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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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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: 2] [Impact Index Per Article: 0.7] [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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Abstract
Fluorochemicals are a widely distributed class of compounds and have been utilized across a wide range of industries for decades. Given the environmental toxicity and adverse health threats of some fluorochemicals, the development of new methods for their decomposition is significant to public health. However, the carbon-fluorine (C-F) bond is among the most chemically robust bonds; consequently, the degradation of fluorinated hydrocarbons is exceptionally difficult. Here, metalloenzymes that catalyze the cleavage of this chemically challenging bond are reviewed. These enzymes include histidine-ligated heme-dependent dehaloperoxidase and tyrosine hydroxylase, thiolate-ligated heme-dependent cytochrome P450, and four nonheme oxygenases, namely, tetrahydrobiopterin-dependent aromatic amino acid hydroxylase, 2-oxoglutarate-dependent hydroxylase, Rieske dioxygenase, and thiol dioxygenase. While much of the literature regarding the aforementioned enzymes highlights their ability to catalyze C-H bond activation and functionalization, in many cases, the C-F bond cleavage has been shown to occur on fluorinated substrates. A copper-dependent laccase-mediated system representing an unnatural radical defluorination approach is also described. Detailed discussions on the structure-function relationships and catalytic mechanisms provide insights into biocatalytic defluorination, which may inspire drug design considerations and environmental remediation of halogenated contaminants.
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX 78249, USA.
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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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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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Wang Y, Davis I, Chan Y, Naik SG, Griffith WP, Liu A. Characterization of the nonheme iron center of cysteamine dioxygenase and its interaction with substrates. J Biol Chem 2020; 295:11789-11802. [PMID: 32601061 DOI: 10.1074/jbc.ra120.013915] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/25/2020] [Indexed: 12/15/2022] Open
Abstract
Cysteamine dioxygenase (ADO) has been reported to exhibit two distinct biological functions with a nonheme iron center. It catalyzes oxidation of both cysteamine in sulfur metabolism and N-terminal cysteine-containing proteins or peptides, such as regulator of G protein signaling 5 (RGS5). It thereby preserves oxygen homeostasis in a variety of physiological processes. However, little is known about its catalytic center and how it interacts with these two types of primary substrates in addition to O2 Here, using electron paramagnetic resonance (EPR), Mössbauer, and UV-visible spectroscopies, we explored the binding mode of cysteamine and RGS5 to human and mouse ADO proteins in their physiologically relevant ferrous form. This characterization revealed that in the presence of nitric oxide as a spin probe and oxygen surrogate, both the small molecule and the peptide substrates coordinate the iron center with their free thiols in a monodentate binding mode, in sharp contrast to binding behaviors observed in other thiol dioxygenases. We observed a substrate-bound B-type dinitrosyl iron center complex in ADO, suggesting the possibility of dioxygen binding to the iron ion in a side-on mode. Moreover, we observed substrate-mediated reduction of the iron center from ferric to the ferrous oxidation state. Subsequent MS analysis indicated corresponding disulfide formation of the substrates, suggesting that the presence of the substrate could reactivate ADO to defend against oxidative stress. The findings of this work contribute to the understanding of the substrate interaction in ADO and fill a gap in our knowledge of the substrate specificity of thiol dioxygenases.
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, University of Texas at San Antonio, Texas, USA
| | - Ian Davis
- Department of Chemistry, University of Texas at San Antonio, Texas, USA.,Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Yan Chan
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Sunil G Naik
- Department of Chemistry, University of Texas at San Antonio, Texas, USA
| | | | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, Texas, USA .,Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
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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: 21] [Impact Index Per Article: 4.2] [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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