1
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Li J, Duan R, Liu A. Cobalt(II)-Substituted Cysteamine Dioxygenase Oxygenation Proceeds through a Cobalt(III)-Superoxo Complex. J Am Chem Soc 2024; 146:18292-18297. [PMID: 38941563 DOI: 10.1021/jacs.4c01871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
We investigated the metal-substituted catalytic activity of human cysteamine dioxygenase (ADO), an enzyme pivotal in regulating thiol metabolism and contributing to oxygen homeostasis. Our findings demonstrate the catalytic competence of cobalt(II)- and nickel(II)-substituted ADO in cysteamine oxygenation. Notably, Co(II)-ADO exhibited superiority over Ni(II)-ADO despite remaining significantly less active than the natural enzyme. Structural analyses through X-ray crystallography and cobalt K-edge excitation confirmed successful metal substitution with minimal structural perturbations. This provided a robust structural basis, supporting a conserved catalytic mechanism tailored to distinct metal centers. This finding challenges the proposed high-valent ferryl-based mechanism for thiol dioxygenases, suggesting a non-high-valent catalytic pathway in the native enzyme. Further investigation of the cysteamine-bound or a peptide mimic of N-terminus RGS5 bound Co(II)-ADO binary complex revealed the metal center's high-spin (S = 3/2) state. Upon reaction with O2, a kinetically and spectroscopically detectable intermediate emerged with a ground spin state of S = 1/2. This intermediate exhibits a characteristic 59Co hyperfine splitting (A = 67 MHz) structure in the EPR spectrum alongside UV-vis features, consistent with known low-spin Co(III)-superoxo complexes. This observation, unique for protein-bound thiolate-ligated cobalt centers in a protein, unveils the capacities for O2 activation in such metal environments. These findings provide valuable insights into the non-heme iron-dependent thiol dioxygenase mechanistic landscape, furthering our understanding of thiol metabolism regulation. The exploration of metal-substituted ADO sheds light on the intricate interplay between metal and catalytic activity in this essential enzyme.
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Affiliation(s)
- Jiasong Li
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Ran Duan
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
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2
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Miller JR, Schnorrenberg EC, Aschenbrener C, Fox BG, Brunold TC. Kinetic and Spectroscopic Investigation of the Y157F and C93G/Y157F Variants of Cysteine Dioxygenase: Dissecting the Roles of the Second-Sphere Residues C93 and Y157. Biochemistry 2024; 63:1684-1696. [PMID: 38885352 PMCID: PMC11219262 DOI: 10.1021/acs.biochem.4c00177] [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] [Indexed: 06/20/2024]
Abstract
In mammals, l-cysteine (Cys) homeostasis is maintained by the mononuclear nonheme iron enzyme cysteine dioxygenase (CDO), which oxidizes Cys to cysteine sulfinic acid. CDO contains a rare post-translational modification, involving the formation of a thioether cross-link between a Cys residue at position 93 (Mus musculus CDO numbering) and a nearby tyrosine at position 157 (Cys-Tyr cross-link). As-isolated CDO contains both the cross-linked and non-cross-linked isoforms, and formation of the Cys-Tyr cross-link during repeated enzyme turnover increases CDO's catalytic efficiency by ∼10-fold. Interestingly, while the C93G CDO variant lacks the Cys-Tyr cross-link, it is similarly active as cross-linked wild-type (WT) CDO. Alternatively, the Y157F CDO variant, which also lacks the cross-link but maintains the free thiolate at position 93, exhibits a drastically reduced catalytic efficiency. These observations suggest that the untethered thiolate moiety of C93 is detrimental to CDO activity and/or that Y157 is essential for catalysis. To further assess the roles of residues C93 and Y157, we performed a spectroscopic and kinetic characterization of Y157F CDO and the newly designed C93G/Y157F CDO variant. Our results provide evidence that the non-cross-linked C93 thiolate stabilizes a water at the sixth coordination site of Cys-bound Y157F Fe(II)CDO. A water is also present, though more weakly coordinated, in Cys-bound C93G/Y157F Fe(II)CDO. The presence of a water molecule, which must be displaced by cosubstrate O2, likely makes a significant contribution to the ∼15-fold and ∼7-fold reduced catalytic efficiencies of the Y157F and C93G/Y157F CDO variants, respectively, relative to cross-linked WT CDO.
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Affiliation(s)
- Joshua R. Miller
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706, United States
| | | | - Cole Aschenbrener
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706, United States
| | - Brian G. Fox
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706, United States
| | - Thomas C. Brunold
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706, United States
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3
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Duan R, Li J, Liu A. Unveiling the mechanism of cysteamine dioxygenase: A combined HPLC-MS assay and metal-substitution approach. Methods Enzymol 2024; 703:147-166. [PMID: 39260994 DOI: 10.1016/bs.mie.2024.05.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Mammalian cysteamine dioxygenase (ADO), a mononuclear non-heme Fe(II) enzyme with three histidine ligands, plays a key role in cysteamine catabolism and regulation of the N-degron signaling pathway. Despite its importance, the catalytic mechanism of ADO remains elusive. Here, we describe an HPLC-MS assay for characterizing thiol dioxygenase catalytic activities and a metal-substitution approach for mechanistic investigation using human ADO as a model. Two proposed mechanisms for ADO differ in oxygen activation: one involving a high-valent ferryl-oxo intermediate. We hypothesized that substituting iron with a metal that has a disfavored tendency to form high-valent states would discriminate between mechanisms. This chapter details the expression, purification, preparation, and characterization of cobalt-substituted ADO. The new HPLC-MS assay precisely measures enzymatic activity, revealing retained reactivity in the cobalt-substituted enzyme. The results obtained favor the concurrent dioxygen transfer mechanism in ADO. This combined approach provides a powerful tool for studying other non-heme iron thiol oxidizing enzymes.
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Affiliation(s)
- Ran Duan
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, United States
| | - Jiasong Li
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, United States
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, United States.
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4
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Paris JC, Hei Cheung Y, Zhang T, Chang WC, Liu P, Guo Y. New Frontiers in Nonheme Enzymatic Oxyferryl Species. Chembiochem 2024:e202400307. [PMID: 38900645 DOI: 10.1002/cbic.202400307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/13/2024] [Accepted: 06/20/2024] [Indexed: 06/22/2024]
Abstract
Non-heme mononuclear iron dependent (NHM-Fe) enzymes exhibit exceedingly diverse catalytic reactivities. Despite their catalytic versatilities, the mononuclear iron centers in these enzymes show a relatively simple architecture, in which an iron atom is ligated with 2-4 amino acid residues, including histidine, aspartic or glutamic acid. In the past two decades, a common high-valent reactive iron intermediate, the S=2 oxyferryl (Fe(IV)-oxo or Fe(IV)=O) species, has been repeatedly discovered in NHM-Fe enzymes containing a 2-His-Fe or 2-His-1-carboxylate-Fe center. However, for 3-His/4-His-Fe enzymes, no common reactive intermediate has been identified. Recently, we have spectroscopically characterized the first S=1 Fe(IV) intermediate in a 3-His-Fe containing enzyme, OvoA, which catalyzes a novel oxidative carbon-sulfur bond formation. In this review, we summarize the broad reactivities demonstrated by S=2 Fe(IV)-oxo intermediates, the discovery of the first S=1 Fe(IV) intermediate in OvoA and the mechanistic implication of such a discovery, and the intrinsic reactivity differences of the S=2 and the S=1 Fe(IV)-oxo species. Finally, we postulate the possible reasons to utilize an S=1 Fe(IV) species in OvoA and their implications to other 3-His/4-His-Fe enzymes.
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Affiliation(s)
- Jared C Paris
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA, 15213, USA
| | - Yuk Hei Cheung
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA, 02215, USA
| | - Tao Zhang
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA, 02215, USA
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, NC, 27695, USA
| | - Pinghua Liu
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA, 02215, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA, 15213, USA
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5
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Pierce BS, Schmittou AN, York NJ, Madigan RP, Nino PF, Foss FW, Lockart MM. Improved resolution of 3-mercaptopropionate dioxygenase active site provided by ENDOR spectroscopy offers insight into catalytic mechanism. J Biol Chem 2024; 300:105777. [PMID: 38395308 PMCID: PMC10966181 DOI: 10.1016/j.jbc.2024.105777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
3-mercaptopropionate (3MPA) dioxygenase (MDO) is a mononuclear nonheme iron enzyme that catalyzes the O2-dependent oxidation of thiol-bearing substrates to yield the corresponding sulfinic acid. MDO is a member of the cysteine dioxygenase family of small molecule thiol dioxygenases and thus shares a conserved sequence of active site residues (Serine-155, Histidine-157, and Tyrosine-159), collectively referred to as the SHY-motif. It has been demonstrated that these amino acids directly interact with the mononuclear Fe-site, influencing steady-state catalysis, catalytic efficiency, O2-binding, and substrate coordination. However, the underlying mechanism by which this is accomplished is poorly understood. Here, pulsed electron paramagnetic resonance spectroscopy [1H Mims electron nuclear double resonance spectroscopy] is applied to validate density functional theory computational models for the MDO Fe-site simultaneously coordinated by substrate and nitric oxide (NO), (3MPA/NO)-MDO. The enhanced resolution provided by electron nuclear double resonance spectroscopy allows for direct observation of Fe-bound substrate conformations and H-bond donation from Tyr159 to the Fe-bound NO ligand. Further inclusion of SHY-motif residues within the validated model reveals a distinct channel restricting movement of the Fe-bound NO-ligand. It has been argued that the iron-nitrosyl emulates the structure of potential Fe(III)-superoxide intermediates within the MDO catalytic cycle. While the merit of this assumption remains unconfirmed, the model reported here offers a framework to evaluate oxygen binding at the substrate-bound Fe-site and possible reaction mechanisms. It also underscores the significance of hydrogen bonding interactions within the enzymatic active site.
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Affiliation(s)
- Brad S Pierce
- Department of Chemistry & Biochemistry, University of Alabama, Tuscaloosa, Alabama, USA.
| | - Allison N Schmittou
- Department of Chemistry & Biochemistry, University of Alabama, Tuscaloosa, Alabama, USA
| | - Nicholas J York
- Department of Chemistry & Biochemistry, University of Alabama, Tuscaloosa, Alabama, USA
| | - Ryan P Madigan
- Department of Chemistry & Biochemistry, The University of Texas at Arlington, Arlington, Texas, USA
| | - Paula F Nino
- Department of Chemistry & Biochemistry, The University of Texas at Arlington, Arlington, Texas, USA
| | - Frank W Foss
- Department of Chemistry & Biochemistry, The University of Texas at Arlington, Arlington, Texas, USA
| | - Molly M Lockart
- Department of Chemistry and Biochemistry, Samford University, Homewood, Alabama, USA.
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6
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Schultz RL, Sabat G, Fox BG, Brunold TC. A Single DNA Point Mutation Leads to the Formation of a Cysteine-Tyrosine Crosslink in the Cysteine Dioxygenase from Bacillus subtilis. Biochemistry 2023; 62:1964-1975. [PMID: 37285547 PMCID: PMC10697556 DOI: 10.1021/acs.biochem.3c00083] [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] [Indexed: 06/09/2023]
Abstract
Cysteine dioxygenase (CDO) is a non-heme iron-containing enzyme that catalyzes the oxidation of cysteine (Cys) to cysteine sulfinic acid (CSA). Crystal structures of eukaryotic CDOs revealed the presence of an unusual crosslink between the sulfur of a cysteine residue (C93 in Mus musculus CDO, MmCDO) and a carbon atom adjacent to the phenyl group of a tyrosine residue (Y157). Formation of this crosslink occurs over time as a byproduct of catalysis and increases the catalytic efficiency of CDO by at least 10-fold. Interestingly, in bacterial CDOs, the residue corresponding to C93 is replaced by a highly conserved glycine (G82 in Bacillus subtilis CDO, BsCDO), which precludes the formation of a C-Y crosslink in these enzymes; yet bacterial CDOs achieve turnover rates paralleling those of fully crosslinked eukaryotic CDOs. In the present study, we prepared the G82C variant of BsCDO to determine if a single DNA point mutation could lead to C-Y crosslink formation in this enzyme. We used gel electrophoresis, peptide mass spectrometry, electron paramagnetic resonance spectroscopy, and kinetic assays to characterize this variant alongside the natively crosslinked wild-type (WT) MmCDO and the natively non-crosslinked WT BsCDO. Collectively, our results provide compelling evidence that the G82C BsCDO variant is indeed capable of C-Y crosslink formation. Our kinetic studies indicate that G82C BsCDO has a reduced catalytic efficiency compared to WT BsCDO and that activity increases as the ratio of crosslinked to non-crosslinked enzyme increases. Finally, by carrying out a bioinformatic analysis of the CDO family, we were able to identify a large number of putatively crosslinked bacterial CDOs, the majority of which are from Gram-negative pathogenic bacteria.
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Affiliation(s)
- Rebecca L. Schultz
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Grzegorz Sabat
- Mass Spectrometry Core, Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Brian G. Fox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Thomas C. Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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7
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Miller JR, Brunold TC. Spectroscopic analysis of the mammalian enzyme cysteine dioxygenase. Methods Enzymol 2023; 682:101-135. [PMID: 36948699 PMCID: PMC11230041 DOI: 10.1016/bs.mie.2023.01.002] [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] [Indexed: 02/17/2023]
Abstract
l-Cysteine (Cys) is an essential building block for the synthesis of new proteins and serves as a precursor for several biologically important sulfur-containing molecules, such as coenzyme A, taurine, glutathione, and inorganic sulfate. However, organisms must tightly regulate the concentration of free Cys, as elevated levels of this semi-essential amino acid can be extremely harmful. The non-heme iron enzyme cysteine dioxygenase (CDO) serves to maintain the proper levels of Cys by catalyzing its oxidation to cysteine sulfinic acid. Crystal structures of resting and substrate-bound mammalian CDO revealed two surprising structural motifs in the first and second coordination spheres of the Fe center. The first is the existence of a neutral three histidine (3-His) facial triad that coordinates the Fe ion, as opposed to an anionic 2-His-1-carboxylate facial triad that is typically observed in mononuclear non-heme Fe(II) dioxygenases. The second unusual structural feature exhibited by mammalian CDO is the presence of a covalent crosslink between the sulfur of a Cys residue and an ortho-carbon of a tyrosine residue. Spectroscopic studies of CDO have provided invaluable insights into the roles that these unusual features play with regards to substrate Cys and co-substrate O2 binding and activation. In this chapter, we summarize results obtained from electronic absorption, electron paramagnetic resonance, magnetic circular dichroism, resonance Raman, and Mössbauer spectroscopic studies of mammalian CDO carried out in the last two decades. Pertinent results obtained from complementary computational studies are also briefly summarized.
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Affiliation(s)
- Joshua R Miller
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States.
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8
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Fernandez RL, Juntunen ND, Brunold TC. Differences in the Second Coordination Sphere Tailor the Substrate Specificity and Reactivity of Thiol Dioxygenases. Acc Chem Res 2022; 55:2480-2490. [PMID: 35994511 PMCID: PMC9583696 DOI: 10.1021/acs.accounts.2c00359] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In recent years, considerable progress has been made toward elucidating the geometric and electronic structures of thiol dioxygenases (TDOs). TDOs catalyze the conversion of substrates with a sulfhydryl group to their sulfinic acid derivatives via the addition of both oxygen atoms from molecular oxygen. All TDOs discovered to date belong to the family of cupin-type mononuclear nonheme Fe(II)-dependent metalloenzymes. While most members of this enzyme family bind the Fe cofactor by two histidines and one carboxylate side chain (2-His-1-carboxylate) to provide a monoanionic binding motif, TDOs feature a neutral three histidine (3-His) facial triad. In this Account, we present a bioinformatics analysis and multiple sequence alignment that highlight the significance of the secondary coordination sphere in tailoring the substrate specificity and reactivity among the different TDOs. These insights provide the framework within which important structural and functional features of the distinct TDOs are discussed.The best studied TDO is cysteine dioxygenase (CDO), which catalyzes the conversion of cysteine to cysteine sulfinic acid in both eukaryotes and prokaryotes. Crystal structures of resting and substrate-bound mammalian CDOs revealed two surprising structural motifs in the first- and second coordination spheres of the Fe center. The first is the presence of the abovementioned neutral 3-His facial triad that coordinates the Fe ion. The second is the existence of a covalent cross-link between the sulfur of Cys93 and an ortho carbon of Tyr157 (mouse CDO numbering scheme). While the exact role of this cross-link remains incompletely understood, various studies established that it is needed for proper substrate Cys positioning and gating solvent access to the active site. Intriguingly, bacterial CDOs lack the Cys-Tyr cross-link; yet, they are as active as cross-linked eukaryotic CDOs.The other known mammalian TDO is cysteamine dioxygenase (ADO). Initially, it was believed that ADO solely catalyzes the oxidation of cysteamine to hypotaurine. However, it has recently been shown that ADO additionally oxidizes N-terminal cysteine (Nt-Cys) peptides, which indicates that ADO may play a much more significant role in mammalian physiology than was originally anticipated. Though predicted on the basis of sequence alignment, site-directed mutagenesis, and spectroscopic studies, it was not until last year that two crystal structures, one of wild-type mouse ADO (solved by us) and the other of a variant of nickel-substituted human ADO, finally provided direct evidence that this enzyme also features a 3-His facial triad. These structures additionally revealed several features that are unique to ADO, including a putative cosubstrate O2 access tunnel that is lined by two Cys residues. Disulfide formation under conditions of high O2 levels may serve as a gating mechanism to prevent ADO from depleting organisms of Nt-Cys-containing molecules.The combination of kinetic and spectroscopic studies in conjunction with structural characterizations of TDOs has furthered our understanding of enzymatic sulfhydryl substrate regulation. In this article, we take advantage of the fact that the ADO X-ray crystal structures provided the final piece needed to compare and contrast key features of TDOs, an essential family of metalloenzymes found across all kingdoms of life.
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Affiliation(s)
- Rebeca L. Fernandez
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Nicholas D. Juntunen
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Thomas C. Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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9
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Sajed S, Kolahdouz M, Sadeghi MA. Prediction of Arsenic Concentration in Water Samples Using Digital Imaging Colorimetry and Multi‐Variable Regression. ChemistrySelect 2022. [DOI: 10.1002/slct.202201376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Samira Sajed
- School of Electrical and Computer Engineering College of Engineering University of Tehran Tehran Iran
| | - Mohammadreza Kolahdouz
- School of Electrical and Computer Engineering College of Engineering University of Tehran Tehran Iran
| | - Mohammad Amin Sadeghi
- School of Electrical and Computer Engineering College of Engineering University of Tehran Tehran Iran
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10
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Correy GJ, Kneller DW, Phillips G, Pant S, Russi S, Cohen AE, Meigs G, Holton JM, Gahbauer S, Thompson MC, Ashworth A, Coates L, Kovalevsky A, Meilleur F, Fraser JS. The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature. SCIENCE ADVANCES 2022; 8:eabo5083. [PMID: 35622909 PMCID: PMC9140965 DOI: 10.1126/sciadv.abo5083] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/11/2022] [Indexed: 05/04/2023]
Abstract
The nonstructural protein 3 (NSP3) macrodomain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Mac1) removes adenosine diphosphate (ADP) ribosylation posttranslational modifications, playing a key role in the immune evasion capabilities of the virus responsible for the coronavirus disease 2019 pandemic. Here, we determined neutron and x-ray crystal structures of the SARS-CoV-2 NSP3 macrodomain using multiple crystal forms, temperatures, and pHs, across the apo and ADP-ribose-bound states. We characterize extensive solvation in the Mac1 active site and visualize how water networks reorganize upon binding of ADP-ribose and non-native ligands, inspiring strategies for displacing waters to increase the potency of Mac1 inhibitors. Determining the precise orientations of active site water molecules and the protonation states of key catalytic site residues by neutron crystallography suggests a catalytic mechanism for coronavirus macrodomains distinct from the substrate-assisted mechanism proposed for human MacroD2. These data provoke a reevaluation of macrodomain catalytic mechanisms and will guide the optimization of Mac1 inhibitors.
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Affiliation(s)
- Galen J. Correy
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
| | - Swati Pant
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - George Meigs
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James M. Holton
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael C. Thompson
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA 95343, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Leighton Coates
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
- Second Target Station, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
| | - Flora Meilleur
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
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11
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Abstract
Here, the choice of the first coordination shell of the metal center is analyzed from the perspective of charge maintenance in a binary enzyme-substrate complex and an O2-bound ternary complex in the nonheme iron oxygenases. Comparing homogentisate 1,2-dioxygenase and gentisate dioxygenase highlights the significance of charge maintenance after substrate binding as an important factor that drives the reaction coordinate. We then extend the charge analysis to several common types of nonheme iron oxygenases containing either a 2-His-1-carboxylate facial triad or a 3-His or 4-His ligand motif, including extradiol and intradiol ring-cleavage dioxygenases, thiol dioxygenases, α-ketoglutarate-dependent oxygenases, and carotenoid cleavage oxygenases. After forming the productive enzyme-substrate complex, the overall charge of the iron complex at the 0, +1, or +2 state is maintained in the remaining catalytic steps. Hence, maintaining a constant charge is crucial to promote the reaction of the iron center beginning from the formation of the Michaelis or ternary complex. The charge compensation to the iron ion is tuned not only by protein-derived carboxylate ligands but also by substrates. Overall, these analyses indicate that charge maintenance at the iron center is significant when all the necessary components form a productive complex. This charge maintenance concept may apply to most oxygen-activating metalloenzymes systems that do not draw electrons and protons step-by-step from a separate reactant, such as NADH, via a reductase. The charge maintenance perception may also be useful in proposing catalytic pathways or designing prototypical reactions using artificial or engineered enzymes for biotechnological applications.
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Affiliation(s)
- Ephrahime S. Traore
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Aimin Liu
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
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12
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Correy GJ, Kneller DW, Phillips G, Pant S, Russi S, Cohen AE, Meigs G, Holton JM, Gahbauer S, Thompson MC, Ashworth A, Coates L, Kovalevsky A, Meilleur F, Fraser JS. The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and X-ray diffraction at room temperature. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.02.07.479477. [PMID: 35169801 PMCID: PMC8845425 DOI: 10.1101/2022.02.07.479477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The NSP3 macrodomain of SARS CoV 2 (Mac1) removes ADP-ribosylation post-translational modifications, playing a key role in the immune evasion capabilities of the virus responsible for the COVID-19 pandemic. Here, we determined neutron and X-ray crystal structures of the SARS-CoV-2 NSP3 macrodomain using multiple crystal forms, temperatures, and pHs, across the apo and ADP-ribose-bound states. We characterize extensive solvation in the Mac1 active site, and visualize how water networks reorganize upon binding of ADP-ribose and non-native ligands, inspiring strategies for displacing waters to increase potency of Mac1 inhibitors. Determining the precise orientations of active site water molecules and the protonation states of key catalytic site residues by neutron crystallography suggests a catalytic mechanism for coronavirus macrodomains distinct from the substrate-assisted mechanism proposed for human MacroD2. These data provoke a re-evaluation of macrodomain catalytic mechanisms and will guide the optimization of Mac1 inhibitors.
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Affiliation(s)
- Galen J Correy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Daniel W Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Swati Pant
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - George Meigs
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, CA 94158, USA
| | - James M Holton
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, CA 94158, USA
| | - Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Michael C Thompson
- Department of Chemistry and Chemical Biology, University of California Merced, CA 95343, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer, University of California San Francisco, CA 94158, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Flora Meilleur
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
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13
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Wang Y, Shin I, Li J, Liu A. Crystal structure of human cysteamine dioxygenase provides a structural rationale for its function as an oxygen sensor. J Biol Chem 2021; 297:101176. [PMID: 34508780 PMCID: PMC8503633 DOI: 10.1016/j.jbc.2021.101176] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/03/2021] [Accepted: 09/05/2021] [Indexed: 01/03/2023] Open
Abstract
Cysteamine dioxygenase (ADO) plays a vital role in regulating thiol metabolism and preserving oxygen homeostasis in humans by oxidizing the sulfur of cysteamine and N-terminal cysteine-containing proteins to their corresponding sulfinic acids using O2 as a cosubstrate. However, as the only thiol dioxygenase that processes both small-molecule and protein substrates, how ADO handles diverse substrates of disparate sizes to achieve various reactions is not understood. The knowledge gap is mainly due to the three-dimensional structure not being solved, as ADO cannot be directly compared with other known thiol dioxygenases. Herein, we report the first crystal structure of human ADO at a resolution of 1.78 Å with a nickel-bound metal center. Crystallization was achieved through both metal substitution and C18S/C239S double mutations. The metal center resides in a tunnel close to an entry site flanked by loops. While ADO appears to use extensive flexibility to handle substrates of different sizes, it also employs proline and proline pairs to maintain the core protein structure and to retain the residues critical for catalysis in place. This feature distinguishes ADO from thiol dioxygenases that only oxidize small-molecule substrates, possibly explaining its divergent substrate specificity. Our findings also elucidate the structural basis for ADO functioning as an oxygen sensor by modifying N-degron substrates to transduce responses to hypoxia. Thus, this work fills a gap in structure–function relationships of the thiol dioxygenase family and provides a platform for further mechanistic investigation and therapeutic intervention targeting impaired oxygen sensing.
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, The University of Texas at San Antonio, Texas, USA
| | - Inchul Shin
- Department of Chemistry, The University of Texas at San Antonio, Texas, USA
| | - Jiasong Li
- Department of Chemistry, The University of Texas at San Antonio, Texas, USA
| | - Aimin Liu
- Department of Chemistry, The University of Texas at San Antonio, Texas, USA.
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14
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Gunawardana DM, Heathcote KC, Flashman E. Emerging roles for thiol dioxygenases as oxygen sensors. FEBS J 2021; 289:5426-5439. [PMID: 34346181 DOI: 10.1111/febs.16147] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/21/2021] [Accepted: 08/03/2021] [Indexed: 12/22/2022]
Abstract
Cysteine dioxygenases, 3-mercaptopropionate dioxygenases and mercaptosuccinate dioxygenases are all thiol dioxygenases (TDOs) that catalyse oxidation of thiol molecules to sulphinates. They are Fe(II)-dependent dioxygenases with a cupin fold that supports a 3xHis metal-coordinating triad at the active site. They also have other, broadly common features including arginine residues involved in substrate carboxylate binding and a conserved trio of residues at the active site featuring a tyrosine important in substrate binding catalysis. Recently, N-terminal cysteinyl dioxygenase enzymes (NCOs) have been identified in plants (plant cysteine oxidases, PCOs), while human 2-aminoethanethiol dioxygenase (ADO) has been shown to act as both an NCO and a small molecule TDO. Although the cupin fold and 3xHis Fe(II)-binding triad seen in the small molecule TDOs are conserved in NCOs, other active site features and aspects of the overall protein architecture are quite different. Furthermore, the PCOs and ADO appear to act as biological O2 sensors, as shown by kinetic analyses and hypoxic regulation of the stability of their biological targets (N-terminal cysteine oxidation triggers protein degradation via the N-degron pathway). Here, we discuss the emergence of these two subclasses of TDO including structural features that could dictate their ability to bind small molecule or polypeptide substrates. These structural features may also underpin the O2 -sensing capability of the NCOs. Understanding how these enzymes interact with their substrates, including O2 , could reveal strategies to manipulate their activity, relevant to hypoxic disease states and plant adaptive responses to flooding.
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15
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York NJ, Lockart MM, Sardar S, Khadka N, Shi W, Stenkamp RE, Zhang J, Kiser PD, Pierce BS. Structure of 3-mercaptopropionic acid dioxygenase with a substrate analog reveals bidentate substrate binding at the iron center. J Biol Chem 2021; 296:100492. [PMID: 33662397 PMCID: PMC8050391 DOI: 10.1016/j.jbc.2021.100492] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/18/2021] [Accepted: 02/26/2021] [Indexed: 12/20/2022] Open
Abstract
Thiol dioxygenases are a subset of nonheme iron oxygenases that catalyze the formation of sulfinic acids from sulfhydryl-containing substrates and dioxygen. Among this class, cysteine dioxygenases (CDOs) and 3-mercaptopropionic acid dioxygenases (3MDOs) are the best characterized, and the mode of substrate binding for CDOs is well understood. However, the manner in which 3-mercaptopropionic acid (3MPA) coordinates to the nonheme iron site in 3MDO remains a matter of debate. A model for bidentate 3MPA coordination at the 3MDO Fe-site has been proposed on the basis of computational docking, whereas steady-state kinetics and EPR spectroscopic measurements suggest a thiolate-only coordination of the substrate. To address this gap in knowledge, we determined the structure of Azobacter vinelandii 3MDO (Av3MDO) in complex with the substrate analog and competitive inhibitor, 3-hydroxypropionic acid (3HPA). The structure together with DFT computational modeling demonstrates that 3HPA and 3MPA associate with iron as chelate complexes with the substrate-carboxylate group forming an additional interaction with Arg168 and the thiol bound at the same position as in CDO. A chloride ligand was bound to iron in the coordination site assigned as the O2-binding site. Supporting HYSCORE spectroscopic experiments were performed on the (3MPA/NO)-bound Av3MDO iron nitrosyl (S = 3/2) site. In combination with spectroscopic simulations and optimized DFT models, this work provides an experimentally verified model of the Av3MDO enzyme-substrate complex, effectively resolving a debate in the literature regarding the preferred substrate-binding denticity. These results elegantly explain the observed 3MDO substrate specificity, but leave unanswered questions regarding the mechanism of substrate-gated reactivity with dioxygen.
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Affiliation(s)
- Nicholas J York
- Department of Chemistry & Biochemistry, University of Alabama, Tuscaloosa, Alabama, USA
| | - Molly M Lockart
- Department of Chemistry & Biochemistry, University of Alabama, Tuscaloosa, Alabama, USA
| | - Sinjinee Sardar
- Department of Chemistry & Biochemistry, The University of Texas at Arlington, Arlington, Texas, USA
| | - Nimesh Khadka
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Wuxian Shi
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, New York, USA
| | - Ronald E Stenkamp
- Departments of Biological Structure and Biochemistry, University of Washington, Seattle, Washington, USA
| | - Jianye Zhang
- Department of Ophthalmology, School of Medicine, University of California, Irvine, Irvine, California, USA
| | - Philip D Kiser
- Department of Ophthalmology, School of Medicine, University of California, Irvine, Irvine, California, USA; Department of Physiology & Biophysics, School of Medicine, University of California, Irvine, Irvine, California, USA; Research Service, VA Long Beach Healthcare System, Long Beach, California, USA.
| | - Brad S Pierce
- Department of Chemistry & Biochemistry, University of Alabama, Tuscaloosa, Alabama, USA.
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16
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Kneller DW, Phillips G, O’Neill HM, Tan K, Joachimiak A, Coates L, Kovalevsky A. Room-temperature X-ray crystallography reveals the oxidation and reactivity of cysteine residues in SARS-CoV-2 3CL M pro: insights into enzyme mechanism and drug design. IUCRJ 2020; 7:S2052252520012634. [PMID: 33063790 PMCID: PMC7553146 DOI: 10.1107/s2052252520012634] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/16/2020] [Indexed: 05/12/2023]
Abstract
The emergence of the novel coronavirus SARS-CoV-2 has resulted in a worldwide pandemic not seen in generations. Creating treatments and vaccines to battle COVID-19, the disease caused by the virus, is of paramount importance in order to stop its spread and save lives. The viral main protease, 3CL Mpro, is indispensable for the replication of SARS-CoV-2 and is therefore an important target for the design of specific protease inhibitors. Detailed knowledge of the structure and function of 3CL Mpro is crucial to guide structure-aided and computational drug-design efforts. Here, the oxidation and reactivity of the cysteine residues of the protease are reported using room-temperature X-ray crystallography, revealing that the catalytic Cys145 can be trapped in the peroxysulfenic acid oxidation state at physiological pH, while the other surface cysteines remain reduced. Only Cys145 and Cys156 react with the alkylating agent N-ethylmaleimide. It is suggested that the zwitterionic Cys145-His45 catalytic dyad is the reactive species that initiates catalysis, rather than Cys145-to-His41 proton transfer via the general acid-base mechanism upon substrate binding. The structures also provide insight into the design of improved 3CL Mpro inhibitors.
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Affiliation(s)
- Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Hugh M. O’Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Kemin Tan
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
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17
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White MD, Dalle Carbonare L, Lavilla Puerta M, Iacopino S, Edwards M, Dunne K, Pires E, Levy C, McDonough MA, Licausi F, Flashman E. Structures of Arabidopsis thaliana oxygen-sensing plant cysteine oxidases 4 and 5 enable targeted manipulation of their activity. Proc Natl Acad Sci U S A 2020; 117:23140-23147. [PMID: 32868422 PMCID: PMC7502726 DOI: 10.1073/pnas.2000206117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In higher plants, molecular responses to exogenous hypoxia are driven by group VII ethylene response factors (ERF-VIIs). These transcriptional regulators accumulate in the nucleus under hypoxia to activate anaerobic genes but are destabilized in normoxic conditions through the action of oxygen-sensing plant cysteine oxidases (PCOs). The PCOs catalyze the reaction of oxygen with the conserved N-terminal cysteine of ERF-VIIs to form cysteine sulfinic acid, triggering degradation via the Cys/Arg branch of the N-degron pathway. The PCOs are therefore a vital component of the plant oxygen signaling system, connecting environmental stimulus with cellular and physiological response. Rational manipulation of PCO activity could regulate ERF-VII levels and improve flood tolerance, but requires detailed structural information. We report crystal structures of the constitutively expressed PCO4 and PCO5 from Arabidopsis thaliana to 1.24 and 1.91 Å resolution, respectively. The structures reveal that the PCOs comprise a cupin-like scaffold, which supports a central metal cofactor coordinated by three histidines. While this overall structure is consistent with other thiol dioxygenases, closer inspection of the active site indicates that other catalytic features are not conserved, suggesting that the PCOs may use divergent mechanisms to oxidize their substrates. Conservative substitution of two active site residues had dramatic effects on PCO4 function both in vitro and in vivo, through yeast and plant complementation assays. Collectively, our data identify key structural elements that are required for PCO activity and provide a platform for engineering crops with improved hypoxia tolerance.
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Affiliation(s)
- Mark D White
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- School of Chemistry, University of Sydney, Sydney NSW 2006, Australia
| | | | - Mikel Lavilla Puerta
- Plantlab, Institute of Life Sciences, Scuola Superiore Sant'Anna, 56010 Pisa, Italy
| | - Sergio Iacopino
- Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom
| | - Martin Edwards
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Kate Dunne
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Elisabete Pires
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Colin Levy
- Manchester Institute of Biotechnology, University of Manchester, M1 7DN Manchester, United Kingdom
| | - Michael A McDonough
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Francesco Licausi
- Plantlab, Institute of Life Sciences, Scuola Superiore Sant'Anna, 56010 Pisa, Italy
- Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom
| | - Emily Flashman
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom;
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18
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Müller L, Hoof S, Keck M, Herwig C, Limberg C. Enhancing Tris(pyrazolyl)borate-Based Models of Cysteine/Cysteamine Dioxygenases through Steric Effects: Increased Reactivities, Full Product Characterization and Hints to Initial Superoxide Formation. Chemistry 2020; 26:11851-11861. [PMID: 32432367 PMCID: PMC7540079 DOI: 10.1002/chem.202001818] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 02/03/2023]
Abstract
The design of biomimetic model complexes for the cysteine dioxygenase (CDO) and cysteamine dioxygenase (ADO) is reported, where the 3-His coordination of the iron ion is simulated by three pyrazole donors of a trispyrazolyl borate ligand (Tp) and protected cysteine and cysteamine represent substrate ligands. It is found that the replacement of phenyl groups-attached at the 3-positions of the pyrazole units in a previous model-by mesityl residues has massive consequences, as the latter arrange to a more spacious reaction pocket. Thus, the reaction with O2 proceeds much faster and afterwards the first structural characterization of an iron(II) η2 -O,O-sulfinate product became possible. If one of the three Tp-mesityl groups is placed in the 5-position, an even larger reaction pocket results, which leads to yet faster rates and accumulation of a reaction intermediate at low temperatures, as shown by UV/Vis and Mössbauer spectroscopy. After comparison with the results of investigations on the cobalt analogues this intermediate is tentatively assigned to an iron(III) superoxide species.
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Affiliation(s)
- Lars Müller
- Institut für ChemieHumboldt-Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Santina Hoof
- Institut für ChemieHumboldt-Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Matthias Keck
- Institut für ChemieHumboldt-Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Christian Herwig
- Institut für ChemieHumboldt-Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Christian Limberg
- Institut für ChemieHumboldt-Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
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19
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Flückger S, Igareta NV, Seebeck FP. Convergent Evolution of Fungal Cysteine Dioxygenases. Chembiochem 2020; 21:3082-3086. [PMID: 32543095 DOI: 10.1002/cbic.202000317] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/11/2020] [Indexed: 12/16/2022]
Abstract
Cupin-type cysteine dioxygenases (CDOs) are non-heme iron enzymes that occur in animals, plants, bacteria and in filamentous fungi. In this report, we show that agaricomycetes contain an entirely unrelated type of CDO that emerged by convergent evolution from enzymes involved in the biosynthesis of ergothioneine. The activity of this CDO type is dependent on the ergothioneine precursor N-α-trimethylhistidine. The metabolic link between ergothioneine production and cysteine oxidation suggests that the two processes might be part of the same chemical response in fungi, for example against oxidative stress.
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Affiliation(s)
- Sebastian Flückger
- Department for Chemistry, University of Basel, Mattenstrasse 24a, 4002, Basel, Switzerland
| | - Nico V Igareta
- Department for Chemistry, University of Basel, Mattenstrasse 24a, 4002, Basel, Switzerland
| | - Florian P Seebeck
- Department for Chemistry, University of Basel, Mattenstrasse 24a, 4002, Basel, Switzerland
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20
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Fernandez RL, Dillon SL, Stipanuk MH, Fox BG, Brunold TC. Spectroscopic Investigation of Cysteamine Dioxygenase. Biochemistry 2020; 59:2450-2458. [PMID: 32510930 DOI: 10.1021/acs.biochem.0c00267] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thiol dioxygenases are mononuclear non-heme FeII-dependent metalloenzymes that initiate the oxidative catabolism of thiol-containing substrates to their respective sulfinates. Cysteine dioxygenase (CDO), the best characterized mammalian thiol dioxygenase, contains a three-histidine (3-His) coordination environment rather than the 2-His-1-carboxylate facial triad seen in most mononuclear non-heme FeII enzymes. A similar 3-His active site is found in the bacterial thiol dioxygenase 3-mercaptopropionate dioxygenase (MDO), which converts 3-mercaptopropionate into 3-sulfinopropionic acid as part of the bacterial sulfur metabolism pathway. In this study, we have investigated the active site geometric and electronic structures of a third non-heme FeII-dependent thiol dioxygenase, cysteamine dioxygenase (ADO), by using a spectroscopic approach. Although a 3-His facial triad had previously been implicated on the basis of sequence alignment and site-directed mutagenesis studies, little is currently known about the active site environment of ADO. Our magnetic circular dichroism and electron paramagnetic resonance data provide compelling evidence that ADO features a 3-His facial triad, like CDO and MDO. Despite this similar coordination environment, spectroscopic results obtained for ADO incubated with various substrate analogues are distinct from those obtained for the other FeII-dependent thiol dioxygenases. This finding suggests that the secondary coordination sphere of ADO is distinct from those of CDO and MDO, demonstrating the significant role that secondary-sphere residues play in dictating substrate specificity.
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Affiliation(s)
- Rebeca L Fernandez
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Stephanie L Dillon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Martha H Stipanuk
- Department of Nutritional Sciences, Cornell University, Ithaca, New York 14853, United States
| | - Brian G Fox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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21
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Forbes DL, Meneely KM, Chilton AS, Lamb AL, Ellis HR. The 3-His Metal Coordination Site Promotes the Coupling of Oxygen Activation to Cysteine Oxidation in Cysteine Dioxygenase. Biochemistry 2020; 59:2022-2031. [PMID: 32368901 DOI: 10.1021/acs.biochem.9b01085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cysteine dioxygenase (CDO) structurally resembles cupin enzymes that use a 3-His/1-Glu coordination scheme. However, the glutamate ligand is substituted with a cysteine (Cys93) residue, which forms a thioether bond with tyrosine (Tyr157) under physiological conditions. The reversion variant, C93E CDO, was generated in order to reestablish the more common 3-His/1-Glu metal ligands of the cupin superfamily. This variant provides a framework for testing the structural and functional significance of Cys93 and the cross-link in CDO. Although dioxygen consumption was observed with C93E CDO, it was not coupled with l-cysteine oxidation. Substrate analogues (d-cysteine, cysteamine, and 3-mercaptopropionate) were not viable substrates for the C93E CDO variant, although they showed variable coordinations to the iron center. The structures of C93E and cross-linked and non-cross-linked wild-type CDO were solved by X-ray crystallography to 1.91, 2.49, and 2.30 Å, respectively. The C93E CDO variant had similar overall structural properties compared to cross-linked CDO; however, the iron was coordinated by a 3-His/1-Glu geometry, leaving only two coordination sites available for dioxygen and bidentate l-cysteine binding. The hydroxyl group of Tyr157 shifted in both non-cross-linked and C93E CDO, and this displacement prevented the residue from participating in substrate stabilization. Based on these results, the divergence of the metal center of cysteine dioxygenase from the 3-His/1-Glu geometry seen with many cupin enzymes was essential for effective substrate binding. The substitution of Glu with Cys in CDO allows for a third coordination site on the iron for bidentate cysteine and monodentate oxygen binding.
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Affiliation(s)
- Dianna L Forbes
- The Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Kathleen M Meneely
- Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas 66045, United States
| | - Annemarie S Chilton
- Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas 66045, United States
| | - Audrey L Lamb
- Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas 66045, United States
| | - Holly R Ellis
- The Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
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22
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Visser SP. Second‐Coordination Sphere Effects on Selectivity and Specificity of Heme and Nonheme Iron Enzymes. Chemistry 2020; 26:5308-5327. [DOI: 10.1002/chem.201905119] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/04/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Sam P. Visser
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical ScienceThe University of Manchester 131 Princess Street Manchester M1 7DN UK
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23
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Sardar S, Weitz A, Hendrich MP, Pierce BS. Outer-Sphere Tyrosine 159 within the 3-Mercaptopropionic Acid Dioxygenase S-H-Y Motif Gates Substrate-Coordination Denticity at the Non-Heme Iron Active Site. Biochemistry 2019; 58:5135-5150. [PMID: 31750652 PMCID: PMC10071547 DOI: 10.1021/acs.biochem.9b00674] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thiol dioxygenases are non-heme mononuclear iron enzymes that catalyze the O2-dependent oxidation of free thiols (-SH) to produce the corresponding sulfinic acid (-SO2-). Regardless of the phylogenic domain, the active site for this enzyme class is typically comprised of two major features: (1) a mononuclear ferrous iron coordinated by three protein-derived histidines and (2) a conserved sequence of outer Fe-coordination-sphere amino acids (Ser-His-Tyr) spatially adjacent to the iron site (∼3 Å). Here, we utilize a promiscuous 3-mercaptopropionic acid dioxygenase cloned from Azotobacter vinelandii (Av MDO) to explore the function of the conserved S-H-Y motif. This enzyme exhibits activity with 3-mercaptopropionic acid (3mpa), l-cysteine (cys), as well as several other thiol-bearing substrates, thus making it an ideal system to study the influence of residues within the highly conserved S-H-Y motif (H157 and Y159) on substrate specificity and reactivity. The pKa values for these residues were determined by pH-dependent steady-state kinetics, and their assignments verified by comparison to H157N and Y159F variants. Complementary electron paramagnetic resonance and Mössbauer studies demonstrate a network of hydrogen bonds connecting H157-Y159 and Fe-bound ligands within the enzymatic Fe site. Crucially, these experiments suggest that the hydroxyl group of Y159 hydrogen bonds to Fe-bound NO and, by extension, Fe-bound oxygen during native catalysis. This interaction alters both the NO binding affinity and rhombicity of the 3mpa-bound iron-nitrosyl site. In addition, Fe coordination of cys is switched from thiolate only to bidentate (thiolate/amine) for the Y159F variant, indicating that perturbations within the S-H-Y proton relay network also influence cys Fe binding denticity.
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Affiliation(s)
- Sinjinee Sardar
- Department of Chemistry and Biochemistry , The University of Texas at Arlington , 700 Planetarium Place , Arlington , Texas 76019 , United States
| | - Andrew Weitz
- Department of Chemistry , Carnegie Mellon University , 4400 Fifth Avenue , Pittsburgh , Pennsylvania 15213 , United States
| | - Michael P Hendrich
- Department of Chemistry , Carnegie Mellon University , 4400 Fifth Avenue , Pittsburgh , Pennsylvania 15213 , United States
| | - Brad S Pierce
- Department of Chemistry and Biochemistry , University of Alabama , 250 Hackberry Lane , Tuscaloosa , Alabama 35487 , United States
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24
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Fischer AA, Miller JR, Jodts RJ, Ekanayake DM, Lindeman SV, Brunold TC, Fiedler AT. Spectroscopic and Computational Comparisons of Thiolate-Ligated Ferric Nonheme Complexes to Cysteine Dioxygenase: Second-Sphere Effects on Substrate (Analogue) Positioning. Inorg Chem 2019; 58:16487-16499. [PMID: 31789510 DOI: 10.1021/acs.inorgchem.9b02432] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Parallel spectroscopic and computational studies of iron(III) cysteine dioxygenase (CDO) and synthetic models are presented. The synthetic complexes utilize the ligand tris(4,5-diphenyl-1-methylimidazol-2-yl)phosphine (Ph2TIP), which mimics the facial three-histidine triad of CDO and other thiol dioxygenases. In addition to the previously reported [FeII(CysOEt)(Ph2TIP)]BPh4 (1; CysOEt is the ethyl ester of anionic l-cysteine), the formation and crystallographic characterization of [FeII(2-MTS)(Ph2TIP)]BPh4 (2) is reported, where the methyl 2-thiosalicylate anion (2-MTS) resembles the substrate of 3-mercaptopropionate dioxygenase (MDO). One-electron chemical oxidation of 1 and 2 yields ferric species that bind cyanide and azide anions, which have been used as spectroscopic probes of O2 binding in prior studies of FeIII-CDO. The six-coordinate FeIII-CN and FeIII-N3 adducts are examined with UV-vis absorption, electron paramagnetic resonance (EPR), and resonance Raman (rRaman) spectroscopies. In addition, UV-vis and rRaman studies of cysteine- and cyanide-bound FeIII-CDO are reported for both the wild-type (WT) enzyme and C93G variant, which lacks the Cys-Tyr cross-link that is present in the second coordination sphere of the WT active site. Density functional theory (DFT) and ab initio calculations are employed to provide geometric and electronic structure descriptions of the synthetic and enzymatic FeIII adducts. In particular, it is shown that the complete active space self-consistent field (CASSCF) method, in tandem with n-electron valence state second-order perturbation theory (NEVPT2), is capable of elucidating the structural basis of subtle shifts in EPR g values for low-spin FeIII species.
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Affiliation(s)
- Anne A Fischer
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53201 , United States
| | - Joshua R Miller
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Richard J Jodts
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Danushka M Ekanayake
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53201 , United States
| | - Sergey V Lindeman
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53201 , United States
| | - Thomas C Brunold
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Adam T Fiedler
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53201 , United States
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25
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Zhao C, Fang H, Wang J, Zhang S, Zhao X, Li Z, Lin C, Shen Z, Cheng L. Application of fermentation process control to increase l-tryptophan production in Escherichia coli. Biotechnol Prog 2019; 36:e2944. [PMID: 31804750 DOI: 10.1002/btpr.2944] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 11/04/2019] [Accepted: 11/26/2019] [Indexed: 11/11/2022]
Abstract
In this study, process engineering and process control were applied to increase the production of l-tryptophan using Escherichia coli Dmtr/pta-Y. Different dissolved oxygen (DO) and pH control strategies were applied in l-tryptophan production. DO and pH were maintained at [20% (0-20 hr); 30% (20-40 hr)] and [7.0 (0-20 hr), 6.5 (20-40 hr)], respectively, which increased l-tryptophan production, glucose conversion percentage [g (l-tryptophan)/g (glucose)], and transcription levels of key genes for tryptophan biosynthesis and tryptophan biosynthesis flux, and decreased the accumulation of acetate and transcription levels of genes related to acetate synthesis and acetate synthesis flux. Using E. coli Dmtr/pta-Y with optimized DO [20% (0-20 hr); 30% (20-40 hr)] and pH [7.0 (0-20 hr), 6.5 (20-40 hr)] values, the highest l-tryptophan production (52.57 g/L) and glucose conversion percentage (20.15%) were obtained. The l-tryptophan production was increased by 26.58%, the glucose conversion percentage was increased by 22.64%, and the flux of tryptophan biosynthesis was increased to 21.5% compared with different conditions for DO [50% (0-20 hr), 20% (20-40 hr)] and pH [7.0].
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Affiliation(s)
- Chunguang Zhao
- Key Laboratory of Fermentation Engineering, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China.,School of Agriculture, Ningxia University, Ningxia Eppen Biotech Co., Ltd, Yinchuan, China
| | - Haitian Fang
- School of Agriculture, Ningxia University, Ningxia Eppen Biotech Co., Ltd, Yinchuan, China
| | - Jing Wang
- Key Laboratory of Fermentation Engineering, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China.,Department of Critical Care Medicine, Affiliated Hospital of Binzhou Medical University, Binzhou, China
| | - Shasha Zhang
- Key Laboratory of Fermentation Engineering, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Xiubao Zhao
- Key Laboratory of Fermentation Engineering, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Zengliang Li
- Shandong Research Center of High Cell Density Fermentation and Efficient Expression Technology, Shandong Lvdu Bio-science and Technology Co., Ltd, Binzhou, China
| | - Chuwen Lin
- Key Laboratory of Fermentation Engineering, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China.,Shandong Research Center of High Cell Density Fermentation and Efficient Expression Technology, Shandong Lvdu Bio-science and Technology Co., Ltd, Binzhou, China
| | - Zhiqiang Shen
- Key Laboratory of Fermentation Engineering, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China.,Shandong Research Center of High Cell Density Fermentation and Efficient Expression Technology, Shandong Lvdu Bio-science and Technology Co., Ltd, Binzhou, China
| | - Likun Cheng
- Key Laboratory of Fermentation Engineering, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China.,Shandong Research Center of High Cell Density Fermentation and Efficient Expression Technology, Shandong Lvdu Bio-science and Technology Co., Ltd, Binzhou, China
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26
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Anandababu K, Ramasubramanian R, Wadepohl H, Comba P, Johnee Britto N, Jaccob M, Mayilmurugan R. A Structural and Functional Model for the Tris-Histidine Motif in Cysteine Dioxygenase. Chemistry 2019; 25:9540-9547. [PMID: 31090109 DOI: 10.1002/chem.201901005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/23/2019] [Indexed: 01/14/2023]
Abstract
The iron(II) complexes [Fe(L)(MeCN)3 ](SO3 CF3 )2 (L are two derivatives of tris(2-pyridyl)-based ligands) have been synthesized as models for cysteine dioxygenase (CDO). The molecular structure of one of the complexes exhibits octahedral coordination geometry and the Fe-Npy bond lengths [1.953(4)-1.972(4) Å] are similar to those in the Cys-bound FeII -CDO; Fe-NHis : 1.893-2.199 Å. The iron(II) centers of the model complexes exhibit relatively high FeIII/II redox potentials (E1/2 =0.988-1.380 V vs. ferrocene/ferrocenium electrode, Fc/Fc+ ), within the range for O2 activation and typical for the corresponding nonheme iron enzymes. The reaction of in situ generated [Fe(L)(MeCN)(SPh)]+ with excess O2 in acetonitrile (MeCN) yields selectively the doubly oxygenated phenylsulfinic acid product. Isotopic labeling studies using 18 O2 confirm the incorporation of both oxygen atoms of O2 into the product. Kinetic and preliminary DFT studies reveal the involvement of an FeIII peroxido intermediate with a rhombic S= 1 / 2 FeIII center (687-696 nm; g≈2.46-2.48, 2.13-2.15, 1.92-1.94), similar to the spectroscopic signature of the low-spin Cys-bound FeIII CDO (650 nm, g≈2.47, 2.29, 1.90). The proposed FeIII peroxido intermediates have been trapped, and the O-O stretching frequencies are in the expected range (approximately 920 and 820 cm-1 for the alkyl- and hydroperoxido species, respectively). The model complexes have a structure similar to that of the enzyme and structural aspects as well as the reactivity are discussed.
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Affiliation(s)
- Karunanithi Anandababu
- Bioinorganic Chemistry Laboratory/Physical Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai, 625021, India
| | - Ramamoorthy Ramasubramanian
- Bioinorganic Chemistry Laboratory/Physical Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai, 625021, India
| | - Hubert Wadepohl
- Anorganisch-Chemisches Institut and Interdisciplinary Center for Scientific Computing, Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Peter Comba
- Anorganisch-Chemisches Institut and Interdisciplinary Center for Scientific Computing, Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | | | - Madhavan Jaccob
- Department of Chemistry, Loyola College, Chennai, 600034, India
| | - Ramasamy Mayilmurugan
- Bioinorganic Chemistry Laboratory/Physical Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai, 625021, India
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27
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Aloi S, Davies CG, Karplus PA, Wilbanks SM, Jameson GNL. Substrate Specificity in Thiol Dioxygenases. Biochemistry 2019; 58:2398-2407. [PMID: 31045343 DOI: 10.1021/acs.biochem.9b00079] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thiol dioxygenases make up a class of ferrous iron-dependent enzymes that oxidize thiols to their corresponding sulfinates. X-ray diffraction structures of cysteine-bound cysteine dioxygenase show how cysteine is coordinated via its thiolate and amine to the iron and oriented correctly for O atom transfer. There are currently no structures with 3-mercaptopropionic acid or mercaptosuccinic acid bound to their respective enzymes, 3-mercaptopropionate dioxygenase or mercaptosuccinate dioxygenase. Sequence alignments and comparisons of known structures have led us to postulate key structural features that define substrate specificity. Here, we compare the rates and reactivities of variants of Rattus norvegicus cysteine dioxygenase and 3-mercaptopropionate dioxygenases from Pseudomonas aureginosa and Ralstonia eutropha (JMP134) and show how binary variants of three structural features correlate with substrate specificity and reactivity. They are (1) the presence or absence of a cis-peptide bond between residues Ser158 and Pro159, (2) an Arg or Gln at position 60, and (3) a Cys or Arg at position 164 (all RnCDO numbering). Different permutations of these features allow sulfination of l-cysteine, 3-mercaptopropionic acid, and ( R)-mercaptosuccinic acid to be promoted or impeded.
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Affiliation(s)
- Sekotilani Aloi
- Department of Chemistry , University of Otago , P.O. Box 56, Dunedin 9054 , New Zealand
| | - Casey G Davies
- Department of Chemistry , University of Otago , P.O. Box 56, Dunedin 9054 , New Zealand
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics , Oregon State University , 2011 Ag & Life Sciences Building , Corvallis , Oregon 97331 , United States
| | - Sigurd M Wilbanks
- Department of Biochemistry , University of Otago , P.O. Box 56, Dunedin 9054 , New Zealand
| | - Guy N L Jameson
- Department of Chemistry , University of Otago , P.O. Box 56, Dunedin 9054 , New Zealand.,School of Chemistry, Bio21 Molecular Science and Biotechnology Institute , The University of Melbourne , 30 Flemington Road , Parkville , VIC 3010 , Australia
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28
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Li J, Koto T, Davis I, Liu A. Probing the Cys-Tyr Cofactor Biogenesis in Cysteine Dioxygenase by the Genetic Incorporation of Fluorotyrosine. Biochemistry 2019; 58:2218-2227. [PMID: 30946568 DOI: 10.1021/acs.biochem.9b00006] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cysteine dioxygenase (CDO) is a nonheme iron enzyme that adds two oxygen atoms from dioxygen to the sulfur atom of l-cysteine. Adjacent to the iron site of mammalian CDO, there is a post-translationally generated Cys-Tyr cofactor, whose presence substantially enhances the oxygenase activity. The formation of the Cys-Tyr cofactor in CDO is an autocatalytic process, and it is challenging to study by traditional techniques because the cross-linking reaction is a side, uncoupled, single-turnover oxidation buried among multiple turnovers of l-cysteine oxygenation. Here, we take advantage of our recent success in obtaining a purely uncross-linked human CDO due to site-specific incorporation of 3,5-difluoro-l-tyrosine (F2-Tyr) at the cross-linking site through the genetic code expansion strategy. Using EPR spectroscopy, we show that nitric oxide (•NO), an oxygen surrogate, similarly binds to uncross-linked F2-Tyr157 CDO as in wild-type human CDO. We determined X-ray crystal structures of uncross-linked F2-Tyr157 CDO and mature wild-type CDO in complex with both l-cysteine and •NO. These structural data reveal that the active site cysteine (Cys93 in the human enzyme), rather than the generally expected tyrosine (i.e., Tyr157), is well-aligned to be oxidized should the normal oxidation reaction uncouple. This structure-based understanding is further supported by a computational study with models built on the uncross-linked ternary complex structure. Together, these results strongly suggest that the first target to oxidize during the iron-assisted Cys-Tyr cofactor biogenesis is Cys93. Based on these data, a plausible reaction mechanism implementing a cysteine radical involved in the cross-link formation is proposed.
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Affiliation(s)
- Jiasong Li
- Department of Chemistry , University of Texas at San Antonio , San Antonio , Texas 78249 , United States
| | - Teruaki Koto
- Department of Chemistry , University of Texas at San Antonio , San Antonio , Texas 78249 , United States
| | - Ian Davis
- Department of Chemistry , University of Texas at San Antonio , San Antonio , Texas 78249 , United States
| | - Aimin Liu
- Department of Chemistry , University of Texas at San Antonio , San Antonio , Texas 78249 , United States
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29
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Zhao J, Han Y, Ma X, Zhou Y, Yuan S, Shen Q, Ye G, Liu H, Fu P, Zhang G, Qiao B, Liu A. Cysteine Dioxygenase Regulates the Epithelial Morphogenesis of Mammary Gland via Cysteine Sulfinic Acid. iScience 2019; 13:173-189. [PMID: 30849621 PMCID: PMC6406049 DOI: 10.1016/j.isci.2019.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 12/18/2022] Open
Abstract
Epithelial morphogenesis is a common feature in various organs and contributes to functional formation. However, the molecular mechanisms behind epithelial morphogenesis remain largely unknown. Mammary gland is an excellent model system to investigate the molecular mechanisms of epithelial morphogenesis. In this study, we found that cysteine dioxygenase (CDO), a key enzyme in cysteine oxidative metabolism, was involved in mammary epithelial morphogenesis. CDO knockout (KO) females exhibited severe defects in mammary branching morphogenesis and ductal elongation, resulting in poor lactation. CDO contributes to the luminal epithelial cell differentiation, proliferation, and apoptosis mainly through its downstream product cysteine sulfinic acid (CSA). Exogenous supplementation of CSA not only rescued the defects in CDO KO mouse but also enhanced ductal growth in wild-type mouse. It suggests that CDO regulates luminal epithelial differentiation and regeneration via CSA and consequently contributes to mammary development, which raises important implications for epithelial morphogenesis and pathogenesis of breast cancer. Cysteine dioxygenase (CDO) is necessary for mammary epithelial morphogenesis Cysteine sulfinic acid (CSA) supplementation rescues the mammary defects in CDO KO mouse CDO retains lumen character and maintains luminal cell differentiation via CSA CDO maintains epithelial cell renewal via CSA
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Affiliation(s)
- Jianjun Zhao
- College of Animal Science, Southwest University, Chongqing, China.
| | - Yuzhu Han
- College of Animal Science, Southwest University, Chongqing, China
| | - Xingyu Ma
- College of Animal Science, Southwest University, Chongqing, China
| | - Yang Zhou
- College of Animal Science, Southwest University, Chongqing, China
| | - Shukai Yuan
- College of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Qian Shen
- Department of Microbiology, Ohio State University, Columbus, OH, United States
| | - Guogen Ye
- College of Animal Science, Southwest University, Chongqing, China
| | - Hongrun Liu
- College of Animal Science, Southwest University, Chongqing, China
| | - Penghui Fu
- College of Animal Science, Southwest University, Chongqing, China
| | - Gongwei Zhang
- College of Animal Science, Southwest University, Chongqing, China
| | - Bingke Qiao
- College of Animal Science, Southwest University, Chongqing, China
| | - Anfang Liu
- College of Animal Science, Southwest University, Chongqing, China.
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30
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Cleavage of a carbon-fluorine bond by an engineered cysteine dioxygenase. Nat Chem Biol 2018; 14:853-860. [PMID: 29942080 PMCID: PMC6103799 DOI: 10.1038/s41589-018-0085-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 05/04/2018] [Indexed: 11/08/2022]
Abstract
Cysteine dioxygenase (CDO) plays an essential role in sulfur metabolism by regulating homeostatic levels of cysteine. Human CDO contains a post-translationally generated Cys93-Tyr157 cross-linked cofactor. Here, we investigated this Cys-Tyr cross-linking by incorporating unnatural tyrosines in place of Tyr157 via a genetic method. The catalytically active variants were obtained with a thioether bond between Cys93 and the halogen-substituted Tyr157, and we determined the crystal structures of both wild-type and engineered CDO variants in the purely uncross-linked form and with a mature cofactor. Along with mass spectrometry and 19F NMR, these data indicated that the enzyme could catalyze oxidative C-F or C-Cl bond cleavage, resulting in a substantial conformational change of both Cys93 and Tyr157 during cofactor assembly. These findings provide insights into the mechanism of Cys-Tyr cofactor biogenesis and may aid the development of bioinspired aromatic carbon-halogen bond activation.
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31
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de Visser SP. Mechanistic Insight on the Activity and Substrate Selectivity of Nonheme Iron Dioxygenases. CHEM REC 2018; 18:1501-1516. [PMID: 29878456 DOI: 10.1002/tcr.201800033] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/18/2018] [Indexed: 01/05/2023]
Abstract
Nonheme iron dioxygenases catalyze vital reactions for human health particularly related to aging processes. They are involved in the biosynthesis of amino acids, but also the biodegradation of toxic compounds. Typically they react with their substrate(s) through oxygen atom transfer, although often with the assistance of a co-substrate like α-ketoglutarate that is converted to succinate and CO2 . Many reaction processes catalyzed by the nonheme iron dioxygenases are stereoselective or regiospecific and hence understanding the mechanism and protein involvement in the selectivity is important for the design of biotechnological applications of these enzymes. To this end, I will review recent work of our group on nonheme iron dioxygenases and include background information on their general structure and catalytic cycle. Examples of stereoselective and regiospecific reaction mechanisms we elucidated are for the AlkB repair enzyme, prolyl-4-hydroxylase and the ergothioneine biosynthesis enzyme. Finally, I cover an example where we bioengineered S-p-hydroxymandelate synthase into the R-p-hydroxymandelate synthase.
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Affiliation(s)
- Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
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32
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Abstract
Signaling by H2S is proposed to occur via persulfidation, a posttranslational modification of cysteine residues (RSH) to persulfides (RSSH). Persulfidation provides a framework for understanding the physiological and pharmacological effects of H2S. Due to the inherent instability of persulfides, their chemistry is understudied. In this review, we discuss the biologically relevant chemistry of H2S and the enzymatic routes for its production and oxidation. We cover the chemical biology of persulfides and the chemical probes for detecting them. We conclude by discussing the roles ascribed to protein persulfidation in cell signaling pathways.
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Affiliation(s)
- Milos R. Filipovic
- Univeristy of Bordeaux, IBGC, UMR 5095, F-33077 Bordeaux, France
- CNRS, IBGC, UMR 5095, F-33077 Bordeaux, France
| | - Jasmina Zivanovic
- Univeristy of Bordeaux, IBGC, UMR 5095, F-33077 Bordeaux, France
- CNRS, IBGC, UMR 5095, F-33077 Bordeaux, France
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Facultad de Ciencias and Center for Free Radical and Biomedical Research, Universidad de la Republica, 11400 Montevideo, Uruguay
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600, United States
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33
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Pietra F. On the Dynamical Behavior of the Cysteine Dioxygenase-l-Cysteine Complex in the Presence of Free Dioxygen and l-Cysteine. Chem Biodivers 2017; 14. [PMID: 28857465 DOI: 10.1002/cbdv.201700290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/23/2017] [Indexed: 11/11/2022]
Abstract
In this work, viable models of cysteine dioxygenase (CDO) and its complex with l-cysteine dianion were built for the first time, under strict adherence to the crystal structure from X-ray diffraction studies, for all atom molecular dynamics (MD). Based on the CHARMM36 FF, the active site, featuring an octahedral dummy Fe(II) model, allowed us observing water exchange, which would have escaped attention with the more popular bonded models. Free dioxygen (O2 ) and l-cysteine, added at the active site, could be observed being expelled toward the solvating medium under Random Accelerated Molecular Dynamics (RAMD) along major and minor pathways. Correspondingly, free dioxygen (O2 ), added to the solvating medium, could be observed to follow the same above pathways in getting to the active site under unbiased MD. For the bulky l-cysteine, 600 ns of trajectory were insufficient for protein penetration, and the molecule was stuck at the protein borders. These models pave the way to free energy studies of ligand associations, devised to better clarify how this cardinal enzyme behaves in human metabolism.
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Affiliation(s)
- Francesco Pietra
- Accademia Lucchese di Scienze, Lettere e Arti, Classe di Scienze, Palazzo Pretorio, via Vittorio Veneto 1, 55100, Lucca, Italy
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34
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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.
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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.
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35
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Morrow WP, Sardar S, Thapa P, Hossain MS, Foss FW, Pierce BS. Thiol dioxygenase turnover yields benzothiazole products from 2-mercaptoaniline and O 2-dependent oxidation of primary alcohols. Arch Biochem Biophys 2017; 631:66-74. [PMID: 28826737 PMCID: PMC5616182 DOI: 10.1016/j.abb.2017.08.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 08/15/2017] [Accepted: 08/16/2017] [Indexed: 10/19/2022]
Abstract
Thiol dioxygenases are non-heme mononuclear iron enzymes that catalyze the O2-dependent oxidation of free thiols (-SH) to produce the corresponding sulfinic acid (-SO2-). Previous chemical rescue studies identified a putative FeIII-O2- intermediate that precedes substrate oxidation in Mus musculus cysteine dioxygenase (Mm CDO). Given that a similar reactive intermediate has been identified in the extradiol dioxygenase 2, 3-HCPD, it is conceivable that these enzymes share other mechanistic features with regard to substrate oxidation. To explore this possibility, enzymatic reactions with Mm CDO (as well as the bacterial 3-mercaptopropionic acid dioxygenase, Av MDO) were performed using a substrate analogue (2-mercaptoaniline, 2ma). This aromatic thiol closely approximates the catecholic substrate of homoprotocatechuate of 2, 3-HPCD while maintaining the 2-carbon thiol-amine separation preferred by Mm CDO. Remarkably, both enzymes exhibit 2ma-gated O2-consumption; however, none of the expected products for thiol dioxygenase or intra/extradiol dioxygenase reactions were observed. Instead, benzothiazoles are produced by the condensation of 2ma with aldehydes formed by an off-pathway oxidation of primary alcohols added to aqueous reactions to solubilize the substrate. The observed oxidation of 1º-alcohols in 2ma-reactions is consistent with the formation of a high-valent intermediate similar to what has been reported for cytochrome P450 and mononuclear iron model complexes.
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Affiliation(s)
- William P Morrow
- Department of Chemistry & Biochemistry, College of Science, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Sinjinee Sardar
- Department of Chemistry & Biochemistry, College of Science, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Pawan Thapa
- Department of Chemistry & Biochemistry, College of Science, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Mohammad S Hossain
- Department of Chemistry & Biochemistry, College of Science, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Frank W Foss
- Department of Chemistry & Biochemistry, College of Science, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Brad S Pierce
- Department of Chemistry & Biochemistry, College of Science, The University of Texas at Arlington, Arlington, TX 76019, United States.
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36
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Faponle AS, Seebeck FP, de Visser SP. Sulfoxide Synthase versus Cysteine Dioxygenase Reactivity in a Nonheme Iron Enzyme. J Am Chem Soc 2017; 139:9259-9270. [PMID: 28602090 DOI: 10.1021/jacs.7b04251] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The sulfoxide synthase EgtB represents a unique family of nonheme iron enzymes that catalyze the formation of a C-S bond between N-α-trimethyl histidine and γ-glutamyl cysteine, which is the key step in the biosynthesis of ergothioneine, an important amino acid related to aging. A controversy has arisen regarding its catalytic mechanism related to the function of the active-site Tyr377 residue. The biosynthesis of ergothioneine in EgtB shows structural similarities to cysteine dioxygenase which transfers two oxygen atoms to the thiolate group of cysteine. The question, therefore, is how do EgtB enzymes catalyze the C-S bond-formation reaction, while also preventing a dioxygenation of its cysteinate substrate? In this work we present a quantum mechanics/molecular mechanics study into the mechanism of sulfoxide synthase enzymes as compared to cysteine dioxygenase enzymes and present pathways for both reaction channels in EgtB. We show that EgtB contains a conserved tyrosine residue that reacts via proton-coupled electron transfer with the iron(III)-superoxo species and creates an iron(III)-hydroperoxo intermediate, thereby preventing the possible thiolate dioxygenation side reaction. The nucleophilic C-S bond-formation step happens subsequently concomitant to relay of the proton of the iron(II)-hydroperoxo back to Tyr377. This is the rate-determining step in the reaction cycle and is followed by hydrogen-atom transfer from the CE1-H group of trimethyl histidine substrate to iron(II)-superoxo. In the final step, a quick and almost barrierless sulfoxidation leads to the sulfoxide product complexes. The work highlights a unique machinery and active-site setup of the enzyme that drives the sulfoxide synthase reaction.
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Affiliation(s)
- Abayomi S Faponle
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Florian P Seebeck
- Department for Chemistry, University of Basel , St. Johanns-Ring 19, Basel 4056, Switzerland
| | - Sam P de Visser
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
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Wang Y, Li J, Liu A. Oxygen activation by mononuclear nonheme iron dioxygenases involved in the degradation of aromatics. J Biol Inorg Chem 2017; 22:395-405. [PMID: 28084551 DOI: 10.1007/s00775-017-1436-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/03/2017] [Indexed: 11/25/2022]
Abstract
Molecular oxygen is utilized in numerous metabolic pathways fundamental for life. Mononuclear nonheme iron-dependent oxygenase enzymes are well known for their involvement in some of these pathways, activating O2 so that oxygen atoms can be incorporated into their primary substrates. These reactions often initiate pathways that allow organisms to use stable organic molecules as sources of carbon and energy for growth. From the myriad of reactions in which these enzymes are involved, this perspective recounts the general mechanisms of aromatic dihydroxylation and oxidative ring cleavage, both of which are ubiquitous chemical reactions found in life-sustaining processes. The organic substrate provides all four electrons required for oxygen activation and insertion in the reactions mediated by extradiol and intradiol ring-cleaving catechol dioxygenases. In contrast, two of the electrons are provided by NADH in the cis-dihydroxylation mechanism of Rieske dioxygenases. The catalytic nonheme Fe center, with the aid of active site residues, facilitates these electron transfers to O2 as key elements of the activation processes. This review discusses some general questions for the catalytic strategies of oxygen activation and insertion into aromatic compounds employed by mononuclear nonheme iron-dependent dioxygenases. These include: (1) how oxygen is activated, (2) whether there are common intermediates before oxygen transfer to the aromatic substrate, and (3) are these key intermediates unique to mononuclear nonheme iron dioxygenases?
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Jiasong Li
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA.
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38
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Fischer AA, Lindeman SV, Fiedler AT. Spectroscopic and computational studies of reversible O2 binding by a cobalt complex of relevance to cysteine dioxygenase. Dalton Trans 2017; 46:13229-13241. [DOI: 10.1039/c7dt01600j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Spectroscopic and computational studies of reversible O2 binding by a cobalt active-site mimic shed light on the catalytic mechanism of cysteine dioxygenases.
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Fischer AA, Stracey N, Lindeman SV, Brunold TC, Fiedler AT. Synthesis, X-ray Structures, Electronic Properties, and O 2/NO Reactivities of Thiol Dioxygenase Active-Site Models. Inorg Chem 2016; 55:11839-11853. [PMID: 27801576 DOI: 10.1021/acs.inorgchem.6b01931] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Mononuclear non-heme iron complexes that serve as structural and functional mimics of the thiol dioxygenases (TDOs), cysteine dioxygenase (CDO) and cysteamine dioxygenase (ADO), have been prepared and characterized with crystallographic, spectroscopic, kinetic, and computational methods. The high-spin Fe(II) complexes feature the facially coordinating tris(4,5-diphenyl-1-methylimidazol-2-yl)phosphine (Ph2TIP) ligand that replicates the three histidine (3His) triad of the TDO active sites. Further coordination with bidentate l-cysteine ethyl ester (CysOEt) or cysteamine (CysAm) anions yielded five-coordinate (5C) complexes that resemble the substrate-bound forms of CDO and ADO, respectively. Detailed electronic-structure descriptions of the [Fe(Ph2TIP)(LS,N)]BPh4 complexes, where LS,N = CysOEt (1) or CysAm (2), were generated through a combination of spectroscopic techniques [electronic absorption, magnetic circular dichroism (MCD)] and density functional theory (DFT). Complexes 1 and 2 decompose in the presence of O2 to yield the corresponding sulfinic acid (RSO2H) products, thereby emulating the reactivity of the TDO enzymes and related complexes. Rate constants and activation parameters for the dioxygenation reactions were measured and interpreted with the aid of DFT calculations for O2-bound intermediates. Treatment of the TDO models with nitric oxide (NO)-a well-established surrogate of O2-led to a mixture of high-spin and low-spin {FeNO}7 species at low temperature (-70 °C), as indicated by electron paramagnetic resonance (EPR) spectroscopy. At room temperature, these Fe/NO adducts convert to a common species with EPR and infrared (IR) features typical of cationic dinitrosyl iron complexes (DNICs). To complement these results, parallel spectroscopic, computational, and O2/NO reactivity studies were carried out using previously reported TDO models that feature an anionic hydrotris(3-phenyl-5-methyl-pyrazolyl)borate (Ph,MeTp-) ligand. Though the O2 reactivities of the Ph2TIP- and Ph,MeTp-based complexes are quite similar, the supporting ligand perturbs the energies of Fe 3d-based molecular orbitals and modulates Fe-S bond covalency, suggesting possible rationales for the presence of neutral 3His coordination in CDO and ADO.
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Affiliation(s)
- Anne A Fischer
- Department of Chemistry, Marquette University , Milwaukee, Wisconsin 53201, United States
| | - Nuru Stracey
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Sergey V Lindeman
- Department of Chemistry, Marquette University , Milwaukee, Wisconsin 53201, United States
| | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Adam T Fiedler
- Department of Chemistry, Marquette University , Milwaukee, Wisconsin 53201, United States
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40
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Perkins A, Parsonage D, Nelson KJ, Ogba OM, Cheong PHY, Poole LB, Karplus PA. Peroxiredoxin Catalysis at Atomic Resolution. Structure 2016; 24:1668-1678. [PMID: 27594682 DOI: 10.1016/j.str.2016.07.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/24/2016] [Accepted: 07/17/2016] [Indexed: 12/23/2022]
Abstract
Peroxiredoxins (Prxs) are ubiquitous cysteine-based peroxidases that guard cells against oxidative damage, are virulence factors for pathogens, and are involved in eukaryotic redox regulatory pathways. We have analyzed catalytically active crystals to capture atomic resolution snapshots of a PrxQ subfamily enzyme (from Xanthomonas campestris) proceeding through thiolate, sulfenate, and sulfinate species. These analyses provide structures of unprecedented accuracy for seeding theoretical studies, and reveal conformational intermediates giving insight into the reaction pathway. Based on a highly non-standard geometry seen for the sulfenate intermediate, we infer that the sulfenate formation itself can strongly promote local unfolding of the active site to enhance productive catalysis. Further, these structures reveal that preventing local unfolding, in this case via crystal contacts, results in facile hyperoxidative inactivation even for Prxs normally resistant to such inactivation. This supports previous proposals that conformation-specific inhibitors may be useful for achieving selective inhibition of Prxs that are drug targets.
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Affiliation(s)
- Arden Perkins
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Derek Parsonage
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Kimberly J Nelson
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - O Maduka Ogba
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA
| | | | - Leslie B Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA.
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41
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Driggers CM, Kean KM, Hirschberger LL, Cooley RB, Stipanuk MH, Karplus PA. Structure-Based Insights into the Role of the Cys-Tyr Crosslink and Inhibitor Recognition by Mammalian Cysteine Dioxygenase. J Mol Biol 2016; 428:3999-4012. [PMID: 27477048 DOI: 10.1016/j.jmb.2016.07.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 07/15/2016] [Accepted: 07/18/2016] [Indexed: 10/21/2022]
Abstract
In mammals, the non-heme iron enzyme cysteine dioxygenase (CDO) helps regulate Cys levels through converting Cys to Cys sulfinic acid. Its activity is in part modulated by the formation of a Cys93-Tyr157 crosslink that increases its catalytic efficiency over 10-fold. Here, 21 high-resolution mammalian CDO structures are used to gain insight into how the Cys-Tyr crosslink promotes activity and how select competitive inhibitors bind. Crystal structures of crosslink-deficient C93A and Y157F variants reveal similar ~1.0-Å shifts in the side chain of residue 157, and both variant structures have a new chloride ion coordinating the active site iron. Cys binding is also different from wild-type CDO, and no Cys-persulfenate forms in the C93A or Y157F active sites at pH6.2 or 8.0. We conclude that the crosslink enhances activity by positioning the Tyr157 hydroxyl to enable proper Cys binding, proper oxygen binding, and optimal chemistry. In addition, structures are presented for homocysteine (Hcy), D-Cys, thiosulfate, and azide bound as competitive inhibitors. The observed binding modes of Hcy and D-Cys clarify why they are not substrates, and the binding of azide shows that in contrast to what has been proposed, it does not bind in these crystals as a superoxide mimic.
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Affiliation(s)
- Camden M Driggers
- Department of Biochemistry and Biophysics, 2011 Ag & Life Sciences Building, Oregon State University, Corvallis, OR 97331, USA
| | - Kelsey M Kean
- Department of Biochemistry and Biophysics, 2011 Ag & Life Sciences Building, Oregon State University, Corvallis, OR 97331, USA
| | - Lawrence L Hirschberger
- Department of Nutritional Sciences, 227 Savage Hall, Cornell University, Ithaca, NY 14853, USA
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, 2011 Ag & Life Sciences Building, Oregon State University, Corvallis, OR 97331, USA
| | - Martha H Stipanuk
- Department of Nutritional Sciences, 227 Savage Hall, Cornell University, Ithaca, NY 14853, USA.
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, 2011 Ag & Life Sciences Building, Oregon State University, Corvallis, OR 97331, USA.
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42
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Crowell JK, Sardar S, Hossain MS, Foss FW, Pierce BS. Non-chemical proton-dependent steps prior to O2-activation limit Azotobacter vinelandii 3-mercaptopropionic acid dioxygenase (MDO) catalysis. Arch Biochem Biophys 2016; 604:86-94. [PMID: 27311613 DOI: 10.1016/j.abb.2016.06.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 06/09/2016] [Accepted: 06/10/2016] [Indexed: 11/26/2022]
Abstract
3-mercaptopropionate dioxygenase from Azotobacter vinelandii (Av MDO) is a non-heme mononuclear iron enzyme that catalyzes the O2-dependent oxidation of 3-mercaptopropionate (3mpa) to produce 3-sulfinopropionic acid (3spa). With one exception, the active site residues of MDO are identical to bacterial cysteine dioxygenase (CDO). Specifically, the CDO Arg-residue (R50) is replaced by Gln (Q67) in MDO. Despite this minor active site perturbation, substrate-specificity of Av MDO is more relaxed as compared to CDO. In order to investigate the relative timing of chemical and non-chemical events in Av MDO catalysis, the pH/D-dependence of steady-state kinetic parameters (kcat and kcat/KM) and viscosity effects are measured using two different substrates [3mpa and l-cysteine (cys)]. The pL-dependent activity of Av MDO in these reactions can be rationalized assuming a diprotic enzyme model in which three ionic forms of the enzyme are present [cationic, E((z+1)); neutral, E(z); and anionic, E((z-1))]. The activities observed for each substrate appear to be dominated by electrostatic interactions within the enzymatic active site. Given the similarity between MDO and the more extensively characterized mammalian CDO, a tentative model for the role of the conserved 'catalytic triad' is proposed.
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Affiliation(s)
- Joshua K Crowell
- Department of Chemistry & Biochemistry, College of Science, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Sinjinee Sardar
- Department of Chemistry & Biochemistry, College of Science, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Mohammad S Hossain
- Department of Chemistry & Biochemistry, College of Science, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Frank W Foss
- Department of Chemistry & Biochemistry, College of Science, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Brad S Pierce
- Department of Chemistry & Biochemistry, College of Science, The University of Texas at Arlington, Arlington, TX 76019, USA.
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43
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Fellner M, Siakkou E, Faponle AS, Tchesnokov EP, de Visser SP, Wilbanks SM, Jameson GNL. Influence of cysteine 164 on active site structure in rat cysteine dioxygenase. J Biol Inorg Chem 2016; 21:501-10. [PMID: 27193596 DOI: 10.1007/s00775-016-1360-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/07/2016] [Indexed: 11/29/2022]
Abstract
Cysteine dioxygenase is a non-heme mononuclear iron enzyme with unique structural features, namely an intramolecular thioether cross-link between cysteine 93 and tyrosine 157, and a disulfide bond between substrate L-cysteine and cysteine 164 in the entrance channel to the active site. We investigated how these posttranslational modifications affect catalysis through a kinetic, crystallographic and computational study. The enzyme kinetics of a C164S variant are identical to WT, indicating that disulfide formation at C164 does not significantly impair access to the active site at physiological pH. However, at high pH, the cysteine-tyrosine cross-link formation is enhanced in C164S. This supports the view that disulfide formation at position 164 can limit access to the active site. The C164S variant yielded crystal structures of unusual clarity in both resting state and with cysteine bound. Both show that the iron in the cysteine-bound complex is a mixture of penta- and hexa-coordinate with a water molecule taking up the final site (60 % occupancy), which is where dioxygen is believed to coordinate during turnover. The serine also displays stronger hydrogen bond interactions to a water bound to the amine of the substrate cysteine. However, the interactions between cysteine and iron appear unchanged. DFT calculations support this and show that WT and C164S have similar binding energies for the water molecule in the final site. This variant therefore provides evidence that WT also exists in an equilibrium between penta- and hexa-coordinate forms and the presence of the sixth ligand does not strongly affect dioxygen binding.
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Affiliation(s)
- Matthias Fellner
- Department of Chemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Eleni Siakkou
- Department of Chemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Abayomi S Faponle
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Egor P Tchesnokov
- Department of Chemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Sigurd M Wilbanks
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Guy N L Jameson
- Department of Chemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand.
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Expression of genes, encoding the enzymes of cysteine metabolism in human placenta in the first and third trimesters of uncomplicated pregnancy. UKRAINIAN BIOCHEMICAL JOURNAL 2016; 88:88-98. [DOI: 10.15407/ubj88.01.088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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45
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Fellner M, Aloi S, Tchesnokov EP, Wilbanks SM, Jameson GNL. Substrate and pH-Dependent Kinetic Profile of 3-Mercaptopropionate Dioxygenase from Pseudomonas aeruginosa. Biochemistry 2016; 55:1362-71. [DOI: 10.1021/acs.biochem.5b01203] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matthias Fellner
- Department of Chemistry and ‡Department of
Biochemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Sekotilani Aloi
- Department of Chemistry and ‡Department of
Biochemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Egor P. Tchesnokov
- Department of Chemistry and ‡Department of
Biochemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Sigurd M. Wilbanks
- Department of Chemistry and ‡Department of
Biochemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Guy N. L. Jameson
- Department of Chemistry and ‡Department of
Biochemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
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46
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Goncharenko KV, Seebeck FP. Conversion of a non-heme iron-dependent sulfoxide synthase into a thiol dioxygenase by a single point mutation. Chem Commun (Camb) 2016; 52:1945-8. [DOI: 10.1039/c5cc07772a] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
EgtB from Mycobacterium thermoresistibile catalyzes O2-dependent sulfur–carbon bond formation between the side chains of Nα-trimethyl histidine and γ-glutamyl cysteine as a central step in ergothioneine biosynthesis.
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47
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Pierce BS, Subedi BP, Sardar S, Crowell JK. The "Gln-Type" Thiol Dioxygenase from Azotobacter vinelandii is a 3-Mercaptopropionic Acid Dioxygenase. Biochemistry 2015; 54:7477-90. [PMID: 26624219 DOI: 10.1021/acs.biochem.5b00636] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Cysteine dioxygenase (CDO) is a non-heme iron enzyme that catalyzes the O2-dependent oxidation of l-cysteine to produce cysteinesulfinic acid. Bacterial CDOs have been subdivided as either "Arg-type" or "Gln-type" on the basis of the identity of conserved active site residues. To date, "Gln-type" enzymes remain largely uncharacterized. It was recently noted that the "Gln-type" enzymes are more homologous with another thiol dioxygenase [3-mercaptopropionate dioxygenase (MDO)] identified in Variovorax paradoxus, suggesting that enzymes of the "Gln-type" subclass are in fact MDOs. In this work, a putative "Gln-type" thiol dioxygenase from Azotobacter vinelandii (Av) was purified to homogeneity and characterized. Steady-state assays were performed using three substrates [3-mercaptopropionic acid (3mpa), l-cysteine (cys), and cysteamine (ca)]. Despite comparable maximal velocities, the "Gln-type" Av enzyme exhibited a specificity for 3mpa (kcat/KM = 72000 M(-1) s(-1)) nearly 2 orders of magnitude greater than those for cys (110 M(-1) s(-1)) and ca (11 M(-1) s(-1)). Supporting X-band electron paramagnetic resonance (EPR) studies were performed using nitric oxide (NO) as a surrogate for O2 binding to confirm obligate-ordered addition of substrate prior to NO. Stoichimetric addition of NO to solutions of 3mpa-bound enzyme quantitatively yields an iron-nitrosyl species (Av ES-NO) with EPR features consistent with a mononuclear (S = (3)/2) {FeNO}(7) site. Conversely, two distinct substrate-bound conformations were observed in Av ES-NO samples prepared with cys and ca, suggesting heterogeneous binding within the enzymatic active site. Analytical EPR simulations are provided to establish the relative binding affinity for each substrate (3map > cys > ca). Both kinetic and spectroscopic results presented here are consistent with 3mpa being the preferred substrate for this enzyme.
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Affiliation(s)
- Brad S Pierce
- Department of Chemistry and Biochemistry, College of Sciences, The University of Texas at Arlington , Arlington, Texas 76019, United States
| | - Bishnu P Subedi
- Department of Chemistry and Biochemistry, College of Sciences, The University of Texas at Arlington , Arlington, Texas 76019, United States
| | - Sinjinee Sardar
- Department of Chemistry and Biochemistry, College of Sciences, The University of Texas at Arlington , Arlington, Texas 76019, United States
| | - Joshua K Crowell
- Department of Chemistry and Biochemistry, College of Sciences, The University of Texas at Arlington , Arlington, Texas 76019, United States
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48
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Tchesnokov EP, Fellner M, Siakkou E, Kleffmann T, Martin LW, Aloi S, Lamont IL, Wilbanks SM, Jameson GNL. The cysteine dioxygenase homologue from Pseudomonas aeruginosa is a 3-mercaptopropionate dioxygenase. J Biol Chem 2015; 290:24424-37. [PMID: 26272617 PMCID: PMC4591825 DOI: 10.1074/jbc.m114.635672] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Revised: 08/02/2015] [Indexed: 02/02/2023] Open
Abstract
Thiol dioxygenation is the initial oxidation step that commits a thiol to important catabolic or biosynthetic pathways. The reaction is catalyzed by a family of specific non-heme mononuclear iron proteins each of which is reported to react efficiently with only one substrate. This family of enzymes includes cysteine dioxygenase, cysteamine dioxygenase, mercaptosuccinate dioxygenase, and 3-mercaptopropionate dioxygenase. Using sequence alignment to infer cysteine dioxygenase activity, a cysteine dioxygenase homologue from Pseudomonas aeruginosa (p3MDO) has been identified. Mass spectrometry of P. aeruginosa under standard growth conditions showed that p3MDO is expressed in low levels, suggesting that this metabolic pathway is available to the organism. Purified recombinant p3MDO is able to oxidize both cysteine and 3-mercaptopropionic acid in vitro, with a marked preference for 3-mercaptopropionic acid. We therefore describe this enzyme as a 3-mercaptopropionate dioxygenase. Mössbauer spectroscopy suggests that substrate binding to the ferrous iron is through the thiol but indicates that each substrate could adopt different coordination geometries. Crystallographic comparison with mammalian cysteine dioxygenase shows that the overall active site geometry is conserved but suggests that the different substrate specificity can be related to replacement of an arginine by a glutamine in the active site.
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Affiliation(s)
| | | | | | - Torsten Kleffmann
- Biochemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Lois W Martin
- Biochemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | | | - Iain L Lamont
- Biochemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Sigurd M Wilbanks
- Biochemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
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Gogoi P, Chandravanshi M, Mandal SK, Srivastava A, Kanaujia SP. Heterogeneous behavior of metalloproteins toward metal ion binding and selectivity: insights from molecular dynamics studies. J Biomol Struct Dyn 2015; 34:1470-85. [PMID: 26248730 DOI: 10.1080/07391102.2015.1080629] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
About one-third of the existing proteins require metal ions as cofactors for their catalytic activities and structural complexities. While many of them bind only to a specific metal, others bind to multiple (different) metal ions. However, the exact mechanism of their metal preference has not been deduced to clarity. In this study, we used molecular dynamics (MD) simulations to investigate whether a cognate metal (bound to the structure) can be replaced with other similar metal ions. We have chosen seven different proteins (phospholipase A2, sucrose phosphatase, pyrazinamidase, cysteine dioxygenase (CDO), plastocyanin, monoclonal anti-CD4 antibody Q425, and synaptotagmin 1 C2B domain) bound to seven different divalent metal ions (Ca(2+), Mg(2+), Zn(2+), Fe(2+), Cu(2+), Ba(2+), and Sr(2+), respectively). In total, 49 MD simulations each of 50 ns were performed and each trajectory was analyzed independently. Results demonstrate that in some cases, cognate metal ions can be exchanged with similar metal ions. On the contrary, some proteins show binding affinity specifically to their cognate metal ions. Surprisingly, two proteins CDO and plastocyanin which are known to bind Fe(2+) and Cu(2+), respectively, do not exhibit binding affinity to any metal ion. Furthermore, the study reveals that in some cases, the active site topology remains rigid even without cognate metals, whereas, some require them for their active site stability. Thus, it will be interesting to experimentally verify the accuracy of these observations obtained computationally. Moreover, the study can help in designing novel active sites for proteins to sequester metal ions particularly of toxic nature.
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Affiliation(s)
- Prerana Gogoi
- a Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam 781039 , India
| | - Monika Chandravanshi
- a Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam 781039 , India
| | - Suraj Kumar Mandal
- a Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam 781039 , India
| | - Ambuj Srivastava
- a Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam 781039 , India
| | - Shankar Prasad Kanaujia
- a Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam 781039 , India
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Hidaka T, Shimada A, Nakata Y, Kodama H, Kurihara H, Tokihiro T, Ihara S. Simple model of pH-induced protein denaturation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:012709. [PMID: 26274205 DOI: 10.1103/physreve.92.012709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Indexed: 06/04/2023]
Abstract
The pH-induced conformational changes of proteins are systematically studied in the framework of a hydrophobic-polar (HP) model, in which proteins are dramatically simplified as chains of hydrophobic (H) and polar (P) beads on a lattice. We express the electrostatic interaction, the principal driving force of pH-induced unfolding that is not included in the conventional HP model, as the repulsive energy term between P monomers. As a result of the exact enumeration of all of the 14- to 18-mers, it is found that lowest-energy states in many sequences change from single "native" conformations to multiple sets of "denatured" conformations with an increase in the electrostatic repulsion. The switching of the lowest-energy states occurs in quite a similar way to real proteins: it is almost always between two states, while in a small fraction of ≥16-mers it is between three states. We also calculate the structural fluctuations for all of the denatured states and find that the denatured states contain a broad range of incompletely unfolded conformations, similar to "molten globule" states referred to in acid or alkaline denatured real proteins. These results show that the proposed model provides a simple physical picture of pH-induced protein denaturation.
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Affiliation(s)
- T Hidaka
- Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - A Shimada
- Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Y Nakata
- Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904, Japan
- Graduate School of Mathematical Sciences, The University of Tokyo, Komaba, Tokyo 153-8902, Japan
| | - H Kodama
- Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904, Japan
- Graduate School of Mathematical Sciences, The University of Tokyo, Komaba, Tokyo 153-8902, Japan
| | - H Kurihara
- Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
- Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo 102-0076, Japan
| | - T Tokihiro
- Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904, Japan
- Graduate School of Mathematical Sciences, The University of Tokyo, Komaba, Tokyo 153-8902, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo 102-0076, Japan
| | - S Ihara
- Institute for Biology and Mathematics of Dynamic Cellular Processes (iBMath), The University of Tokyo, Komaba, Tokyo 153-8904, Japan
- Graduate School of Mathematical Sciences, The University of Tokyo, Komaba, Tokyo 153-8902, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, Komaba, Tokyo 153-8904, Japan
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