respective monophosphate products. Additionally, it can hydrolyze canonical nucleotides dCTP and CTP, with a suggested role in sustaining their optimal levels in the nucleotide pool. The structures of M. smegmatis MutT2 and its complexes with cytosine derivatives have been determined at resolutions ranging from 1.10 Å to 1.73 Å. The apo enzyme and its complexes with products (dCMP, CMP and 5 m-dCMP) crystallize in space group P21212, while those involving substrates (dCTP, CTP and 5 m-dCTP) crystallize in space group P21. The molecule takes an α/β/α sandwich fold arrangement, as observed in other MutT homologs. The nucleoside moiety of the ligands is similarly located in all the complexes, while the location of the remaining tail exhibits variability. This is the first report of a MutT2-type protein in complex with ligands. A critical interaction involving Asp116 confers the specificity of the enzyme towards cytosine moieties. A conserved set of enzyme-ligand interactions along with concerted movements of important water molecules provide insights into the mechanism of action.
Collapse
Affiliation(s)
- Amandeep Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | | | - Pau Biak Sang
- Dept. of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Umesh Varshney
- Dept. of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - M Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
| |
Collapse
|
402
|
Thompson AP, Wegener KL, Booker GW, Polyak SW, Bruning JB. Precipitant-ligand exchange technique reveals the ADP binding mode in Mycobacterium tuberculosis dethiobiotin synthetase. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:965-972. [PMID: 30289406 DOI: 10.1107/s2059798318010136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/13/2018] [Indexed: 11/10/2022]
Abstract
Dethiobiotin synthetase from Mycobacterium tuberculosis (MtDTBS) is a promising antituberculosis drug target. Small-molecule inhibitors that target MtDTBS provide a route towards new therapeutics for the treatment of antibiotic-resistant tuberculosis. Adenosine diphosphate (ADP) is an inhibitor of MtDTBS; however, structural studies into its mechanism of inhibition have been unsuccessful owing to competitive binding to the enzyme by crystallographic precipitants such as citrate and sulfate. Here, a crystallographic technique termed precipitant-ligand exchange has been developed to exchange protein-bound precipitants with ligands of interest. Proof of concept for the exchange method was demonstrated using cytidine triphosphate (CTP), which adopted the same binding mechanism as that obtained with traditional crystal-soaking techniques. Precipitant-ligand exchange also yielded the previously intractable structure of MtDTBS in complex with ADP solved to 2.4 Å resolution. This result demonstrates the utility of precipitant-ligand exchange, which may be widely applicable to protein crystallography.
Collapse
Affiliation(s)
- Andrew P Thompson
- Molecular and Biomedical Science, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
| | - Kate L Wegener
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Grant W Booker
- Molecular and Biomedical Science, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
| | - Steven W Polyak
- Molecular and Biomedical Science, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
| | - John B Bruning
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| |
Collapse
|
403
|
González JM, Marti-Arbona R, Chen JCH, Broom-Peltz B, Unkefer CJ. Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase. Acta Crystallogr F Struct Biol Commun 2018; 74:610-616. [PMID: 30279311 PMCID: PMC6168771 DOI: 10.1107/s2053230x18011809] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/20/2018] [Indexed: 11/10/2022] Open
Abstract
Three high-resolution X-ray crystal structures of malate dehydrogenase (MDH; EC 1.1.1.37) from the methylotroph Methylobacterium extorquens AM1 are presented. By comparing the structures of apo MDH, a binary complex of MDH and NAD+, and a ternary complex of MDH and oxaloacetate with ADP-ribose occupying the pyridine nucleotide-binding site, conformational changes associated with the formation of the catalytic complex were characterized. While the substrate-binding site is accessible in the enzyme resting state or NAD+-bound forms, the substrate-bound form exhibits a closed conformation. This conformational change involves the transition of an α-helix to a 310-helix, which causes the adjacent loop to close the active site following coenzyme and substrate binding. In the ternary complex, His284 forms a hydrogen bond to the C2 carbonyl of oxaloacetate, placing it in a position to donate a proton in the formation of (2S)-malate.
Collapse
Affiliation(s)
- Javier M. González
- Instituto de Bionanotecnología del NOA, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Santiago del Estero, G4206XCP Santiago del Estero, Argentina
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Julian C.-H. Chen
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Brian Broom-Peltz
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Clifford J. Unkefer
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| |
Collapse
|
404
|
Shabalin IG, Porebski PJ, Minor W. Refining the macromolecular model - achieving the best agreement with the data from X-ray diffraction experiment. CRYSTALLOGR REV 2018; 24:236-262. [PMID: 30416256 DOI: 10.1080/0889311x.2018.1521805] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Refinement of macromolecular X-ray crystal structures involves using complex software with hundreds of different settings. The complexity of underlying concepts and the sheer amount sof instructions may make it difficult for less experienced crystallographers to achieve optimal results in their refinements. This tutorial review offers guidelines for choosing the best settings for the reciprocal-space refinement of macromolecular models and provides practical tips for manual model correction. To help aspiring crystallographers navigate the process, some of the most practically important concepts of protein structure refinement are described. Among the topics covered are the use and purpose of R-free, geometrical restraints, restraints on atomic displacement parameters (ADPs), refinement weights, various parametrizations of ADPs (full anisotropic refinement and TLS), and omit maps. We also give practical tips for manual model correction in Coot, modelling of side-chains with poor or missing density, and ligand identification, fitting, and refinement.
Collapse
Affiliation(s)
- Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, United States
| | - Przemyslaw J Porebski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, United States
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, United States
| |
Collapse
|
405
|
Ragwan ER, Arai E, Kung Y. New Crystallographic Snapshots of Large Domain Movements in Bacterial 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase. Biochemistry 2018; 57:5715-5725. [PMID: 30199631 DOI: 10.1021/acs.biochem.8b00869] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase (HMGR) catalyzes the first committed step of the mevalonate pathway, which is used across biology in the biosynthesis of countless metabolites. HMGR consumes 2 equiv of the cofactor NAD(P)H to perform the four-electron reduction of HMG-CoA to mevalonate toward the production of steroids and isoprenoids, the largest class of natural products. Recent structural data have shown that HMGR contains a highly mobile C-terminal domain (CTD) that is believed to adopt many different conformations to permit binding and dissociation of the substrate, cofactors, and products at specific points during the reaction cycle. Here, we have characterized the HMGR from Delftia acidovorans as an NADH-specific enzyme and determined crystal structures of the enzyme in unbound, mevalonate-bound, and NADH- and citrate-bound states. Together, these structures depict ligand binding in both the active site and the cofactor-binding site while illustrating how a conserved helical motif confers NAD(P)H cofactor specificity. Unexpectedly, the NADH-bound structure also reveals a new conformation of the CTD, in which the domain has "flipped" upside-down, while directly binding the cofactor. By capturing these structural snapshots, this work not only expands the known range of HMGR domain movement but also provides valuable insight into the catalytic mechanism of this biologically important enzyme.
Collapse
Affiliation(s)
- Edwin R Ragwan
- Department of Chemistry , Bryn Mawr College , 101 North Merion Avenue , Bryn Mawr , Pennsylvania 19010 , United States
| | - Eri Arai
- Department of Chemistry , Bryn Mawr College , 101 North Merion Avenue , Bryn Mawr , Pennsylvania 19010 , United States
| | - Yan Kung
- Department of Chemistry , Bryn Mawr College , 101 North Merion Avenue , Bryn Mawr , Pennsylvania 19010 , United States
| |
Collapse
|
406
|
Snapshots of a modified nucleotide moving through the confines of a DNA polymerase. Proc Natl Acad Sci U S A 2018; 115:9992-9997. [PMID: 30224478 PMCID: PMC6176618 DOI: 10.1073/pnas.1811518115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Despite being evolved to process the four canonical nucleotides, DNA polymerases are known to incorporate and extend from modified nucleotides, which is the key to numerous core biotechnology applications. The structural basis for postincorporation elongation remained elusive. We successfully crystallized KlenTaq DNA polymerase in six complexes, providing high-resolution snapshots of the modification “moving” from the 3′ terminus upstream to the sixth nucleotide in the primer strand. Combining these data with quantum mechanics/molecular mechanics calculations and biochemical studies elucidates how the enzyme and the modified substrate mutually modulate their conformations without compromising the enzyme’s activity. This highlights the unexpected plasticity of the system as origin of the broad substrate properties of the DNA polymerase and guide for the design of improved systems. DNA polymerases have evolved to process the four canonical nucleotides accurately. Nevertheless, these enzymes are also known to process modified nucleotides, which is the key to numerous core biotechnology applications. Processing of modified nucleotides includes incorporation of the modified nucleotide and postincorporation elongation to proceed with the synthesis of the nascent DNA strand. The structural basis for postincorporation elongation is currently unknown. We addressed this issue and successfully crystallized KlenTaq DNA polymerase in six closed ternary complexes containing the enzyme, the modified DNA substrate, and the incoming nucleotide. Each structure shows a high-resolution snapshot of the elongation of a modified primer, where the modification “moves” from the 3′-primer terminus upstream to the sixth nucleotide in the primer strand. Combining these data with quantum mechanics/molecular mechanics calculations and biochemical studies elucidates how the enzyme and the modified substrate mutually modulate their conformations without compromising the enzyme’s activity significantly. The study highlights the plasticity of the system as origin of the broad substrate properties of DNA polymerases and facilitates the design of improved systems.
Collapse
|
407
|
Thomaston JL, Polizzi NF, Konstantinidi A, Wang J, Kolocouris A, DeGrado WF. Inhibitors of the M2 Proton Channel Engage and Disrupt Transmembrane Networks of Hydrogen-Bonded Waters. J Am Chem Soc 2018; 140:15219-15226. [PMID: 30165017 DOI: 10.1021/jacs.8b06741] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Water-mediated interactions play key roles in drug binding. In protein sites with sparse polar functionality, a small-molecule approach is often viewed as insufficient to achieve high affinity and specificity. Here we show that small molecules can enable potent inhibition by targeting key waters. The M2 proton channel of influenza A is the target of the antiviral drugs amantadine and rimantadine. Structural studies of drug binding to the channel using X-ray crystallography have been limited because of the challenging nature of the target, with the one previously solved crystal structure limited to 3.5 Å resolution. Here we describe crystal structures of amantadine bound to M2 in the Inwardclosed conformation (2.00 Å), rimantadine bound to M2 in both the Inwardclosed (2.00 Å) and Inwardopen (2.25 Å) conformations, and a spiro-adamantyl amine inhibitor bound to M2 in the Inwardclosed conformation (2.63 Å). These X-ray crystal structures of the M2 proton channel with bound inhibitors reveal that ammonium groups bind to water-lined sites that are hypothesized to stabilize transient hydronium ions formed in the proton-conduction mechanism. Furthermore, the ammonium and adamantyl groups of the adamantyl-amine class of drugs are free to rotate in the channel, minimizing the entropic cost of binding. These drug-bound complexes provide the first high-resolution structures of drugs that interact with and disrupt networks of hydrogen-bonded waters that are widely utilized throughout nature to facilitate proton diffusion within proteins.
Collapse
Affiliation(s)
- Jessica L Thomaston
- Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94158 , United States
| | - Nicholas F Polizzi
- Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94158 , United States
| | - Athina Konstantinidi
- Department of Pharmaceutical Chemistry , National and Kapodistrian University of Athens , 15771 Athens , Greece
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy , University of Arizona , Tucson , Arizona 85721 , United States
| | - Antonios Kolocouris
- Department of Pharmaceutical Chemistry , National and Kapodistrian University of Athens , 15771 Athens , Greece
| | - William F DeGrado
- Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94158 , United States
| |
Collapse
|
408
|
Afanador GA, Tomchick DR, Phillips MA. Trypanosomatid Deoxyhypusine Synthase Activity Is Dependent on Shared Active-Site Complementation between Pseudoenzyme Paralogs. Structure 2018; 26:1499-1512.e5. [PMID: 30197036 DOI: 10.1016/j.str.2018.07.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/07/2018] [Accepted: 07/25/2018] [Indexed: 12/30/2022]
Abstract
Trypanosoma brucei is a neglected tropical disease endemic to Africa. The polyamine spermidine is essential for post-translational hypusine modification of eukaryotic initiation factor 5A (eIF5A), which is catalyzed by deoxyhypusine synthase (TbDHS). In trypanosomatids, deoxyhypusine synthase (DHS) activity is dependent on heterotetramer formation between two paralogs, DHSc and DHSp, both with minimal activity on their own due to missing catalytic residues. We determined the X-ray structure of TbDHS showing a single functional shared active site is formed at the DHSc/DHSp heterodimer interface, with deficiencies in one subunit complemented by the other. Each heterodimer contains two NAD+ binding sites, one housed in the functional catalytic site and the second bound in a remnant dead site that lacks key catalytic residues. Functional analysis of these sites by site-directed mutagenesis identified long-range contributions to the catalytic site from the dead site. Differences between trypanosomatid and human DHS that could be exploited for drug discovery were identified.
Collapse
Affiliation(s)
- Gustavo A Afanador
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Margaret A Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
409
|
Cheng Z, VanPelt J, Bergstrom A, Bethel C, Katko A, Miller C, Mason K, Cumming E, Zhang H, Kimble RL, Fullington S, Bretz SL, Nix JC, Bonomo RA, Tierney DL, Page RC, Crowder MW. A Noncanonical Metal Center Drives the Activity of the Sediminispirochaeta smaragdinae Metallo-β-lactamase SPS-1. Biochemistry 2018; 57:5218-5229. [PMID: 30106565 PMCID: PMC6314204 DOI: 10.1021/acs.biochem.8b00728] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In an effort to evaluate whether a recently reported putative metallo-β-lactamase (MβL) contains a novel MβL active site, SPS-1 from Sediminispirochaeta smaragdinae was overexpressed, purified, and characterized using spectroscopic and crystallographic studies. Metal analyses demonstrate that recombinant SPS-1 binds nearly 2 equiv of Zn(II), and steady-state kinetic studies show that the enzyme hydrolyzes carbapenems and certain cephalosporins but not β-lactam substrates with bulky substituents at the 6/7 position. Spectroscopic studies of Co(II)-substituted SPS-1 suggest a novel metal center in SPS-1, with a reduced level of spin coupling between the metal ions and a novel Zn1 metal binding site. This site was confirmed with a crystal structure of the enzyme. The structure shows a Zn2 site that is similar to that in NDM-1 and other subclass B1 MβLs; however, the Zn1 metal ion is coordinated by two histidine residues and a water molecule, which is held in position by a hydrogen bond network. The Zn1 metal is displaced nearly 1 Å from the position reported in other MβLs. The structure also shows extended helices above the active site, which create a binding pocket that precludes the binding of substrates with large, bulky substituents at the 6/7 position of β-lactam antibiotics. This study reveals a novel metal binding site in MβLs and suggests that the targeting of metal binding sites in MβLs with inhibitors is now more challenging with the identification of this new MβL.
Collapse
Affiliation(s)
- Zishuo Cheng
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Jamie VanPelt
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Alexander Bergstrom
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Christopher Bethel
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106
| | - Andrew Katko
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Callie Miller
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Kelly Mason
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Erin Cumming
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Huan Zhang
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Robert L. Kimble
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Sarah Fullington
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Stacey Lowery Bretz
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Jay C. Nix
- Molecular Biology Consortium, Beamline 4.2.2, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106
- Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, Proteomics and Bioinformatics, and the CWRU-Cleveland VAMC Center of Antimicrobial Resistance and Epidemiology, Cleveland, OH 44106
| | - David L. Tierney
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Richard C. Page
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| |
Collapse
|
410
|
Frkic RL, Chua BS, Shin Y, Pascal BD, Novick SJ, Kamenecka TM, Griffin PR, Bruning JB. Structural and Dynamic Elucidation of a Non-acid PPAR γ Partial Agonist: SR1988. NUCLEAR RECEPTOR RESEARCH 2018; 5. [PMID: 30906767 PMCID: PMC6428214 DOI: 10.11131/2018/101350] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Targeting peroxisome proliferator-activated receptor γ (PPARγ) by synthetic compounds has been shown to elicit insulin sensitising properties in type 2 diabetics. Treatment with a class of these compounds, the thiazolidinediones (TZDs), has shown adverse side effects such as weight gain, fluid retention, and congestive heart failure. This is due to their full agonist properties on the receptor, where a number of genes are upregulated beyond normal physiological levels. Lessened transactivation of PPARγ by partial agonists has proved beneficial in terms of reducing side effects, while still maintaining insulin sensitising properties. However, some partial agonists have been associated with unfavourable pharmacokinetic profiles due to their acidic moieties, often causing partitioning to the liver. Here we present SR1988, a new partial agonist with favourable non-acid chemical properties. We used a combination of X-ray crystallography and hydrogen/deuterium exchange (HDX) to elucidate the structural basis for reduced activation of PPARγ by SR1988. This structural analysis reveals a mechanism that decreases stabilisation of the AF2 coactivator binding surface by the ligand.
Collapse
Affiliation(s)
- Rebecca L Frkic
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Benjamin S Chua
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Youseung Shin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Bruce D Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, United States.,Omics Informatics LLC, 1050 Bishop Street #517, Honolulu, HI, 96813, Hawaii
| | - Scott J Novick
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Theodore M Kamenecka
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - John B Bruning
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| |
Collapse
|
411
|
Raczynska JE, Shabalin IG, Minor W, Wlodawer A, Jaskolski M. A close look onto structural models and primary ligands of metallo-β-lactamases. Drug Resist Updat 2018; 40:1-12. [PMID: 30466711 PMCID: PMC6260963 DOI: 10.1016/j.drup.2018.08.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 08/14/2018] [Accepted: 08/16/2018] [Indexed: 10/28/2022]
Abstract
β-Lactamases are hydrolytic enzymes capable of opening the β-lactam ring of antibiotics such as penicillin, thus endowing the bacteria that produce them with antibiotic resistance. Of particular medical concern are metallo-β-lactamases (MBLs), with an active site built around coordinated Zn cations. MBLs are pan-reactive enzymes that can break down almost all classes of β-lactams, including such last-resort antibiotics as carbapenems. They are not only broad-spectrum-reactive but are often plasmid-borne (e.g., the New Delhi enzyme, NDM), and can spread horizontally even among unrelated bacteria. Acquired MBLs are encoded by mobile genetic elements, which often include other resistance genes, making the microbiological situation particularly alarming. There is an urgent need to develop MBL inhibitors in order to rescue our antibiotic armory. A number of such efforts have been undertaken, most notably using the 3D structures of various MBLs as drug-design targets. Structure-guided drug discovery depends on the quality of the structures that are collected in the Protein Data Bank (PDB) and on the consistency of the information in dedicated β-lactamase databases. We conducted a careful review of the crystal structures of class B β-lactamases, concluding that the quality of these structures varies widely, especially in the regions where small molecules interact with the macromolecules. In a number of examples the interpretation of the bound ligands (e.g., inhibitors, substrate/product analogs) is doubtful or even incorrect, and it appears that in some cases the modeling of ligands was not supported by electron density. For ten MBL structures, alternative interpretations of the original diffraction data could be proposed and the new models have been deposited in the PDB. In four cases, these models, prepared jointly with the authors of the original depositions, superseded the previous deposits. This review emphasizes the importance of critical assessment of structural models describing key drug design targets at the level of the raw experimental data. Since the structures reviewed here are the basis for ongoing design of new MBL inhibitors, it is important to identify and correct the problems with ambiguous crystallographic interpretations, thus enhancing reproducibility in this highly medically relevant area.
Collapse
Affiliation(s)
- Joanna E Raczynska
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; Center for Structural Genomics of Infectious Diseases, Charlottesville, VA 22908, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; Center for Structural Genomics of Infectious Diseases, Charlottesville, VA 22908, USA
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland; Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.
| |
Collapse
|
412
|
Hussein WM, Feder D, Schenk G, Guddat LW, McGeary RP. Purple acid phosphatase inhibitors as leads for osteoporosis chemotherapeutics. Eur J Med Chem 2018; 157:462-479. [DOI: 10.1016/j.ejmech.2018.08.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/14/2018] [Accepted: 08/01/2018] [Indexed: 11/24/2022]
|
413
|
Tsai CJ, Pamula F, Nehmé R, Mühle J, Weinert T, Flock T, Nogly P, Edwards PC, Carpenter B, Gruhl T, Ma P, Deupi X, Standfuss J, Tate CG, Schertler GFX. Crystal structure of rhodopsin in complex with a mini-G o sheds light on the principles of G protein selectivity. SCIENCE ADVANCES 2018; 4:eaat7052. [PMID: 30255144 PMCID: PMC6154990 DOI: 10.1126/sciadv.aat7052] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/10/2018] [Indexed: 05/20/2023]
Abstract
Selective coupling of G protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptors (GPCRs) to specific Gα-protein subtypes is critical to transform extracellular signals, carried by natural ligands and clinical drugs, into cellular responses. At the center of this transduction event lies the formation of a signaling complex between the receptor and G protein. We report the crystal structure of light-sensitive GPCR rhodopsin bound to an engineered mini-Go protein. The conformation of the receptor is identical to all previous structures of active rhodopsin, including the complex with arrestin. Thus, rhodopsin seems to adopt predominantly one thermodynamically stable active conformation, effectively acting like a "structural switch," allowing for maximum efficiency in the visual system. Furthermore, our analysis of the well-defined GPCR-G protein interface suggests that the precise position of the carboxyl-terminal "hook-like" element of the G protein (its four last residues) relative to the TM7/helix 8 (H8) joint of the receptor is a significant determinant in selective G protein activation.
Collapse
Affiliation(s)
- Ching-Ju Tsai
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
- Corresponding author. (C.-J.T.); (G.F.X.S.)
| | - Filip Pamula
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
- Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, 8093 Zürich, Switzerland
| | - Rony Nehmé
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jonas Mühle
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
| | - Tilman Flock
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
- Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, 8093 Zürich, Switzerland
- Fitzwilliam College, University of Cambridge, Cambridge, UK
| | - Przemyslaw Nogly
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
- Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, 8093 Zürich, Switzerland
| | - Patricia C. Edwards
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Byron Carpenter
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Thomas Gruhl
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
- Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, 8093 Zürich, Switzerland
| | - Pikyee Ma
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
| | - Xavier Deupi
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
- Condensed Matter Theory Group, PSI, 5232 Villigen PSI, Switzerland
| | - Jörg Standfuss
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
| | - Christopher G. Tate
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Gebhard F. X. Schertler
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
- Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, 8093 Zürich, Switzerland
- Corresponding author. (C.-J.T.); (G.F.X.S.)
| |
Collapse
|
414
|
Capture and characterization of a reactive haem–carbenoid complex in an artificial metalloenzyme. Nat Catal 2018. [DOI: 10.1038/s41929-018-0105-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
415
|
Tararina MA, Xue S, Smith LC, Muellers SN, Miranda PO, Janda KD, Allen KN. Crystallography Coupled with Kinetic Analysis Provides Mechanistic Underpinnings of a Nicotine-Degrading Enzyme. Biochemistry 2018; 57:3741-3751. [PMID: 29812904 PMCID: PMC6295333 DOI: 10.1021/acs.biochem.8b00384] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Nicotine oxidoreductase (NicA2) is a bacterial flavoenzyme, which catalyzes the first step of nicotine catabolism by oxidizing S-nicotine into N-methyl-myosmine. It has been proposed as a biotherapeutic for nicotine addiction because of its nanomolar substrate binding affinity. The first crystal structure of NicA2 has been reported, establishing NicA2 as a member of the monoamine oxidase (MAO) family. However, substrate specificity and structural determinants of substrate binding and/or catalysis have not been explored. Herein, analysis of the pH-rate profile, single-turnover kinetics, and binding data establish that pH does not significantly affect the catalytic rate and product release is not rate-limiting. The X-ray crystal structure of NicA2 with S-nicotine refined to 2.65 Å resolution reveals a hydrophobic binding site with a solvent exclusive cavity. Hydrophobic interactions predominantly orient the substrate, promoting the binding of a deprotonated species and supporting a hydride-transfer mechanism. Notably, NicA2 showed no activity against neurotransmitters oxidized by the two isoforms of human MAO. To further probe the substrate range of NicA2, enzyme activity was evaluated using a series of substrate analogues, indicating that S-nicotine is the optimal substrate and substitutions within the pyridyl ring abolish NicA2 activity. Moreover, mutagenesis and kinetic analysis of active-site residues reveal that removal of a hydrogen bond between the pyridyl ring of S-nicotine and the hydroxyl group of T381 has a 10-fold effect on KM, supporting the role of this bond in positioning the catalytically competent form of the substrate. Together, crystallography combined with kinetic analysis provides a deeper understanding of this enzyme's remarkable specificity.
Collapse
Affiliation(s)
- Margarita A. Tararina
- Program in Biomolecular Pharmacology, Boston University School of Medicine, 72 East Concord Street, Boston, Massachusetts 02118, United States
| | - Song Xue
- Departments of Chemistry and Immunology and The Skaggs Institute for Chemical Biology
| | - Lauren C. Smith
- Departments of Chemistry and Immunology and The Skaggs Institute for Chemical Biology
| | - Samantha N. Muellers
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Pedro O. Miranda
- Departments of Chemistry and Immunology and The Skaggs Institute for Chemical Biology
| | - Kim D. Janda
- Departments of Chemistry and Immunology and The Skaggs Institute for Chemical Biology
- Worm Institute for Medical Research (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, BCC-582, La Jolla, California 92037, United States
| | - Karen N. Allen
- Program in Biomolecular Pharmacology, Boston University School of Medicine, 72 East Concord Street, Boston, Massachusetts 02118, United States
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| |
Collapse
|
416
|
Roca C, Martinez-González L, Daniel-Mozo M, Sastre J, Infantes L, Mansilla A, Chaves-Sanjuan A, González-Rubio JM, Gil C, Cañada FJ, Martinez A, Sanchez-Barrena MJ, Campillo NE. Deciphering the Inhibition of the Neuronal Calcium Sensor 1 and the Guanine Exchange Factor Ric8a with a Small Phenothiazine Molecule for the Rational Generation of Therapeutic Synapse Function Regulators. J Med Chem 2018; 61:5910-5921. [DOI: 10.1021/acs.jmedchem.8b00088] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carlos Roca
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | | | - Miguel Daniel-Mozo
- Instituto de Química Física Rocasolano-CSIC, Serrano 119, 28006 Madrid, Spain
| | - Javier Sastre
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Lourdes Infantes
- Instituto de Química Física Rocasolano-CSIC, Serrano 119, 28006 Madrid, Spain
| | - Alicia Mansilla
- Fundación para la Investigación Biomédica, Hospital Ramón y Cajal, Ctra. de Colmenar Viejo, Km. 9, 28034 Madrid, Spain
| | | | | | - Carmen Gil
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - F. Javier Cañada
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Ana Martinez
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | | | - Nuria E. Campillo
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| |
Collapse
|
417
|
Wang W, Qin B, Wojdyla JA, Wang M, Gao X, Cui S. Structural characterization of free-state and product-state Mycobacterium tuberculosis methionyl-tRNA synthetase reveals an induced-fit ligand-recognition mechanism. IUCRJ 2018; 5:478-490. [PMID: 30002848 PMCID: PMC6038951 DOI: 10.1107/s2052252518008217] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
Mycobacterium tuberculosis (MTB) caused 10.4 million cases of tuberculosis and 1.7 million deaths in 2016. The incidence of multidrug-resistant and extensively drug-resistant MTB is becoming an increasing threat to public health and the development of novel anti-MTB drugs is urgently needed. Methionyl-tRNA synthetase (MetRS) is considered to be a valuable drug target. However, structural characterization of M. tuberculosis MetRS (MtMetRS) was lacking for decades, thus hampering drug design. Here, two high-resolution crystal structures of MtMetRS are reported: the free-state structure (apo form; 1.9 Å resolution) and a structure with the intermediate product methionyl-adenylate (Met-AMP) bound (2.4 Å resolution). It was found that free-state MtMetRS adopts a previously unseen conformation that has never been observed in other MetRS homologues. The pockets for methionine and AMP are not formed in free-state MtMetRS, suggesting that it is in a nonproductive conformation. Combining these findings suggests that MtMetRS employs an induced-fit mechanism in ligand binding. By comparison with the structure of human cytosolic MetRS, additional pockets specific to MtMetRS that could be used for anti-MTB drug design were located.
Collapse
Affiliation(s)
- Wei Wang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Science, No. 9 Dong Dan San Tiao, Dong Cheng Qu, Beijing 100730, People’s Republic of China
| | - Bo Qin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Science, No. 9 Dong Dan San Tiao, Dong Cheng Qu, Beijing 100730, People’s Republic of China
| | | | - Meitian Wang
- Paul Scherrer Institute, Swiss Light Source, CH-5232 Villigen, Switzerland
| | - Xiaopan Gao
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Science, No. 9 Dong Dan San Tiao, Dong Cheng Qu, Beijing 100730, People’s Republic of China
| | - Sheng Cui
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Science, No. 9 Dong Dan San Tiao, Dong Cheng Qu, Beijing 100730, People’s Republic of China
| |
Collapse
|
418
|
Chojnacki K, Wińska P, Wielechowska M, Łukowska-Chojnacka E, Tölzer C, Niefind K, Bretner M. Biological properties and structural study of new aminoalkyl derivatives of benzimidazole and benzotriazole, dual inhibitors of CK2 and PIM1 kinases. Bioorg Chem 2018; 80:266-275. [PMID: 29966873 DOI: 10.1016/j.bioorg.2018.06.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/15/2018] [Accepted: 06/18/2018] [Indexed: 11/30/2022]
Abstract
The new aminoalkyl-substituted derivatives of known CK2 inhibitors 4,5,6,7-tetrabromo-1H-benzimidazole (TBBi) and 4,5,6,7-tetrabromo-1H-benzotriazole (TBBt) were synthesized, and their influence on the activity of recombinant human CK2 α, CK2 holoenzyme and PIM1 kinases was evaluated. All derivatives inhibited the activity of studied kinases and the most efficient were aminopropyl-derivatives 8b and 14b. These compounds also exerted inhibition of cancer cell lines - CCRF-CEM (acute lymphoblastoid leukemia), MCF-7 (human breast cancer), and PC-3 (prostate cancer) proliferation and their EC50 is comparable with the value for clinically studied CK2 inhibitor CX-4945. Preliminary structure activity relationship analysis indicated that the spacer length affected antitumor potency, and two to three methylene units were more favorable. The complex of CK2 α1-335/8b was crystallized, both under high-salt conditions and under low-salt conditions giving crystals which diffracted X-rays to about 2.4 Å resolution, what enabled the determination of the corresponding 3D-structures.
Collapse
Affiliation(s)
- K Chojnacki
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - P Wińska
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - M Wielechowska
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - E Łukowska-Chojnacka
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - C Tölzer
- Department für Chemie, Institut für Biochemie, Universtät zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany
| | - K Niefind
- Department für Chemie, Institut für Biochemie, Universtät zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany
| | - M Bretner
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland.
| |
Collapse
|
419
|
Pascolutti M, Dirr L, Guillon P, Van Den Bergh A, Ve T, Thomson RJ, von Itzstein M. Structural Insights into Human Parainfluenza Virus 3 Hemagglutinin-Neuraminidase Using Unsaturated 3- N-Substituted Sialic Acids as Probes. ACS Chem Biol 2018; 13:1544-1550. [PMID: 29693380 DOI: 10.1021/acschembio.8b00150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A novel approach to human parainfluenza virus 3 (hPIV-3) inhibitor design has been evaluated by targeting an unexplored pocket within the active site region of the hemagglutinin-neuraminidase (HN) of the virus that is normally occluded upon ligand engagement. To explore this opportunity, we developed a highly efficient route to introduce nitrogen-based functionalities at the naturally unsubstituted C-3 position on the neuraminidase inhibitor template N-acyl-2,3-dehydro-2-deoxy-neuraminic acid ( N-acyl-Neu2en), via a regioselective 2,3-bromoazidation. Introduction of triazole substituents at C-3 on this template provided compounds with low micromolar inhibition of hPIV-3 HN neuraminidase activity, with the most potent having 48-fold improved potency over the corresponding C-3 unsubstituted analogue. However, the C-3-triazole N-acyl-Neu2en derivatives were significantly less active against the hemagglutinin function of the virus, with high micromolar IC50 values determined, and showed insignificant in vitro antiviral activity. Given the different pH optima of the HN protein's neuraminidase (acidic pH) and hemagglutinin (neutral pH) functions, the influence of pH on inhibitor binding was examined using X-ray crystallography and STD NMR spectroscopy, providing novel insights into the multifunctionality of hPIV-3 HN. While the 3-phenyltriazole- N-isobutyryl-Neu2en derivative could bind HN at pH 4.6, suitable for neuraminidase inhibition, at neutral pH binding of the inhibitor was substantially reduced. Importantly, this study clearly demonstrates for the first time that potent inhibition of HN neuraminidase activity is not necessarily directly correlated with a strong antiviral activity, and suggests that strong inhibition of the hemagglutinin function of hPIV HN is crucial for potent antiviral activity. This highlights the importance of designing hPIV inhibitors that primarily target the receptor-binding function of hPIV HN.
Collapse
Affiliation(s)
- Mauro Pascolutti
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4222, Australia
| | - Larissa Dirr
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4222, Australia
| | - Patrice Guillon
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4222, Australia
| | - Annelies Van Den Bergh
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4222, Australia
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4222, Australia
| | - Robin J. Thomson
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4222, Australia
| | - Mark von Itzstein
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4222, Australia
| |
Collapse
|
420
|
Osipov EM, Lilina AV, Tsallagov SI, Safonova TN, Sorokin DY, Tikhonova TV, Popov VO. Structure of the flavocytochrome c sulfide dehydrogenase associated with the copper-binding protein CopC from the haloalkaliphilic sulfur-oxidizing bacterium Thioalkalivibrio paradoxusARh 1. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:632-642. [DOI: 10.1107/s2059798318005648] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 04/10/2018] [Indexed: 11/10/2022]
Abstract
Flavocytochrome c sulfide dehydrogenase from Thioalkalivibrio paradoxus (TpFCC) is a heterodimeric protein consisting of flavin- and monohaem c-binding subunits. TpFCC was co-purified and co-crystallized with the dimeric copper-binding protein TpCopC. The structure of the TpFCC–(TpCopC)2 complex was determined by X-ray diffraction at 2.6 Å resolution. The flavin-binding subunit of TpFCC is structurally similar to those determined previously, and the structure of the haem-binding subunit is similar to that of the N-terminal domain of dihaem FCCs. According to classification based on amino-acid sequence, TpCopC belongs to a high-affinity CopC subfamily characterized by the presence of a conserved His1-Xxx-His3 motif at the N-terminus. Apparently, a unique α-helix which is present in each monomer of TpCopC at the interface with TpFCC plays a key role in complex formation. The structure of the copper-binding site in TpCopC is similar to those in other known CopC structures. His3 is not involved in binding to the copper ion and is 6–7 Å away from this ion. Therefore, the His1-Xxx-His3 motif cannot be considered to be a key factor in the high affinity of CopC for copper(II) ions. It is suggested that the TpFCC–(TpCopC)2 heterotetramer may be a component of a large periplasmic complex that is responsible for thiocyanate metabolism.
Collapse
|
421
|
Keedy DA, Hill ZB, Biel JT, Kang E, Rettenmaier TJ, Brandão-Neto J, Pearce NM, von Delft F, Wells JA, Fraser JS. An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering. eLife 2018; 7:36307. [PMID: 29877794 PMCID: PMC6039181 DOI: 10.7554/elife.36307] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/04/2018] [Indexed: 12/28/2022] Open
Abstract
Allostery is an inherent feature of proteins, but it remains challenging to reveal the mechanisms by which allosteric signals propagate. A clearer understanding of this intrinsic circuitry would afford new opportunities to modulate protein function. Here, we have identified allosteric sites in protein tyrosine phosphatase 1B (PTP1B) by combining multiple-temperature X-ray crystallography experiments and structure determination from hundreds of individual small-molecule fragment soaks. New modeling approaches reveal 'hidden' low-occupancy conformational states for protein and ligands. Our results converge on allosteric sites that are conformationally coupled to the active-site WPD loop and are hotspots for fragment binding. Targeting one of these sites with covalently tethered molecules or mutations allosterically inhibits enzyme activity. Overall, this work demonstrates how the ensemble nature of macromolecular structure, revealed here by multitemperature crystallography, can elucidate allosteric mechanisms and open new doors for long-range control of protein function. Proteins perform many important jobs in each of the cells in our bodies, such as transporting other molecules and helping chemical reactions to occur. The part of the protein directly involved in these tasks is called the active site. Other areas of the protein can communicate with the active site to switch the protein on or off. This method of control is known as allostery. Switching proteins on and off could help us to develop treatments for certain diseases. For example, a protein called PTP1B reduces how well cells can respond to insulin. Switching this protein off could therefore help to treat diabetes. However, much like it’s hard to guess how a light switch is wired to a light bulb without seeing behind the walls, it is hard to predict which remote areas of a protein are ‘wired’ to the active site. Keedy, Hill et al. have now used two complementary methods to examine the structure of PTP1B and find new allosteric sites. The first method captured a series of X-ray images from crystallized molecules of the protein held at different temperatures. This revealed areas of PTP1B that can move like windshield wipers to communicate with each other. The second method soaked PTP1B crystals in trays with hundreds of drug-sized molecules and assessed which sites on the protein the molecules bound to. The molecules generally bound to just a few sites of the protein. Further tests on one of these sites showed that it can communicate with the active site to turn the protein on or off. Further work will be needed to develop drugs that could treat diabetes by binding to the newly identified allosteric sites in PTP1B. More generally, the methods developed by Keedy, Hill et al. could be used to study allostery in other important proteins.
Collapse
Affiliation(s)
- Daniel A Keedy
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Zachary B Hill
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Justin T Biel
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Emily Kang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - T Justin Rettenmaier
- Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | | | - Nicholas M Pearce
- Crystal and Structural Chemistry Group, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Frank von Delft
- Diamond Light Source, Didcot, United Kingdom.,Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom.,Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| |
Collapse
|
422
|
Gourinchas G, Heintz U, Winkler A. Asymmetric activation mechanism of a homodimeric red light-regulated photoreceptor. eLife 2018; 7:e34815. [PMID: 29869984 PMCID: PMC6005682 DOI: 10.7554/elife.34815] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 06/03/2018] [Indexed: 12/18/2022] Open
Abstract
Organisms adapt to environmental cues using diverse signaling networks. In order to sense and integrate light for regulating various biological functions, photoreceptor proteins have evolved in a modular way. This modularity is targeted in the development of optogenetic tools enabling the control of cellular events with high spatiotemporal precision. However, the limited understanding of signaling mechanisms impedes the rational design of innovative photoreceptor-effector couples. Here, we reveal molecular details of signal transduction in phytochrome-regulated diguanylyl cyclases. Asymmetric structural changes of the full-length homodimer result in a functional heterodimer featuring two different photoactivation states. Structural changes around the cofactors result in a quasi-translational rearrangement of the distant coiled-coil sensor-effector linker. Eventually, this regulates enzymatic activity by modulating the dimer interface of the output domains. Considering the importance of phytochrome heterodimerization in plant signaling, our mechanistic details of asymmetric photoactivation in a bacterial system reveal novel aspects of the evolutionary adaptation of phytochromes.
Collapse
Affiliation(s)
| | - Udo Heintz
- Max Planck Institute for Medical ResearchHeidelbergGermany
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of TechnologyGrazAustria
| |
Collapse
|
423
|
Punekar AS, Samsudin F, Lloyd AJ, Dowson CG, Scott DJ, Khalid S, Roper DI. The role of the jaw subdomain of peptidoglycan glycosyltransferases for lipid II polymerization. Cell Surf 2018; 2:54-66. [PMID: 30046666 PMCID: PMC6053601 DOI: 10.1016/j.tcsw.2018.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/12/2018] [Accepted: 06/12/2018] [Indexed: 12/27/2022] Open
Abstract
Bacterial peptidoglycan glycosyltransferases (PGT) catalyse the essential polymerization of lipid II into linear glycan chains required for peptidoglycan biosynthesis. The PGT domain is composed of a large head subdomain and a smaller jaw subdomain and can be potently inhibited by the antibiotic moenomycin A (MoeA). We present an X-ray structure of the MoeA-bound Staphylococcus aureus monofunctional PGT enzyme, revealing electron density for a second MoeA bound to the jaw subdomain as well as the PGT donor site. Isothermal titration calorimetry confirms two drug-binding sites with markedly different affinities and positive cooperativity. Hydrophobic cluster analysis suggests that the membrane-interacting surface of the jaw subdomain has structural and physicochemical properties similar to amphipathic cationic α -helical antimicrobial peptides for lipid II recognition and binding. Furthermore, molecular dynamics simulations of the drug-free and -bound forms of the enzyme demonstrate the importance of the jaw subdomain movement for lipid II selection and polymerization process and provide molecular-level insights into the mechanism of peptidoglycan biosynthesis by PGTs.
Collapse
Affiliation(s)
- Avinash S. Punekar
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Firdaus Samsudin
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Adrian J. Lloyd
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | | | - David J. Scott
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
- ISIS Neutron and Muon Spallation Source and Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, United Kingdom
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - David I. Roper
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| |
Collapse
|
424
|
Huang P, Zheng S, Wierbowski BM, Kim Y, Nedelcu D, Aravena L, Liu J, Kruse AC, Salic A. Structural Basis of Smoothened Activation in Hedgehog Signaling. Cell 2018; 174:312-324.e16. [PMID: 29804838 DOI: 10.1016/j.cell.2018.04.029] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/03/2018] [Accepted: 04/20/2018] [Indexed: 12/21/2022]
Abstract
The seven-transmembrane-spanning protein Smoothened is the central transducer in Hedgehog signaling, a pathway fundamental in development and in cancer. Smoothened is activated by cholesterol binding to its extracellular cysteine-rich domain (CRD). How this interaction leads to changes in the transmembrane domain and Smoothened activation is unknown. Here, we report crystal structures of sterol-activated Smoothened. The CRD undergoes a dramatic reorientation, allosterically causing the transmembrane domain to adopt a conformation similar to active G-protein-coupled receptors. We show that Smoothened contains a unique inhibitory π-cation lock, which is broken on activation and is disrupted in constitutively active oncogenic mutants. Smoothened activation opens a hydrophobic tunnel, suggesting a pathway for cholesterol movement from the inner membrane leaflet to the CRD. All Smoothened antagonists bind the transmembrane domain and block tunnel opening, but cyclopamine also binds the CRD, inducing the active transmembrane conformation. Together, these results define the mechanisms of Smoothened activation and inhibition.
Collapse
Affiliation(s)
- Pengxiang Huang
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Sanduo Zheng
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Bradley M Wierbowski
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Youngchang Kim
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Daniel Nedelcu
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Laura Aravena
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Jing Liu
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Adrian Salic
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
| |
Collapse
|
425
|
Enzymatic control of dioxygen binding and functionalization of the flavin cofactor. Proc Natl Acad Sci U S A 2018; 115:4909-4914. [PMID: 29686059 DOI: 10.1073/pnas.1801189115] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The reactions of enzymes and cofactors with gaseous molecules such as dioxygen (O2) are challenging to study and remain among the most contentious subjects in biochemistry. To date, it is largely enigmatic how enzymes control and fine-tune their reactions with O2, as exemplified by the ubiquitous flavin-dependent enzymes that commonly facilitate redox chemistry such as the oxygenation of organic substrates. Here we employ O2-pressurized X-ray crystallography and quantum mechanical calculations to reveal how the precise positioning of O2 within a flavoenzyme's active site enables the regiospecific formation of a covalent flavin-oxygen adduct and oxygenating species (i.e., the flavin-N5-oxide) by mimicking a critical transition state. This study unambiguously demonstrates how enzymes may control the O2 functionalization of an organic cofactor as prerequisite for oxidative catalysis. Our work thus illustrates how O2 reactivity can be harnessed in an enzymatic environment and provides crucial knowledge for future rational design of O2-reactive enzymes.
Collapse
|
426
|
Human N-acetylglucosaminyltransferase II substrate recognition uses a modular architecture that includes a convergent exosite. Proc Natl Acad Sci U S A 2018; 115:4637-4642. [PMID: 29666272 DOI: 10.1073/pnas.1716988115] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Asn-linked oligosaccharides are extensively modified during transit through the secretory pathway, first by trimming of the nascent glycan chains and subsequently by initiating and extending multiple oligosaccharide branches from the trimannosyl glycan core. Trimming and branching pathway steps are highly ordered and hierarchal based on the precise substrate specificities of the individual biosynthetic enzymes. A key committed step in the synthesis of complex-type glycans is catalyzed by N-acetylglucosaminyltransferase II (MGAT2), an enzyme that generates the second GlcNAcβ1,2- branch from the trimannosyl glycan core using UDP-GlcNAc as the sugar donor. We determined the structure of human MGAT2 as a Mn2+-UDP donor analog complex and as a GlcNAcMan3GlcNAc2-Asn acceptor complex to reveal the structural basis for substrate recognition and catalysis. The enzyme exhibits a GT-A Rossmann-like fold that employs conserved divalent cation-dependent substrate interactions with the UDP-GlcNAc donor. MGAT2 interactions with the extended glycan acceptor are distinct from other related glycosyltransferases. These interactions are composed of a catalytic subsite that binds the Man-α1,6- monosaccharide acceptor and a distal exosite pocket that binds the GlcNAc-β1,2Man-α1,3Manβ- substrate "recognition arm." Recognition arm interactions are similar to the enzyme-substrate interactions for Golgi α-mannosidase II, a glycoside hydrolase that acts just before MGAT2 in the Asn-linked glycan biosynthetic pathway. These data suggest that substrate binding by MGAT2 employs both conserved and convergent catalytic subsite modules to provide substrate selectivity and catalysis. More broadly, the MGAT2 active-site architecture demonstrates how glycosyltransferases create complementary modular templates for regiospecific extension of glycan structures in mammalian cells.
Collapse
|
427
|
Che S, Chen Y, Liang Y, Zhang Q, Bartlam M. Crystal structure of RecR, a member of the RecFOR DNA-repair pathway, from Pseudomonas aeruginosa PAO1. Acta Crystallogr F Struct Biol Commun 2018; 74:222-230. [PMID: 29633970 PMCID: PMC5894107 DOI: 10.1107/s2053230x18003503] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 02/28/2018] [Indexed: 11/10/2022] Open
Abstract
DNA damage is usually lethal to all organisms. Homologous recombination plays an important role in the DNA damage-repair process in prokaryotic organisms. Two pathways are responsible for homologous recombination in Pseudomonas aeruginosa: the RecBCD pathway and the RecFOR pathway. RecR is an important regulator in the RecFOR homologous recombination pathway in P. aeruginosa. It forms complexes with RecF and RecO that can facilitate the loading of RecA onto ssDNA in the RecFOR pathway. Here, the crystal structure of RecR from P. aeruginosa PAO1 (PaRecR) is reported. PaRecR crystallizes in space group P6122, with two monomers per asymmetric unit. Analytical ultracentrifugation data show that PaRecR forms a stable dimer, but can exist as a tetramer in solution. The crystal structure shows that dimeric PaRecR forms a ring-like tetramer architecture via crystal symmetry. The presence of a ligand in the Walker B motif of one RecR subunit suggests a putative nucleotide-binding site.
Collapse
Affiliation(s)
- Shiyou Che
- College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, People’s Republic of China
| | - Yujing Chen
- College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, People’s Republic of China
| | - Yakun Liang
- College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, People’s Republic of China
| | - Qionglin Zhang
- College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, People’s Republic of China
| | - Mark Bartlam
- College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, People’s Republic of China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 38 Tongyan Road, Tianjin 300350, People’s Republic of China
| |
Collapse
|
428
|
Wolf NM, Gutka HJ, Movahedzadeh F, Abad-Zapatero C. Structures of the Mycobacterium tuberculosis GlpX protein (class II fructose-1,6-bisphosphatase): implications for the active oligomeric state, catalytic mechanism and citrate inhibition. Acta Crystallogr D Struct Biol 2018; 74:321-331. [PMID: 29652259 PMCID: PMC5892879 DOI: 10.1107/s2059798318002838] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/16/2018] [Indexed: 11/19/2022] Open
Abstract
The crystal structures of native class II fructose-1,6-bisphosphatase (FBPaseII) from Mycobacterium tuberculosis at 2.6 Å resolution and two active-site protein variants are presented. The variants were complexed with the reaction product fructose 6-phosphate (F6P). The Thr84Ala mutant is inactive, while the Thr84Ser mutant has a lower catalytic activity. The structures reveal the presence of a 222 tetramer, similar to those described for fructose-1,6/sedoheptulose-1,7-bisphosphatase from Synechocystis (strain 6803) as well as the equivalent enzyme from Thermosynechococcus elongatus. This homotetramer corresponds to a homologous oligomer that is present but not described in the crystal structure of FBPaseII from Escherichia coli and is probably conserved in all FBPaseIIs. The constellation of amino-acid residues in the active site of FBPaseII from M. tuberculosis (MtFBPaseII) is conserved and is analogous to that described previously for the E. coli enzyme. Moreover, the structure of the active site of the partially active (Thr84Ser) variant and the analysis of the kinetics are consistent with the previously proposed catalytic mechanism. The presence of metabolites in the crystallization medium (for example citrate and malonate) and in the corresponding crystal structures of MtFBPaseII, combined with their observed inhibitory effect, could suggest the existence of an uncharacterized inhibition of this class of enzymes besides the allosteric inhibition by adenosine monophosphate observed for the Synechocystis enzyme. The structural and functional insights derived from the structure of MtFBPaseII will provide critical information for the design of lead inhibitors, which will be used to validate this target for future chemical intervention.
Collapse
Affiliation(s)
- Nina M. Wolf
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Hiten J. Gutka
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, USA
- Oncobiologics Inc., Cranbury, New Jersey, USA
| | - Farahnaz Movahedzadeh
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Celerino Abad-Zapatero
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| |
Collapse
|
429
|
Cretu C, Agrawal AA, Cook A, Will CL, Fekkes P, Smith PG, Lührmann R, Larsen N, Buonamici S, Pena V. Structural Basis of Splicing Modulation by Antitumor Macrolide Compounds. Mol Cell 2018; 70:265-273.e8. [DOI: 10.1016/j.molcel.2018.03.011] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/07/2018] [Accepted: 03/07/2018] [Indexed: 12/22/2022]
|
430
|
Leisico F, V Vieira D, Figueiredo TA, Silva M, Cabrita EJ, Sobral RG, Ludovice AM, Trincão J, Romão MJ, de Lencastre H, Santos-Silva T. First insights of peptidoglycan amidation in Gram-positive bacteria - the high-resolution crystal structure of Staphylococcus aureus glutamine amidotransferase GatD. Sci Rep 2018; 8:5313. [PMID: 29593310 PMCID: PMC5871853 DOI: 10.1038/s41598-018-22986-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 02/27/2018] [Indexed: 12/05/2022] Open
Abstract
Gram-positive bacteria homeostasis and antibiotic resistance mechanisms are dependent on the intricate architecture of the cell wall, where amidated peptidoglycan plays an important role. The amidation reaction is carried out by the bi-enzymatic complex MurT-GatD, for which biochemical and structural information is very scarce. In this work, we report the first crystal structure of the glutamine amidotransferase member of this complex, GatD from Staphylococcus aureus, at 1.85 Å resolution. A glutamine molecule is found close to the active site funnel, hydrogen-bonded to the conserved R128. In vitro functional studies using 1H-NMR spectroscopy showed that S. aureus MurT-GatD complex has glutaminase activity even in the absence of lipid II, the MurT substrate. In addition, we produced R128A, C94A and H189A mutants, which were totally inactive for glutamine deamidation, revealing their essential role in substrate sequestration and catalytic reaction. GatD from S. aureus and other pathogenic bacteria share high identity to enzymes involved in cobalamin biosynthesis, which can be grouped in a new sub-family of glutamine amidotransferases. Given the ubiquitous presence of GatD, these results provide significant insights into the molecular basis of the so far undisclosed amidation mechanism, contributing to the development of alternative therapeutics to fight infections.
Collapse
Affiliation(s)
- Francisco Leisico
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Diana V Vieira
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
- Oxford Protein Production Facility, Research Complex at Harwell, Didcot, United Kingdom
| | - Teresa A Figueiredo
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
- Laboratory of Molecular Genetics, Microbiology of Human Pathogens Unit, Instituto de Tecnologia Química e Biológica António Xavier da Universidade Nova de Lisboa, Oeiras, Portugal
| | - Micael Silva
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Eurico J Cabrita
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Rita G Sobral
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Ana Madalena Ludovice
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | | | - Maria João Romão
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Microbiology of Human Pathogens Unit, Instituto de Tecnologia Química e Biológica António Xavier da Universidade Nova de Lisboa, Oeiras, Portugal.
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, USA.
| | - Teresa Santos-Silva
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.
| |
Collapse
|
431
|
Banda-Vázquez J, Shanmugaratnam S, Rodríguez-Sotres R, Torres-Larios A, Höcker B, Sosa-Peinado A. Redesign of LAOBP to bind novel l-amino acid ligands. Protein Sci 2018. [PMID: 29524280 DOI: 10.1002/pro.3403] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Computational protein design is still a challenge for advancing structure-function relationships. While recent advances in this field are promising, more information for genuine predictions is needed. Here, we discuss different approaches applied to install novel glutamine (Gln) binding into the Lysine/Arginine/Ornithine binding protein (LAOBP) from Salmonella typhimurium. We studied the ligand binding behavior of two mutants: a binding pocket grafting design based on a structural superposition of LAOBP to the Gln binding protein QBP from Escherichia coli and a design based on statistical coupled positions. The latter showed the ability to bind Gln even though the protein was not very stable. Comparison of both approaches highlighted a nonconservative shared point mutation between LAOBP_graft and LAOBP_sca. This context dependent L117K mutation in LAOBP turned out to be sufficient for introducing Gln binding, as confirmed by different experimental techniques. Moreover, the crystal structure of LAOBP_L117K in complex with its ligand is reported.
Collapse
Affiliation(s)
| | - Sooruban Shanmugaratnam
- Max Planck Institute for Developmental Biology, Tübingen, Germany.,Universität Bayreuth, Bayreuth, Germany
| | | | | | - Birte Höcker
- Max Planck Institute for Developmental Biology, Tübingen, Germany.,Universität Bayreuth, Bayreuth, Germany
| | | |
Collapse
|
432
|
Galdeano C, Coquelle N, Cieslikiewicz-Bouet M, Bartolini M, Pérez B, Clos MV, Silman I, Jean L, Colletier JP, Renard PY, Muñoz-Torrero D. Increasing Polarity in Tacrine and Huprine Derivatives: Potent Anticholinesterase Agents for the Treatment of Myasthenia Gravis. Molecules 2018. [PMID: 29534488 PMCID: PMC6017698 DOI: 10.3390/molecules23030634] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Symptomatic treatment of myasthenia gravis is based on the use of peripherally-acting acetylcholinesterase (AChE) inhibitors that, in some cases, must be discontinued due to the occurrence of a number of side-effects. Thus, new AChE inhibitors are being developed and investigated for their potential use against this disease. Here, we have explored two alternative approaches to get access to peripherally-acting AChE inhibitors as new agents against myasthenia gravis, by structural modification of the brain permeable anti-Alzheimer AChE inhibitors tacrine, 6-chlorotacrine, and huprine Y. Both quaternization upon methylation of the quinoline nitrogen atom, and tethering of a triazole ring, with, in some cases, the additional incorporation of a polyphenol-like moiety, result in more polar compounds with higher inhibitory activity against human AChE (up to 190-fold) and butyrylcholinesterase (up to 40-fold) than pyridostigmine, the standard drug for symptomatic treatment of myasthenia gravis. The novel compounds are furthermore devoid of brain permeability, thereby emerging as interesting leads against myasthenia gravis.
Collapse
Affiliation(s)
- Carles Galdeano
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain.
| | - Nicolas Coquelle
- Institut de Biologie Structurale, Université Grenoble Alpes, Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'Énergie Atomique (CEA) (UMR 5075), F-38054 Grenoble, France.
- Large-Scale Structures Group, Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France.
| | - Monika Cieslikiewicz-Bouet
- Laboratory COBRA (UMR 6014), Normandie Université, UNIROUEN, Institut National des Sciences Appliquées (INSA) Rouen, CNRS, 76000 Rouen, France.
| | - Manuela Bartolini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy.
| | - Belén Pérez
- Department of Pharmacology, Therapeutics and Toxicology, Neuroscience Institute, Autonomous University of Barcelona, E-08193 Barcelona, Spain.
| | - M Victòria Clos
- Department of Pharmacology, Therapeutics and Toxicology, Neuroscience Institute, Autonomous University of Barcelona, E-08193 Barcelona, Spain.
| | - Israel Silman
- Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel.
| | - Ludovic Jean
- Laboratory COBRA (UMR 6014), Normandie Université, UNIROUEN, Institut National des Sciences Appliquées (INSA) Rouen, CNRS, 76000 Rouen, France.
| | - Jacques-Philippe Colletier
- Institut de Biologie Structurale, Université Grenoble Alpes, Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'Énergie Atomique (CEA) (UMR 5075), F-38054 Grenoble, France.
| | - Pierre-Yves Renard
- Laboratory COBRA (UMR 6014), Normandie Université, UNIROUEN, Institut National des Sciences Appliquées (INSA) Rouen, CNRS, 76000 Rouen, France.
| | - Diego Muñoz-Torrero
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain.
| |
Collapse
|
433
|
Büttner D, Kramer JS, Klingler FM, Wittmann SK, Hartmann MR, Kurz CG, Kohnhäuser D, Weizel L, Brüggerhoff A, Frank D, Steinhilber D, Wichelhaus TA, Pogoryelov D, Proschak E. Challenges in the Development of a Thiol-Based Broad-Spectrum Inhibitor for Metallo-β-Lactamases. ACS Infect Dis 2018; 4:360-372. [PMID: 29172434 DOI: 10.1021/acsinfecdis.7b00129] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Pathogens, expressing metallo-β-lactamases (MBLs), become resistant against most β-lactam antibiotics. Besides the dragging search for new antibiotics, development of MBL inhibitors would be an alternative weapon against resistant bacterial pathogens. Inhibition of resistance enzymes could restore the antibacterial activity of β-lactams. Various approaches to MBL inhibitors are described; among others, the promising motif of a zinc coordinating thiol moiety is very popular. Nevertheless, since the first report of a thiol-based MBL inhibitor (thiomandelic acid) in 2001, no steps in development of thiol based MBL inhibitors were reported that go beyond clinical isolate testing. In this study, we report on the synthesis and biochemical characterization of thiol-based MBL inhibitors and highlight the challenges behind the development of thiol-based compounds, which exhibit good in vitro activity toward a broad spectrum of MBLs, selectivity against human off-targets, and reasonable activity against clinical isolates.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Denia Frank
- Institute of Medical Microbiology and Infection Control, Goethe University Hospital, Paul-Ehrlich-Straße 40, 60596 Frankfurt, Germany
| | | | - Thomas A. Wichelhaus
- Institute of Medical Microbiology and Infection Control, Goethe University Hospital, Paul-Ehrlich-Straße 40, 60596 Frankfurt, Germany
| | | | | |
Collapse
|
434
|
6-Thioguanine is a noncompetitive and slow binding inhibitor of human deubiquitinating protease USP2. Sci Rep 2018; 8:3102. [PMID: 29449607 PMCID: PMC5814560 DOI: 10.1038/s41598-018-21476-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 02/06/2018] [Indexed: 12/20/2022] Open
Abstract
Ubiquitin-specific protease 2 (USP2) belongs to the family of deubiquitinases that can rescue protein targets from proteasomal degradation by reversing their ubiquitination. In various cancers, including prostate cancer and ovarian carcinoma, upregulation of USP2 leads to an increase in the levels of deubiquitinated substrates such as fatty acid synthase, MDM2, cyclin D1 and Aurora-A. USP2 thus plays a critical role in tumor cells’ survival and therefore represents a therapeutic target. Here a leukemia drug, 6-thioguanine, was found to be a potent inhibitor of USP2. Enzyme-kinetic and X-ray crystallographic data suggest that 6-thioguanine displays a noncompetitive and slow-binding inhibitory mechanism against USP2. Our study provides a clear rationale for the clinical evaluation of 6-thioguanine for USP2-upregulated cancers.
Collapse
|
435
|
Marshall AC, Bond CS, Bruning JB. Structure of Aspergillus fumigatus Cytosolic Thiolase: Trapped Tetrahedral Reaction Intermediates and Activation by Monovalent Cations. ACS Catal 2018. [DOI: 10.1021/acscatal.7b02873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Andrew C. Marshall
- Institute
for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Charles S. Bond
- School
of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - John B. Bruning
- Institute
for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| |
Collapse
|
436
|
Ribeiro Filho HV, Bernardi Videira N, Bridi AV, Tittanegro TH, Helena Batista FA, de Carvalho Pereira JG, de Oliveira PSL, Bajgelman MC, Le Maire A, Figueira ACM. Screening for PPAR Non-Agonist Ligands Followed by Characterization of a Hit, AM-879, with Additional No-Adipogenic and cdk5-Mediated Phosphorylation Inhibition Properties. Front Endocrinol (Lausanne) 2018; 9:11. [PMID: 29449830 PMCID: PMC5799700 DOI: 10.3389/fendo.2018.00011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 01/11/2018] [Indexed: 11/13/2022] Open
Abstract
Peroxisome proliferator-activated receptor gamma (PPARγ) is a member of a nuclear receptor superfamily and acts as a ligand-dependent transcription factor, playing key roles in maintenance of adipose tissue and in regulation of glucose and lipid homeostasis. This receptor is the target of thiazolidinediones, a class of antidiabetic drugs, which improve insulin sensitization and regulate glycemia in type 2 diabetes. Despite the beneficial effects of drugs, such as rosiglitazone and pioglitazone, their use is associated with several side effects, including weight gain, heart failure, and liver disease, since these drugs induce full activation of the receptor. By contrast, a promising activation-independent mechanism that involves the inhibition of cyclin-dependent kinase 5 (CDK5)-mediated PPARγ phosphorylation has been related to the insulin-sensitizing effects induced by these drugs. Thus, we aimed to identify novel PPARγ ligands that do not possess agonist properties by conducting a mini-trial with 80 compounds using the sequential steps of thermal shift assay, 8-anilino-1-naphthalenesulfonic acid fluorescence quenching, and a cell-based transactivation assay. We identified two non-agonist PPARγ ligands, AM-879 and P11, and one partial-agonist, R32. Using fluorescence anisotropy, we show that AM-879 does not dissociate the NCOR corepressor in vitro, and it has only a small effect on TRAP coactivator recruitment. In cells, AM-879 could not induce adipocyte differentiation or positively regulate the expression of genes associated with adipogenesis. In addition, AM-879 inhibited CDK5-mediated phosphorylation of PPARγ in vitro. Taken together, these findings supported an interaction between AM-879 and PPARγ; this interaction was identified by the analysis of the crystal structure of the PPARγ:AM-879 complex and evidenced by AM-879's mechanism of action as a putative PPARγ non-agonist with antidiabetic properties. Moreover, we present an optimized assay pipeline capable of detecting ligands that physically bind to PPARγ but do not cause its activation as a new strategy to identify ligands for this nuclear receptor.
Collapse
Affiliation(s)
- Helder Veras Ribeiro Filho
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Post Graduation Program in Biosciences and Technology of Bioactive Products, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Natália Bernardi Videira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Post Graduation Program in Biosciences and Technology of Bioactive Products, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Aline Villanova Bridi
- Post Graduation Program in Biosciences and Technology of Bioactive Products, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Thais Helena Tittanegro
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Post Graduation Program in Biosciences and Technology of Bioactive Products, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | | | - José Geraldo de Carvalho Pereira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Paulo Sérgio Lopes de Oliveira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Marcio Chaim Bajgelman
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Albane Le Maire
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Centre de Biochimie Structurale CNRS, Université de Montpellier, Montpellier, France
| | - Ana Carolina Migliorini Figueira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Post Graduation Program in Biosciences and Technology of Bioactive Products, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| |
Collapse
|
437
|
Wlodawer A, Dauter Z, Porebski PJ, Minor W, Stanfield R, Jaskolski M, Pozharski E, Weichenberger CX, Rupp B. Detect, correct, retract: How to manage incorrect structural models. FEBS J 2018; 285:444-466. [PMID: 29113027 PMCID: PMC5799025 DOI: 10.1111/febs.14320] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 11/01/2017] [Indexed: 12/13/2022]
Abstract
The massive technical and computational progress of biomolecular crystallography has generated some adverse side effects. Most crystal structure models, produced by crystallographers or well-trained structural biologists, constitute useful sources of information, but occasional extreme outliers remind us that the process of structure determination is not fail-safe. The occurrence of severe errors or gross misinterpretations raises fundamental questions: Why do such aberrations emerge in the first place? How did they evade the sophisticated validation procedures which often produce clear and dire warnings, and why were severe errors not noticed by the depositors themselves, their supervisors, referees and editors? Once detected, what can be done to either correct, improve or eliminate such models? How do incorrect models affect the underlying claims or biomedical hypotheses they were intended, but failed, to support? What is the long-range effect of the propagation of such errors? And finally, what mechanisms can be envisioned to restore the validity of the scientific record and, if necessary, retract publications that are clearly invalidated by the lack of experimental evidence? We suggest that cognitive bias and flawed epistemology are likely at the root of the problem. By using examples from the published literature and from public repositories such as the Protein Data Bank, we provide case summaries to guide correction or improvement of structural models. When strong claims are unsustainable because of a deficient crystallographic model, removal of such a model and even retraction of the affected publication are necessary to restore the integrity of the scientific record.
Collapse
Affiliation(s)
- Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Przemyslaw J. Porebski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Robyn Stanfield
- Department of Structural and Computational Biology, BCC206, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, Poznan, 61-614, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan, 61-704, Poland
| | - Edwin Pozharski
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Bernhard Rupp
- CVMO, k.-k.Hofkristallamt, 991 Audrey Place, Vista, CA, 92084, USA
- Department of Genetic Epidemiology, Medical University Innsbruck, Schöpfstr. 41, Innsbruck, 6020, Austria
| |
Collapse
|
438
|
Haywood J, Schmidberger JW, James AM, Nonis SG, Sukhoverkov KV, Elias M, Bond CS, Mylne JS. Structural basis of ribosomal peptide macrocyclization in plants. eLife 2018; 7:32955. [PMID: 29384475 PMCID: PMC5834244 DOI: 10.7554/elife.32955] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/26/2018] [Indexed: 12/14/2022] Open
Abstract
Constrained, cyclic peptides encoded by plant genes represent a new generation of drug leads. Evolution has repeatedly recruited the Cys-protease asparaginyl endopeptidase (AEP) to perform their head-to-tail ligation. These macrocyclization reactions use the substrates amino terminus instead of water to deacylate, so a peptide bond is formed. How solvent-exposed plant AEPs macrocyclize is poorly understood. Here we present the crystal structure of an active plant AEP from the common sunflower, Helianthus annuus. The active site contained electron density for a tetrahedral intermediate with partial occupancy that predicted a binding mode for peptide macrocyclization. By substituting catalytic residues we could alter the ratio of cyclic to acyclic products. Moreover, we showed AEPs from other species lacking cyclic peptides can perform macrocyclization under favorable pH conditions. This structural characterization of AEP presents a logical framework for engineering superior enzymes that generate macrocyclic peptide drug leads. Most proteins are long, chain-like molecules that have two ends respectively called the N-terminus and C-terminus. However, certain proteins can close on themselves to become circular. This requires a chemical reaction between the N- and C-termini, which creates a strong bond between the two extremities. To go through this ‘cyclization’ process, a straight protein attaches to a certain type of protease, a class of enzyme that usually cuts proteins into smaller pieces. In plants that are distantly related, the same group of enzymes – called AEPs – has been selected to perform cyclization. Here, Haywood et al. study an AEP enzyme from sunflowers: they identify what about this enzyme’s structure is important to drive the complex chemical reaction that results in the protein being cyclized rather than simply cut. Using a technique called X-ray crystallography to see the positions of individual atoms in the enzyme, Haywood et al. caught a snapshot of the enzyme. Its structure explained how the enzyme’s shape can guide cyclization. In particular, the part of the enzyme that binds to the proteins, the active site, was relatively flat and open, but also flexible: this helped the N and C-termini react with each other and close the protein. Further experiments artificially mutated specific areas of the enzyme, which helped determine exactly which elements guide this succession of chemical reactions. The activity of AEPs is influenced by their local environment, such as acidity. In fact, Haywood et al. showed that certain AEPs, which do not normally carry out cyclization, can start performing this role when exposed to a different level of acidity. The pharmaceutical industry is increasingly interested in circular proteins, as these are stable, easily used by the body, and can be genetically customized to act only on specific targets. If the cyclization process is better understood, and then harnessed, new drug compounds could be produced.
Collapse
Affiliation(s)
- Joel Haywood
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.,The ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia
| | - Jason W Schmidberger
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.,The ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia
| | - Amy M James
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.,The ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia
| | - Samuel G Nonis
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.,The ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia
| | - Kirill V Sukhoverkov
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.,The ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia
| | - Mikael Elias
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Joshua S Mylne
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.,The ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia
| |
Collapse
|
439
|
Structural basis for recognition of diverse antidepressants by the human serotonin transporter. Nat Struct Mol Biol 2018; 25:170-175. [PMID: 29379174 DOI: 10.1038/s41594-018-0026-8] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 12/27/2017] [Indexed: 12/22/2022]
Abstract
Selective serotonin reuptake inhibitors are clinically prescribed antidepressants that act by increasing the local concentrations of neurotransmitters at synapses and in extracellular spaces via blockade of the serotonin transporter. Here we report X-ray structures of engineered thermostable variants of the human serotonin transporter bound to the antidepressants sertraline, fluvoxamine, and paroxetine. The drugs prevent serotonin binding by occupying the central substrate-binding site and stabilizing the transporter in an outward-open conformation. These structures explain how residues within the central site orchestrate binding of chemically diverse inhibitors and mediate transporter drug selectivity.
Collapse
|
440
|
Green KD, Biswas T, Pang AH, Willby MJ, Reed MS, Stuchlik O, Pohl J, Posey JE, Tsodikov OV, Garneau-Tsodikova S. Acetylation by Eis and Deacetylation by Rv1151c of Mycobacterium tuberculosis HupB: Biochemical and Structural Insight. Biochemistry 2018; 57:781-790. [PMID: 29345920 DOI: 10.1021/acs.biochem.7b01089] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial nucleoid-associated proteins (NAPs) are critical to genome integrity and chromosome maintenance. Post-translational modifications of bacterial NAPs appear to function similarly to their better studied mammalian counterparts. The histone-like NAP HupB from Mycobacterium tuberculosis (Mtb) was previously observed to be acetylated by the acetyltransferase Eis, leading to genome reorganization. We report biochemical and structural aspects of acetylation of HupB by Eis. We also found that the SirT-family NAD+-dependent deacetylase Rv1151c from Mtb deacetylated HupB in vitro and characterized the deacetylation kinetics. We propose that activities of Eis and Rv1151c could regulate the acetylation status of HupB to remodel the mycobacterial chromosome in response to environmental changes.
Collapse
Affiliation(s)
- Keith D Green
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| | - Tapan Biswas
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Allan H Pang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| | | | | | | | | | | | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| |
Collapse
|
441
|
Miller BR, Kung Y. Structural Features and Domain Movements Controlling Substrate Binding and Cofactor Specificity in Class II HMG-CoA Reductase. Biochemistry 2017; 57:654-662. [PMID: 29224355 DOI: 10.1021/acs.biochem.7b00999] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The key mevalonate pathway enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase (HMGR) uses the cofactor NAD(P)H to reduce HMG-CoA to mevalonate in the production of countless metabolites and natural products. Although inhibition of HMGR by statin drugs is well-understood, several mechanistic details of HMGR catalysis remain unresolved, and the structural basis for the wide range of cofactor specificity for either NADH or NADPH among HMGRs from different organisms is also unknown. Here, we present crystal structures of HMGR from Streptococcus pneumoniae (SpHMGR) alongside kinetic data of the enzyme's cofactor preferences. Our structure of SpHMGR bound with its kinetically preferred NADPH cofactor suggests how NADPH-specific binding and recognition are achieved. In addition, our structure of HMG-CoA-bound SpHMGR reveals large, previously unknown conformational domain movements that may control HMGR substrate binding and enable cofactor exchange without intermediate release during the catalytic cycle. Taken together, this work provides critical new insights into both the HMGR reaction mechanism and the structural basis of cofactor specificity.
Collapse
Affiliation(s)
- Bradley R Miller
- Department of Chemistry, Bryn Mawr College , 101 North Merion Avenue, Bryn Mawr, Pennsylvania 19010, United States
| | - Yan Kung
- Department of Chemistry, Bryn Mawr College , 101 North Merion Avenue, Bryn Mawr, Pennsylvania 19010, United States
| |
Collapse
|
442
|
Huber TR, McPherson EC, Keating CE, Snow CD. Installing Guest Molecules at Specific Sites within Scaffold Protein Crystals. Bioconjug Chem 2017; 29:17-22. [DOI: 10.1021/acs.bioconjchem.7b00668] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Thaddaus R. Huber
- Department of Chemical and
Biological Engineering, Colorado State University, 1301 Campus Delivery Fort Collins, Colorado 80523, United States
| | - Eli C. McPherson
- Department of Chemical and
Biological Engineering, Colorado State University, 1301 Campus Delivery Fort Collins, Colorado 80523, United States
| | - Carolyn E. Keating
- Department of Chemical and
Biological Engineering, Colorado State University, 1301 Campus Delivery Fort Collins, Colorado 80523, United States
| | - Christopher D. Snow
- Department of Chemical and
Biological Engineering, Colorado State University, 1301 Campus Delivery Fort Collins, Colorado 80523, United States
| |
Collapse
|
443
|
Stewart AC, Bethel CR, VanPelt J, Bergstrom A, Cheng Z, Miller CG, Williams C, Poth R, Morris M, Lahey O, Nix JC, Tierney DL, Page RC, Crowder MW, Bonomo RA, Fast W. Clinical Variants of New Delhi Metallo-β-Lactamase Are Evolving To Overcome Zinc Scarcity. ACS Infect Dis 2017; 3:927-940. [PMID: 28965402 DOI: 10.1021/acsinfecdis.7b00128] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Use and misuse of antibiotics have driven the evolution of serine β-lactamases to better recognize new generations of β-lactam drugs, but the selective pressures driving evolution of metallo-β-lactamases are less clear. Here, we present evidence that New Delhi metallo-β-lactamase (NDM) is evolving to overcome the selective pressure of zinc(II) scarcity. Studies of NDM-1, NDM-4 (M154L), and NDM-12 (M154L, G222D) demonstrate that the point mutant M154L, contained in 50% of clinical NDM variants, selectively enhances resistance to the penam ampicillin at low zinc(II) concentrations relevant to infection sites. Each of the clinical variants is shown to be progressively more thermostable and to bind zinc(II) more tightly than NDM-1, but a selective enhancement of penam turnover at low zinc(II) concentrations indicates that most of the improvement derives from catalysis rather than stability. X-ray crystallography of NDM-4 and NDM-12, as well as bioinorganic spectroscopy of dizinc(II), zinc(II)/cobalt(II), and dicobalt(II) metalloforms probe the mechanism of enhanced resistance and reveal perturbations of the dinuclear metal cluster that underlie improved catalysis. These studies support the proposal that zinc(II) scarcity, rather than changes in antibiotic structure, is driving the evolution of new NDM variants in clinical settings.
Collapse
Affiliation(s)
- Alesha C. Stewart
- Division of Chemical
Biology and Medicinal Chemistry, College of Pharmacy, and the LaMontagne
Center for Infectious Disease, University of Texas, Austin, Texas 78712, United States
| | - Christopher R. Bethel
- Research Services, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Jamie VanPelt
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Alex Bergstrom
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Callie G. Miller
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Cameron Williams
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Robert Poth
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Matthew Morris
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Olivia Lahey
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Jay C. Nix
- Molecular Biology Consortium, Beamline 4.2.2, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - David L. Tierney
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Richard C. Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Michael W. Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Robert A. Bonomo
- Research Services, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
- Departments
of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry,
Proteomics and Bioinformatics, and the CWRU-Cleveland VAMC Center
for Antimicrobial Resistance and Epidemiology, Cleveland, Ohio 44106, United States
| | - Walter Fast
- Division of Chemical
Biology and Medicinal Chemistry, College of Pharmacy, and the LaMontagne
Center for Infectious Disease, University of Texas, Austin, Texas 78712, United States
| |
Collapse
|
444
|
Naschberger A, Orry A, Lechner S, Bowler MW, Nurizzo D, Novokmet M, Keller MA, Oemer G, Seppi D, Haslbeck M, Pansi K, Dieplinger H, Rupp B. Structural Evidence for a Role of the Multi-functional Human Glycoprotein Afamin in Wnt Transport. Structure 2017; 25:1907-1915.e5. [PMID: 29153507 DOI: 10.1016/j.str.2017.10.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/14/2017] [Accepted: 10/23/2017] [Indexed: 11/19/2022]
Abstract
Afamin, a human plasma glycoprotein and putative transporter of hydrophobic molecules, has been shown to act as extracellular chaperone for poorly soluble, acylated Wnt proteins, forming a stable, soluble complex with functioning Wnt proteins. The 2.1-Å crystal structure of glycosylated human afamin reveals an almost exclusively hydrophobic binding cleft capable of harboring large hydrophobic moieties. Lipid analysis confirms the presence of lipids, and density in the primary binding pocket of afamin was modeled as palmitoleic acid, presenting the native O-acylation on serine 209 in human Wnt3a. The modeled complex between the experimental afamin structure and a Wnt3a homology model based on the XWnt8-Fz8-CRD fragment complex crystal structure is compelling, with favorable interactions comparable with the crystal structure complex. Afamin readily accommodates the conserved palmitoylated serine 209 of Wnt3a, providing a structural basis how afamin solubilizes hydrophobic and poorly soluble Wnt proteins.
Collapse
Affiliation(s)
- Andreas Naschberger
- Division of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstraße 41, 6020 Innsbruck, Austria; Division of Biological Chemistry, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Andrew Orry
- MolSoft LLC, 11199 Sorrento Valley Road, San Diego, CA 92121, USA
| | - Stefan Lechner
- Division of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstraße 41, 6020 Innsbruck, Austria
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38043 Grenoble, France
| | - Didier Nurizzo
- Structural Biology Group, ESRF, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Mislav Novokmet
- Genos, Glycoscience Laboratory, Hondlova 2/11, 10000 Zagreb, Croatia
| | - Markus A Keller
- Division of Human Genetics, Medical University of Innsbruck, Peter-Mayr-Straße 1, 6020 Innsbruck, Austria
| | - Gregor Oemer
- Genos, Glycoscience Laboratory, Hondlova 2/11, 10000 Zagreb, Croatia
| | - Daniele Seppi
- Division of Biological Chemistry, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Martin Haslbeck
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Kathrin Pansi
- Division of Biological Chemistry, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Hans Dieplinger
- Division of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstraße 41, 6020 Innsbruck, Austria
| | - Bernhard Rupp
- Division of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstraße 41, 6020 Innsbruck, Austria; k.-k. Hofkristallamt, San Diego, CA 92084, USA.
| |
Collapse
|
445
|
Do HT, Wang HY, Li H, Chreifi G, Poulos TL, Silverman RB. Improvement of Cell Permeability of Human Neuronal Nitric Oxide Synthase Inhibitors Using Potent and Selective 2-Aminopyridine-Based Scaffolds with a Fluorobenzene Linker. J Med Chem 2017; 60:9360-9375. [PMID: 29091437 DOI: 10.1021/acs.jmedchem.7b01356] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Inhibition of neuronal nitric oxide synthase (nNOS) is a promising therapeutic approach to treat neurodegenerative diseases. Recently, we have achieved considerable progress in improving the potency and isoform selectivity of human nNOS inhibitors bearing a 2-aminopyridine scaffold. However, these inhibitors still suffered from too low cell membrane permeability to enter into CNS drug development. We report herein our studies to improve permeability of nNOS inhibitors as measured by both PAMPA-BBB and Caco-2 assays. The most permeable compound (12) in this study still preserves excellent potency with human nNOS (Ki = 30 nM) and very high selectivity over other NOS isoforms, especially human eNOS (hnNOS/heNOS = 2799, the highest hnNOS/heNOS ratio we have obtained to date). X-ray crystallographic analysis reveals that 12 adopts a similar binding mode in both rat and human nNOS, in which the 2-aminopyridine and the fluorobenzene linker form crucial hydrogen bonds with glutamate and tyrosine residues, respectively.
Collapse
Affiliation(s)
- Ha T Do
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Center for Developmental Therapeutics, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Heng-Yen Wang
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Center for Developmental Therapeutics, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Huiying Li
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine , Irvine California 92697-3900, United States
| | - Georges Chreifi
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine , Irvine California 92697-3900, United States
| | - Thomas L Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine , Irvine California 92697-3900, United States
| | - Richard B Silverman
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Center for Developmental Therapeutics, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| |
Collapse
|
446
|
Drexler DJ, Müller M, Rojas-Cordova CA, Bandera AM, Witte G. Structural and Biophysical Analysis of the Soluble DHH/DHHA1-Type Phosphodiesterase TM1595 from Thermotoga maritima. Structure 2017; 25:1887-1897.e4. [PMID: 29107484 DOI: 10.1016/j.str.2017.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/07/2017] [Accepted: 09/29/2017] [Indexed: 11/26/2022]
Abstract
The concentration of messenger molecules in bacterial cells needs to be tightly regulated. This can be achieved by either controlling the synthesis rate, degradation, or export by specific transporters, respectively. The regulation of the essential second messenger c-di-AMP is achieved by modulation of the diadenylate cyclase activity as well as by specific phosphodiesterases that hydrolyze c-di-AMP in the cell. We provide here structural and biochemical data on the DHH-type phosphodiesterase TmPDE (TM1595) from Thermotoga maritima. Our analysis shows that TmPDE is preferentially degrading linear dinucleotides, such as 5'-pApA, 5'-pGpG, and 5'-pApG, compared with cyclic dinucleotide substrates. The high-resolution structural data provided here describe all steps of the PDE reaction: the ligand-free enzyme, two substrate-bound states, and three post-reaction states. We can furthermore show that Pde2 from Streptococcus pneumoniae shares both structural features and substrate specificity based on small-angle X-ray scattering data and biochemical assays.
Collapse
Affiliation(s)
- David Jan Drexler
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Martina Müller
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Carlos Alberto Rojas-Cordova
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Adrian Maurice Bandera
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Gregor Witte
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany.
| |
Collapse
|
447
|
Tossounian MA, Van Molle I, Wahni K, Jacques S, Gevaert K, Van Breusegem F, Vertommen D, Young D, Rosado LA, Messens J. Disulfide bond formation protects Arabidopsis thaliana glutathione transferase tau 23 from oxidative damage. Biochim Biophys Acta Gen Subj 2017; 1862:775-789. [PMID: 29031766 DOI: 10.1016/j.bbagen.2017.10.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 10/04/2017] [Accepted: 10/10/2017] [Indexed: 12/22/2022]
Abstract
BACKGROUND Glutathione transferases play an important role as detoxifying enzymes. In A. thaliana, elevated levels of reactive oxygen species (ROS), provoked during biotic and abiotic stress, influence the activity of GSTU23. The aim of this study is to determine the impact of oxidative stress on the function and structure of GSTU23. METHODS The impact of oxidation on the function of GSTU23 was studied using a glutathione transferase biochemical assay and mass spectrometry. With kinetics, circular dichroism and thermodynamics, we compared reduced with oxidized GSTU23. X-ray crystal structures of GSTU23 visualize the impact of oxidation on methionines and cysteines. RESULTS In the presence of 100μM H2O2, oxidation of the methionine side-chain to a sulfoxide is the prominent post-translational modification, which can be reduced by C. diphtheriae MsrA and MsrB. However, increasing the level to 200μM H2O2 results in a reversible intramolecular disulfide between Cys65-Cys110, which is substrate for glutaredoxin. Under these oxidizing conditions, GSTU23 undergoes a structural change and forms a more favourable enzyme-substrate complex to overcome kcat decrease. CONCLUSIONS AND SIGNIFICANCE At lower H2O2 levels (100μM), GSTU23 forms methionine sulfoxides. Specifically, oxidation of Met14, located near the catalytic Ser13, could interfere with both GSH binding and catalytic activation. At higher H2O2 levels (200μM), the Cys65-Cys110 disulfide bond protects other cysteines and also methionines from overoxidation. This study shows the impact of oxidative stress on GSTU23 regulated by methionine sulfoxide reductases and glutaredoxin, and the mechanisms involved in maintaining its catalytic functionality under oxidizing conditions.
Collapse
Affiliation(s)
- Maria-Armineh Tossounian
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Brussels Center for Redox Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Inge Van Molle
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Brussels Center for Redox Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Khadija Wahni
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Brussels Center for Redox Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Silke Jacques
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium; VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, B-9052 Ghent, Belgium
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium; VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, B-9052 Ghent, Belgium
| | - Didier Vertommen
- de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - David Young
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Brussels Center for Redox Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Leonardo Astolfi Rosado
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Brussels Center for Redox Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Brussels Center for Redox Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium.
| |
Collapse
|
448
|
Cingolani G, Panella A, Perrone MG, Vitale P, Di Mauro G, Fortuna CG, Armen RS, Ferorelli S, Smith WL, Scilimati A. Structural basis for selective inhibition of Cyclooxygenase-1 (COX-1) by diarylisoxazoles mofezolac and 3-(5-chlorofuran-2-yl)-5-methyl-4-phenylisoxazole (P6). Eur J Med Chem 2017; 138:661-668. [PMID: 28710965 PMCID: PMC5992922 DOI: 10.1016/j.ejmech.2017.06.045] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/21/2017] [Accepted: 06/23/2017] [Indexed: 01/23/2023]
Abstract
The diarylisoxazole molecular scaffold is found in several NSAIDs, especially those with high selectivity for COX-1. Here, we have determined the structural basis for COX-1 binding to two diarylisoxazoles: mofezolac, which is polar and ionizable, and 3-(5-chlorofuran-2-yl)-5-methyl-4-phenylisoxazole (P6) that has very low polarity. X-ray analysis of the crystal structures of COX-1 bound to mofezolac and 3-(5-chlorofuran-2-yl)-5-methyl-4-phenylisoxazole allowed the identification of specific binding determinants within the enzyme active site, relevant to generate structure/activity relationships for diarylisoxazole NSAIDs.
Collapse
Affiliation(s)
- Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; Institute of Biomembranes and Bioenergetics, National Research Council, Via Amendola 165/A, 70125 Bari, Italy
| | - Andrea Panella
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "Aldo Moro", Via E. Orabona 4, 70125 Bari, Italy
| | - Maria Grazia Perrone
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "Aldo Moro", Via E. Orabona 4, 70125 Bari, Italy
| | - Paola Vitale
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "Aldo Moro", Via E. Orabona 4, 70125 Bari, Italy
| | - Giuseppe Di Mauro
- Department of Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Cosimo G Fortuna
- Department of Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Roger S Armen
- Department of Pharmaceutical Sciences, College of Pharmacy, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Savina Ferorelli
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "Aldo Moro", Via E. Orabona 4, 70125 Bari, Italy
| | - William L Smith
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Antonio Scilimati
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "Aldo Moro", Via E. Orabona 4, 70125 Bari, Italy.
| |
Collapse
|
449
|
Porebski PJ, Sroka P, Zheng H, Cooper DR, Minor W. Molstack-Interactive visualization tool for presentation, interpretation, and validation of macromolecules and electron density maps. Protein Sci 2017; 27:86-94. [PMID: 28815771 DOI: 10.1002/pro.3272] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/11/2017] [Accepted: 08/14/2017] [Indexed: 11/07/2022]
Abstract
Our understanding of the world of biomolecular structures is based upon the interpretation of macromolecular models, of which ∼90% are an interpretation of electron density maps. This structural information guides scientific progress and exploration in many biomedical disciplines. The Protein Data Bank's web portals have made these structures available for mass scientific consumption and greatly broaden the scope of information presented in scientific publications. The portals provide numerous quality metrics; however, the portion of the structure that is most vital for interpretation of the function may have the most difficult to interpret electron density and this ambiguity is not reflected by any single metric. The possible consequences of basing research on suboptimal models make it imperative to inspect the agreement of a model with its experimental evidence. Molstack, a web-based interactive publishing platform for structural data, allows users to present density maps and structural models by displaying a collection of maps and models, including different interpretation of one's own data, re-refinements, and corrections of existing structures. Molstack organizes the sharing and dissemination of these structural models along with their experimental evidence as an interactive session. Molstack was designed with three groups of users in mind; researchers can present the evidence of their interpretation, reviewers and readers can independently judge the experimental evidence of the authors' conclusions, and other researchers can present or even publish their new hypotheses in the context of prior results. The server is available at http://molstack.bioreproducibility.org.
Collapse
Affiliation(s)
- Przemyslaw J Porebski
- Department of Biological Physics & Molecular Physiology, University of Virginia, Charlottesville, Virginia
| | - Piotr Sroka
- Department of Biological Physics & Molecular Physiology, University of Virginia, Charlottesville, Virginia
| | - Heping Zheng
- Department of Biological Physics & Molecular Physiology, University of Virginia, Charlottesville, Virginia
| | - David R Cooper
- Department of Biological Physics & Molecular Physiology, University of Virginia, Charlottesville, Virginia
| | - Wladek Minor
- Department of Biological Physics & Molecular Physiology, University of Virginia, Charlottesville, Virginia
| |
Collapse
|
450
|
Structural Basis for the Bidirectional Activity of Bacillus nanoRNase NrnA. Sci Rep 2017; 7:11085. [PMID: 28894100 PMCID: PMC5593865 DOI: 10.1038/s41598-017-09403-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/24/2017] [Indexed: 12/21/2022] Open
Abstract
NanoRNAs are RNA fragments 2 to 5 nucleotides in length that are generated as byproducts of RNA degradation and abortive transcription initiation. Cells have specialized enzymes to degrade nanoRNAs, such as the DHH phosphoesterase family member NanoRNase A (NrnA). This enzyme was originally identified as a 3′ → 5′ exonuclease, but we show here that NrnA is bidirectional, degrading 2–5 nucleotide long RNA oligomers from the 3′ end, and longer RNA substrates from the 5′ end. The crystal structure of Bacillus subtilis NrnA reveals a dynamic bi-lobal architecture, with the catalytic N-terminal DHH domain linked to the substrate binding C-terminal DHHA1 domain via an extended linker. Whereas this arrangement is similar to the structure of RecJ, a 5′ → 3′ DHH family DNase and other DHH family nanoRNases, Bacillus NrnA has gained an extended substrate-binding patch that we posit is responsible for its 3′ → 5′ activity.
Collapse
|