1
|
Killian MM, Brophy MB, Nolan EM, Brunold TC. Spectroscopic and computational investigations of Cobalt(II) binding to the innate immune protein human calprotectin. J Biol Inorg Chem 2024; 29:127-137. [PMID: 38233645 DOI: 10.1007/s00775-023-02034-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/30/2023] [Indexed: 01/19/2024]
Abstract
Human calprotectin (CP) is an innate immune protein that participates in the metal-withholding response to infection by sequestering essential metal nutrients from invading microbial pathogens. CP is comprised of S100A8 (α subunit, 10.8 kDa) and S100A9 (β subunit, 13.2 kDa). Two transition-metal binding sites of CP form at the S100A8/S100A9 dimer interface. Site 1 is a His3Asp motif comprised of His83 and His87 from the S100A8 subunit and His20 and Asp30 from the S100A9 subunit. Site 2 is an unusual hexahistidine motif composed of S100A8 residues His17 and His27 and S100A9 residues His91, His95, His103, and His105. In the present study, the His3Asp and His6 sites of CP were further characterized by utilizing Co2+ as a spectroscopic probe. Magnetic circular dichroism spectroscopy was employed in conjunction with electron paramagnetic resonance spectroscopy and density functional theory computations to characterize the Co2+-bound S100A8(C42S)/S100A9(C3S) CP-Ser variant and six site variants that allowed the His3Asp and His6 sites to be further probed. Our results provide new insight into the metal-binding sites of CP-Ser and the effect of amino acid substitutions on the structure of site 2.
Collapse
Affiliation(s)
- Michelle M Killian
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Megan B Brophy
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Elizabeth M Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| |
Collapse
|
2
|
Pérez AL, Kemmerer A, Zapata AJ, Sartoris R, Gonzalez PJ, Urteaga R, Baggio R, Suarez S, Ramos CA, Dalosto SD, Rizzi AC, Brondino CD. Synthesis, structure, and characterisation of a ferromagnetically coupled dinuclear complex containing Co(II) ions in a high spin configuration and thiodiacetate and phenanthroline as ligands and of a series of isomorphous heterodinuclear complexes containing different Co : Zn ratios. Dalton Trans 2023; 52:14595-14605. [PMID: 37786344 DOI: 10.1039/d3dt02115g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
We report the synthesis, crystal structure, and characterisation of a dinuclear Co(II) compound with thiodiacetate (tda) and phenanthroline (phen) as ligands (1), and of a series of metal complexes isomorphous to 1 with different Co : Zn ratios (2, 4 : 1; 3, 1 : 1; 4, 1 : 4; 5, 1 : 10). General characterisation methodologies and X-ray data showed that all the synthesised complexes are isomorphous to Zn(II) and Cu(II) analogues (CSD codes: DUHXEL and BEBQII). 1 consists of centrosymmetric Co(II) ion dimers in which the ions are 3.214 Å apart, linked by two μ-O bridges. Each cobalt atom is in a distorted octahedral environment of the N2O3S type. UV-vis spectra of 1 and 5 are in line with high spin (S = 3/2) Co(II) ions in octahedral coordination and indicate that the electronic structure of both Co(II) ions in the dinuclear unit does not significantly change relative to that of the magnetically isolated Co(II) ion. EPR spectra of powder samples of 5 (Co : Zn ratio of 1 : 10) together with spectral simulation indicated high spin Co(II) ions with high rhombic distortion of the zfs [E/D = 0.31(1), D > 0]. DC magnetic susceptibility experiments on 1 and analysis of the data constraining the E/D value obtained by EPR yielded g = 2.595(7), |D| = 61(1) cm-1, and an intradimer ferromagnetic exchange coupling of J = 1.39(4) cm-1. EPR spectra as a function of Co : Zn ratio for both powder and single crystal samples confirmed that they result from two effective S' = 1/2 spins that interact through dipolar and isotropic exchange interactions to yield magnetically isolated S' = 1 centres and that interdimeric exchange interactions, putatively mediated by hydrophobic interactions between phen moieties, are negligible. The latter observation contrasts with that observed in the Cu(II) analogue, where a transition from S = 1 to S' = 1/2 was observed. Computational calculations indicated that the absence of the interdimeric exchange interaction in 1 is due to a lower Co(II) ion spin density delocalisation towards the metal ligands.
Collapse
Affiliation(s)
- Ana L Pérez
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, Ciudad Universitaria, S3000ZAA Santa Fe, Argentina.
- Instituto de Física del Litoral, Universidad Nacional del Litoral - CONICET, Güemes 3450, 3000 Santa Fe, Argentina
| | - Axel Kemmerer
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, Ciudad Universitaria, S3000ZAA Santa Fe, Argentina.
| | - Alejandro J Zapata
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, Ciudad Universitaria, S3000ZAA Santa Fe, Argentina.
| | - Rosana Sartoris
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, Ciudad Universitaria, S3000ZAA Santa Fe, Argentina.
| | - Pablo J Gonzalez
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, Ciudad Universitaria, S3000ZAA Santa Fe, Argentina.
| | - Raul Urteaga
- Instituto de Física del Litoral, Universidad Nacional del Litoral - CONICET, Güemes 3450, 3000 Santa Fe, Argentina
- Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santiago del Estero 2829, 3000 Santa Fe, Argentina
| | - Ricardo Baggio
- Gerencia de Investigación y Aplicaciones, Centro Atómico Constituyentes, Comisión Nacional de Energía Atómica, Buenos Aires, Argentina
| | - Sebastián Suarez
- Gerencia de Investigación y Aplicaciones, Centro Atómico Constituyentes, Comisión Nacional de Energía Atómica, Buenos Aires, Argentina
| | - Carlos A Ramos
- Instituto de Nanociencia y Nanotecnología, CNEA-CONICET, Centro Atómico Bariloche, 8400, San Carlos de Bariloche, Río Negro, Argentina
| | - Sergio D Dalosto
- Instituto de Física del Litoral, Universidad Nacional del Litoral - CONICET, Güemes 3450, 3000 Santa Fe, Argentina
- Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santiago del Estero 2829, 3000 Santa Fe, Argentina
| | - Alberto C Rizzi
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, Ciudad Universitaria, S3000ZAA Santa Fe, Argentina.
| | - Carlos D Brondino
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, Ciudad Universitaria, S3000ZAA Santa Fe, Argentina.
| |
Collapse
|
3
|
A de novo binuclear zinc enzyme with DNA cleavage activity. J Biol Inorg Chem 2021; 26:161-167. [PMID: 33469708 DOI: 10.1007/s00775-020-01845-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 12/16/2020] [Indexed: 12/15/2022]
Abstract
Metallohydrolases are broadly used throughout biology, often to catalyze the degradation of macromolecules such as DNA and proteins. Many of these enzymes function with zinc in their active site, and an important subset of these enzymes utilize a binuclear zinc active site. Mimics of these enzymes have been developed, some of which catalyze the digestion of DNA. However, the majority of the mimics that utilize zinc are small molecules, and most are mononuclear. Herein, we report DNA cleavage activity by the de novo designed Due Ferri single-chain (DFsc) protein containing a binuclear zinc active site. This binuclear zinc-protein complex is able to digest plasmid DNA at rates up to 50 ng/h, and these cleavage rates are affected by changes to amino acid residues near the zinc-binding site. These results indicate that the DFsc scaffold is a good model system to carry out careful structure-function relationship studies to understand key structural features that influence reactivity in natural binuclear zinc hydrolases, as it is the first report of a binuclear model system in a protein scaffold.
Collapse
|
4
|
Selleck C, Pedroso MM, Wilson L, Krco S, Knaven EG, Miraula M, Mitić N, Larrabee JA, Brück T, Clark A, Guddat LW, Schenk G. Structure and mechanism of potent bifunctional β-lactam- and homoserine lactone-degrading enzymes from marine microorganisms. Sci Rep 2020; 10:12882. [PMID: 32732933 PMCID: PMC7392888 DOI: 10.1038/s41598-020-68612-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/26/2020] [Indexed: 11/11/2022] Open
Abstract
Genes that confer antibiotic resistance can rapidly be disseminated from one microorganism to another by mobile genetic elements, thus transferring resistance to previously susceptible bacterial strains. The misuse of antibiotics in health care and agriculture has provided a powerful evolutionary pressure to accelerate the spread of resistance genes, including those encoding β-lactamases. These are enzymes that are highly efficient in inactivating most of the commonly used β-lactam antibiotics. However, genes that confer antibiotic resistance are not only associated with pathogenic microorganisms, but are also found in non-pathogenic (i.e. environmental) microorganisms. Two recent examples are metal-dependent β-lactamases (MBLs) from the marine organisms Novosphingobium pentaromativorans and Simiduia agarivorans. Previous studies have demonstrated that their β-lactamase activity is comparable to those of well-known MBLs from pathogenic sources (e.g. NDM-1, AIM-1) but that they also possess efficient lactonase activity, an activity associated with quorum sensing. Here, we probed the structure and mechanism of these two enzymes using crystallographic, spectroscopic and fast kinetics techniques. Despite highly conserved active sites both enzymes demonstrate significant variations in their reaction mechanisms, highlighting both the extraordinary ability of MBLs to adapt to changing environmental conditions and the rather promiscuous acceptance of diverse substrates by these enzymes.
Collapse
Affiliation(s)
- Christopher Selleck
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia. .,Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, QLD, 4072, Australia. .,Sustainable Minerals Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Liam Wilson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Stefan Krco
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Esmée Gianna Knaven
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Manfredi Miraula
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Department of Chemistry, Maynooth University, Maynooth, County Kildare, Ireland
| | - Nataša Mitić
- Department of Chemistry, Maynooth University, Maynooth, County Kildare, Ireland
| | - James A Larrabee
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, 05753, USA
| | - Thomas Brück
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), Lichtenberg Str. 4, 85748, Garching, Germany
| | - Alice Clark
- Sustainable Minerals Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia. .,Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, QLD, 4072, Australia. .,Sustainable Minerals Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia.
| |
Collapse
|
5
|
Plugis NM, Rudd ND, Krzystek J, Swenson DC, Telser J, Larrabee JA. Cobalt(II) "Scorpionate" complexes as electronic ground state models for cobalt-substituted zinc enzymes: Structure investigation by magnetic circular dichroism. J Inorg Biochem 2019; 203:110876. [PMID: 31756558 DOI: 10.1016/j.jinorgbio.2019.110876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/19/2019] [Accepted: 10/01/2019] [Indexed: 12/15/2022]
Abstract
Zinc centers in pseudo-tetrahedral geometry are widely found in biology, often with three histidine ligands from protein. The trispyrazolylborate "scorpionate" ligand is used as a model for this tris(histidine) motif, and spectroscopically active CoII is often used as a substitute for spectroscopically silent ZnII. In this work, four pseudo-tetrahedral scorpionate complexes with the formula (Tpt-Bu,Tn)CoL, where Tpt-Bu,Tn = hydrotris(3-tert-butyl, 5-2'-thienyl-pyrazol-1-yl)borate anion and L = Cl-, N3-, NCO-, or NCS-, were studied using variable-temperature, variable-field magnetic circular dichroism (VTVH MCD) spectroscopy. The major goal was to determine the axial and rhombic zero field splitting (ZFS) parameters (D and E, respectively) of these S = 3/2 systems and compare these ZFS parameters to those determined previously by high-frequency and -field electron paramagnetic resonance (HFEPR) spectroscopy on the same (L = Cl- and NCS-) or closely related complexes. Additionally, HFEPR studies were undertaken here on the complexes with L = N3-, NCO-. Crystal structures for these two complexes are also first reported here. The values of D determined by VTVH MCD were + 12.8 and + 3.6 cm-1 for the L = Cl- and NCS- complexes, respectively. These values are in close agreement with those for the same complexes as previously determined by HFEPR. The values of D determined by VTVH MCD were + 3.0 and + 6.6 cm-1 for the L = N3- and NCO- complexes, respectively. These values were not as close to those determined by HFEPR in the present study, which are 4.2 cm-1 ≤ |D| ≤ 5.6 cm-1 in Tpt-Bu,TnCoN3, and 8.3 cm-1 ≤ |D| ≤ 11.0 cm-1 in Tpt-Bu,TnCoNCO. The bands in MCD spectra of these complexes were assigned in C3v symmetry and a complete ligand-field analysis of the MCD data was made using the Angular Overlap Model (AOM), which is compared to previous results.
Collapse
Affiliation(s)
- Nicholas M Plugis
- Department of Chemistry & Biochemistry, 547 Bicentennial Way, Middlebury College, Middlebury, VT 05753, USA
| | - Nathan D Rudd
- Department of Chemistry & Biochemistry, 547 Bicentennial Way, Middlebury College, Middlebury, VT 05753, USA
| | - J Krzystek
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA
| | - Dale C Swenson
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Joshua Telser
- Department of Biological, Physical and Health Sciences, Roosevelt University, 430 South Michigan Avenue, Chicago, IL 60605, USA
| | - James A Larrabee
- Department of Chemistry & Biochemistry, 547 Bicentennial Way, Middlebury College, Middlebury, VT 05753, USA.
| |
Collapse
|
6
|
Hfidhi N, Korb M, Fitta M, Čižmár E, Lang H, Naïli H. Magneto-electronic properties and structural features of unusual bis(μ-aqua) bis(μ-sulfato) bridges in binuclear cobalt-based 4-aminopyridine. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2018.09.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
7
|
Monteiro Pedroso M, Selleck C, Bilyj J, Harmer JR, Gahan LR, Mitić N, Standish AJ, Tierney DL, Larrabee JA, Schenk G. Reaction mechanism of the metallohydrolase CpsB from Streptococcus pneumoniae, a promising target for novel antimicrobial agents. Dalton Trans 2018; 46:13194-13201. [PMID: 28573276 DOI: 10.1039/c7dt01350g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
CpsB is a metal ion-dependent hydrolase involved in the biosynthesis of capsular polysaccharides in bacterial organisms. The enzyme has been proposed as a promising target for novel chemotherapeutics to combat antibiotic resistance. The crystal structure of CpsB indicated the presence of as many as three closely spaced metal ions, modelled as Mn2+, in the active site. While the preferred metal ion composition in vivo is obscure Mn2+ and Co2+ have been demonstrated to be most effective in reconstituting activity. Using isothermal titration calorimetry (ITC) we have demonstrated that, in contrast to the crystal structure, only two Mn2+ or Co2+ ions bind to a monomer of CpsB. This observation is in agreement with magnetic circular dichroism (MCD) and electron paramagnetic resonance (EPR) data that indicate the presence of two weakly ferromagnetically coupled Co2+ ions in the active site of catalytically active CpsB. While CpsB is known to be a phosphoesterase we have also been able to demonstrate that this enzyme is efficient in hydrolyzing the β-lactam substrate nitrocefin. Steady-state and stopped-flow kinetics measurements further indicated that phosphoesters and nitrocefin undergo catalysis in a conserved manner with a metal ion-bridging hydroxide acting as a nucleophile. Thus, the combined physicochemical studies demonstrate that CpsB is a novel member of the dinuclear metallohydrolase family.
Collapse
Affiliation(s)
- Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Pedroso MM, Selleck C, Enculescu C, Harmer JR, Mitić N, Craig WR, Helweh W, Hugenholtz P, Tyson GW, Tierney DL, Larrabee JA, Schenk G. Characterization of a highly efficient antibiotic-degrading metallo-β-lactamase obtained from an uncultured member of a permafrost community. Metallomics 2017; 9:1157-1168. [DOI: 10.1039/c7mt00195a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Microorganisms in the permafrost contain a potent mechanism to inactivate antibiotics.
Collapse
|
9
|
Selleck C, Larrabee JA, Harmer J, Guddat LW, Mitić N, Helweh W, Ollis DL, Craig WR, Tierney DL, Monteiro Pedroso M, Schenk G. AIM-1: An Antibiotic-Degrading Metallohydrolase That Displays Mechanistic Flexibility. Chemistry 2016; 22:17704-17714. [DOI: 10.1002/chem.201602762] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Christopher Selleck
- School of Chemistry and Molecular Biosciences; The University of Queensland; St. Lucia Queensland 4072 Australia
| | - James A. Larrabee
- Department of Chemistry and Biochemistry; Middlebury College; Middlebury Vermont 05753 USA
| | - Jeffrey Harmer
- Centre for Advanced Imaging; The University of Queensland; St. Lucia Queensland 4072 Australia
| | - Luke W. Guddat
- School of Chemistry and Molecular Biosciences; The University of Queensland; St. Lucia Queensland 4072 Australia
| | - Nataša Mitić
- Department of Chemistry; Maynooth University; Maynooth, Co. Kildare Ireland
| | - Waleed Helweh
- Department of Chemistry and Biochemistry; Middlebury College; Middlebury Vermont 05753 USA
| | - David L. Ollis
- Research School of Chemistry; Australian National University of Canberra; ACT 0200 Australia
| | - Whitney R. Craig
- Department of Chemistry and Biochemistry; Miami University, Oxford; Ohio 45056 USA
| | - David L. Tierney
- Department of Chemistry and Biochemistry; Miami University, Oxford; Ohio 45056 USA
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences; The University of Queensland; St. Lucia Queensland 4072 Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences; The University of Queensland; St. Lucia Queensland 4072 Australia
| |
Collapse
|
10
|
Tadrowski S, Pedroso MM, Sieber V, Larrabee JA, Guddat LW, Schenk G. Metal Ions Play an Essential Catalytic Role in the Mechanism of Ketol-Acid Reductoisomerase. Chemistry 2016; 22:7427-36. [PMID: 27136273 DOI: 10.1002/chem.201600620] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Indexed: 01/13/2023]
Abstract
Ketol-acid reductoisomerase (KARI) is a Mg(2+) -dependent enzyme in the branched-chain amino acid biosynthesis pathway. It catalyses a complex two-part reaction: an alkyl migration followed by a NADPH-dependent reduction. Both reactions occur within the one active site, but in particular, the mechanism of the isomerisation step is poorly understood. Here, using a combination of kinetic, thermodynamic and spectroscopic techniques, the reaction mechanisms of both Escherichia coli and rice KARI have been investigated. We propose a conserved mechanism of catalysis, whereby a hydroxide, bridging the two Mg(2+) ions in the active site, initiates the reaction by abstracting a proton from the C2 alcohol group of the substrate. While the μ-hydroxide-bridged dimetallic centre is pre-assembled in the bacterial enzyme, in plant KARI substrate binding leads to a reduction of the metal-metal distance with the concomitant formation of a hydroxide bridge. Only Mg(2+) is capable of promoting the isomerisation reaction, likely to be due to non-competent substrate binding in the presence of other metal ions.
Collapse
Affiliation(s)
- Sonya Tadrowski
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Marcelo M Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Volker Sieber
- Straubing Center of Science, Technische Universität München, Straubing, Germany
| | - James A Larrabee
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, 05753, USA
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia.
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia.
| |
Collapse
|
11
|
Pedroso MM, Larrabee JA, Ely F, Gwee SE, Mitić N, Ollis DL, Gahan LR, Schenk G. Ca(II) Binding Regulates and Dominates the Reactivity of a Transition-Metal-Ion-Dependent Diesterase from Mycobacterium tuberculosis. Chemistry 2015; 22:999-1009. [PMID: 26662456 DOI: 10.1002/chem.201504001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Indexed: 11/07/2022]
Abstract
The diesterase Rv0805 from Mycobacterium tuberculosis is a dinuclear metallohydrolase that plays an important role in signal transduction by controlling the intracellular levels of cyclic nucleotides. As Rv0805 is essential for mycobacterial growth it is a promising new target for the development of chemotherapeutics to treat tuberculosis. The in vivo metal-ion composition of Rv0805 is subject to debate. Here, we demonstrate that the active site accommodates two divalent transition metal ions with binding affinities ranging from approximately 50 nm for Mn(II) to about 600 nm for Zn(II) . In contrast, the enzyme GpdQ from Enterobacter aerogenes, despite having a coordination sphere identical to that of Rv0805, binds only one metal ion in the absence of substrate, thus demonstrating the significance of the outer sphere to modulate metal-ion binding and enzymatic reactivity. Ca(II) also binds tightly to Rv0805 (Kd ≈40 nm), but kinetic, calorimetric, and spectroscopic data indicate that two Ca(II) ions bind at a site different from the dinuclear transition-metal-ion binding site. Ca(II) acts as an activator of the enzymatic activity but is able to promote the hydrolysis of substrates even in the absence of transition-metal ions, thus providing an effective strategy for the regulation of the enzymatic activity.
Collapse
Affiliation(s)
- Marcelo M Pedroso
- School of Chemistry and Molecular BioSciences, The University of Queensland, St. Lucia, QLD 4072, Australia), Fax
| | - James A Larrabee
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT 05753, USA
| | - Fernanda Ely
- School of Chemistry and Molecular BioSciences, The University of Queensland, St. Lucia, QLD 4072, Australia), Fax
| | - Shuhui E Gwee
- School of Chemistry and Molecular BioSciences, The University of Queensland, St. Lucia, QLD 4072, Australia), Fax
| | - Nataša Mitić
- Department of Chemistry, National University of Ireland-Maynooth, Maynooth, Co. Kildare, Ireland
| | - David L Ollis
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Lawrence R Gahan
- School of Chemistry and Molecular BioSciences, The University of Queensland, St. Lucia, QLD 4072, Australia), Fax
| | - Gerhard Schenk
- School of Chemistry and Molecular BioSciences, The University of Queensland, St. Lucia, QLD 4072, Australia), Fax.
| |
Collapse
|
12
|
Starus A, Nocek B, Bennett B, Larrabee JA, Shaw DL, Sae-Lee W, Russo MT, Gillner DM, Makowska-Grzyska M, Joachimiak A, Holz RC. Inhibition of the dapE-Encoded N-Succinyl-L,L-diaminopimelic Acid Desuccinylase from Neisseria meningitidis by L-Captopril. Biochemistry 2015; 54:4834-44. [PMID: 26186504 DOI: 10.1021/acs.biochem.5b00475] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Binding of the competitive inhibitor L-captopril to the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase from Neisseria meningitidis (NmDapE) was examined by kinetic, spectroscopic, and crystallographic methods. L-Captopril, an angiotensin-converting enzyme (ACE) inhibitor, was previously shown to be a potent inhibitor of the DapE from Haemophilus influenzae (HiDapE) with an IC50 of 3.3 μM and a measured Ki of 1.8 μM and displayed a dose-responsive antibiotic activity toward Escherichia coli. L-Captopril is also a competitive inhibitor of NmDapE with a Ki of 2.8 μM. To examine the nature of the interaction of L-captopril with the dinuclear active site of DapE, we have obtained electron paramagnetic resonance (EPR) and magnetic circular dichroism (MCD) data for the enzymatically hyperactive Co(II)-substituted forms of both HiDapE and NmDapE. EPR and MCD data indicate that the two Co(II) ions in DapE are antiferromagnetically coupled, yielding an S = 0 ground state, and suggest a thiolate bridge between the two metal ions. Verification of a thiolate-bridged dinuclear complex was obtained by determining the three-dimensional X-ray crystal structure of NmDapE in complex with L-captopril at 1.8 Å resolution. Combination of these data provides new insights into binding of L-captopril to the active site of DapE enzymes as well as important inhibitor-active site residue interaction's. Such information is critical for the design of new, potent inhibitors of DapE enzymes.
Collapse
Affiliation(s)
- Anna Starus
- †Department of Chemistry and Biochemistry, Loyola University-Chicago, 1068 West Sheridan Road, Chicago, Illinois 60626, United States
| | - Boguslaw Nocek
- ‡Center for Structural Genomics of Infectious Diseases, Computation Institute, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Brian Bennett
- §Department of Physics, Marquette University, Milwaukee, Wisconsin 53201, United States
| | - James A Larrabee
- ∥Department of Chemistry and Biochemistry, Middlebury College, Middlebury, Vermont 05753, United States
| | - Daniel L Shaw
- ∥Department of Chemistry and Biochemistry, Middlebury College, Middlebury, Vermont 05753, United States
| | - Wisath Sae-Lee
- ∥Department of Chemistry and Biochemistry, Middlebury College, Middlebury, Vermont 05753, United States
| | - Marie T Russo
- ∥Department of Chemistry and Biochemistry, Middlebury College, Middlebury, Vermont 05753, United States
| | - Danuta M Gillner
- ⊥Department of Chemistry, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Magdalena Makowska-Grzyska
- ‡Center for Structural Genomics of Infectious Diseases, Computation Institute, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Andrzej Joachimiak
- ‡Center for Structural Genomics of Infectious Diseases, Computation Institute, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Richard C Holz
- #Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201, United States
| |
Collapse
|