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Yang J, Struwe M, Scheidig A, Mengell J, Clement B, Kirk ML. Active Site Structures of the Escherichia coli N-Hydroxylaminopurine Resistance Molybdoenzyme YcbX. Inorg Chem 2023; 62:5315-5319. [PMID: 36971376 PMCID: PMC10544827 DOI: 10.1021/acs.inorgchem.3c00342] [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: 03/29/2023]
Abstract
X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) data have been used to characterize the coordination environment for the catalytic Mo site of Escherichia coli YcbX in two different oxidation states. In the oxidized state, the Mo(VI) ion is coordinated by two terminal oxo ligands, a thiolate S atom from cysteine, and two S donors from the bidentate pyranopterin ene-1,2-dithiolate (pyranopterin dithiolene). Upon reduction, it is the more basic equatorial oxo ligand that is protonated, with a Mo-Oeq bond distance that is best described as either a short Mo4+-OH2 bond or a long Mo4+-OH bond. Mechanistic implications for substrate reduction are discussed in light of these structural details.
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Affiliation(s)
- Jing Yang
- Department of Chemistry and Chemical Biology, The University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, NM 87131-0001
| | - Michel Struwe
- Zoologisches Institut – Strukturbiologie, Zentrum für Biochemie und Molekularbiologie Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany
- Pharmazeutisches Institut, Christian-Albrechts-Universität zu Kiel, Gutenbergstraße 76, 24118 Kiel, Germany
| | - Axel Scheidig
- Zoologisches Institut – Strukturbiologie, Zentrum für Biochemie und Molekularbiologie Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany
| | - Joshua Mengell
- Department of Chemistry and Chemical Biology, The University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, NM 87131-0001
| | - Bernd Clement
- Pharmazeutisches Institut, Christian-Albrechts-Universität zu Kiel, Gutenbergstraße 76, 24118 Kiel, Germany
| | - Martin L. Kirk
- Department of Chemistry and Chemical Biology, The University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, NM 87131-0001
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Pushie MJ, Doonan CJ, Moquin K, Weiner JH, Rothery R, George GN. Molybdenum Site Structure of Escherichia coli YedY, a Novel Bacterial Oxidoreductase. Inorg Chem 2010; 50:732-40. [DOI: 10.1021/ic101280m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Jake Pushie
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada
| | - Christian J. Doonan
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada
| | - Kamila Moquin
- School of Molecular and Systems Medicine, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Joel H. Weiner
- School of Molecular and Systems Medicine, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Richard Rothery
- School of Molecular and Systems Medicine, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Graham N. George
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada
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Johnson-Winters K, Tollin G, Enemark JH. Elucidating the catalytic mechanism of sulfite oxidizing enzymes using structural, spectroscopic, and kinetic analyses. Biochemistry 2010; 49:7242-54. [PMID: 20666399 DOI: 10.1021/bi1008485] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sulfite oxidizing enzymes (SOEs) are molybdenum cofactor-dependent enzymes that are found in plants, animals, and bacteria. Sulfite oxidase (SO) is found in animals and plants, while sulfite dehydrogenase (SDH) is found in bacteria. In animals, SO catalyzes the oxidation of toxic sulfite to sulfate as the final step in the catabolism of the sulfur-containing amino acids, methionine and cysteine. In humans, sulfite oxidase deficiency is an inherited recessive disorder that produces severe neonatal neurological problems that lead to early death. Plant SO (PSO) also plays an important role in sulfite detoxification and in addition serves as an intermediate enzyme in the assimilatory reduction of sulfate. In vertebrates, the proposed catalytic mechanism of SO involves two intramolecular one-electron transfer (IET) steps from the molybdenum cofactor to the iron of the integral b-type heme. A similar mechanism is proposed for SDH, involving its molybdenum cofactor and c-type heme. However, PSO, which lacks an integral heme cofactor, uses molecular oxygen as its electron acceptor. Here we review recent results for SOEs from kinetic measurements, computational studies, electron paramagnetic resonance (EPR) spectroscopy, electrochemical measurements, and site-directed mutagenesis on active site residues of SOEs and of the flexible polypepetide tether that connects the heme and molybdenum domains of human SO. Rapid kinetic studies of PSO are also discussed.
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Affiliation(s)
- Kayunta Johnson-Winters
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, USA
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Yang J, Rothery R, Sempombe J, Weiner JH, Kirk ML. Spectroscopic characterization of YedY: the role of sulfur coordination in a Mo(V) sulfite oxidase family enzyme form. J Am Chem Soc 2010; 131:15612-4. [PMID: 19860477 DOI: 10.1021/ja903087k] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electronic paramagnetic resonance (EPR), electronic absorption, and magnetic circular dichroism spectroscopies have been performed on YedY, a SUOX fold protein with a Mo domain that is remarkably similar to that found in chicken sulfite oxidase, Arabidopsis thaliana plant sulfite oxidase, and the bacterial sulfite dehydrogenase from Starkeya novella. Low-energy dithiolene --> Mo and cysteine thiolate --> Mo charge-transfer bands have been assigned for the first time in a Mo(V) form of a SUOX fold protein, and the spectroscopic data have been used to interpret the results of bonding calculations. The analysis shows that second coordination sphere effects modulate dithiolene and cysteine sulfur covalency contributions to the Mo bonding scheme. In particular, a more acute O(oxo)-Mo-S(Cys)-C dihedral angle results in increased cysteine thiolate S --> Mo charge transfer and a large g(1) in the EPR spectrum. The spectrosocopic results, coupled with the available structural data, indicate that these second coordination sphere effects may play key roles in modulating the active-site redox potential, facilitating hole superexchange pathways for electron transfer regeneration, and affecting the type of reactions catalyzed by sulfite oxidase family enzymes.
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Affiliation(s)
- Jing Yang
- Department of Chemistry and Chemical Biology, The University of New Mexico, Albuquerque, New Mexico 87131, USA
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Ghosh W, Dam B. Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea. FEMS Microbiol Rev 2009; 33:999-1043. [PMID: 19645821 DOI: 10.1111/j.1574-6976.2009.00187.x] [Citation(s) in RCA: 288] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Lithotrophic sulfur oxidation is an ancient metabolic process. Ecologically and taxonomically diverged prokaryotes have differential abilities to utilize different reduced sulfur compounds as lithotrophic substrates. Different phototrophic or chemotrophic species use different enzymes, pathways and mechanisms of electron transport and energy conservation for the oxidation of any given substrate. While the mechanisms of sulfur oxidation in obligately chemolithotrophic bacteria, predominantly belonging to Beta- (e.g. Thiobacillus) and Gammaproteobacteria (e.g. Thiomicrospira), are not well established, the Sox system is the central pathway in the facultative bacteria from Alphaproteobacteria (e.g. Paracoccus). Interestingly, photolithotrophs such as Rhodovulum belonging to Alphaproteobacteria also use the Sox system, whereas those from Chromatiaceae and Chlorobi use a truncated Sox complex alongside reverse-acting sulfate-reducing systems. Certain chemotrophic magnetotactic Alphaproteobacteria allegedly utilize such a combined mechanism. Sulfur-chemolithotrophic metabolism in Archaea, largely restricted to Sulfolobales, is distinct from those in Bacteria. Phylogenetic and biomolecular fossil data suggest that the ubiquity of sox genes could be due to horizontal transfer, and coupled sulfate reduction/sulfide oxidation pathways, originating in planktonic ancestors of Chromatiaceae or Chlorobi, could be ancestral to all sulfur-lithotrophic processes. However, the possibility that chemolithotrophy, originating in deep sea, is the actual ancestral form of sulfur oxidation cannot be ruled out.
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Affiliation(s)
- Wriddhiman Ghosh
- Department of Microbiology, University of Burdwan, West Bengal, India.
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Preuss B, Berg C, Altenberend F, Gregor M, Stevanovic S, Klein R. Demonstration of autoantibodies to recombinant human sulphite oxidase in patients with chronic liver disorders and analysis of their clinical relevance. Clin Exp Immunol 2007; 150:312-21. [PMID: 17711488 PMCID: PMC2219346 DOI: 10.1111/j.1365-2249.2007.03482.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
It has been shown previously that sera from patients with cholestatic liver diseases react with sulphite oxidase (SO) prepared from chicken liver. In order to analyse this reactivity and the clinical relevance of anti-SO antibodies in more detail, we produced human recombinant SO. Human recombinant SO (60 kDa) was expressed in Escherichia coli and applied to enzyme-linked immunosorbent assay and Western blot. Sera from patients with autoimmune liver disorders [primary biliary cirrhosis (PBC) n = 96; autoimmune hepatitis (AIH) n = 77; primary sclerosing cholangitis (PSC) n = 39], and from patients with other hepatic (n = 154) and non-hepatic chronic inflammatory disorders (n = 113) were investigated. Highest incidence and activities of IgG-anti-SO antibodies were observed in PSC patients. Nine of 16 untreated (56%) and four of 23 PSC patients treated with ursodeoxycholic acid (UDCA) (17%) were positive. Antibody activity decreased significantly during UDCA treatment. Five per cent of PBC and 9% of AIH patients, but also 15% of patients with alcoholic liver disease, were IgG anti-SO-positive. In patients with viral hepatitis and non-hepatic disorders they could be hardly detected. Anti-SO antibodies are further anti-mitochondrial antibodies in chronic liver diseases. They occur predominantly in PSC, and UDCA treatment seams to decrease antibody activity. Whether these antibodies are primary or secondary phenomena and whether they are related to the aetiology or pathogenesis, at least in a subgroup of patients with chronic liver diseases, has still to be evaluated.
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Affiliation(s)
- B Preuss
- Department of Internal Medicine II, University of Tuebingen, Germany
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D'Errico G, Di Salle A, La Cara F, Rossi M, Cannio R. Identification and characterization of a novel bacterial sulfite oxidase with no heme binding domain from Deinococcus radiodurans. J Bacteriol 2006; 188:694-701. [PMID: 16385059 PMCID: PMC1347283 DOI: 10.1128/jb.188.2.694-701.2006] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An open reading frame (draSO) encoding a putative sulfite oxidase (SO) was identified in the sequence of chromosome II of Deinococcus radiodurans; the predicted gene product showed significant amino acid sequence homology to several bacterial and eukaryotic SOs, such as the biochemically and structurally characterized enzyme from Arabidopsis thaliana. Cloning of the Deinococcus SO gene was performed by PCR amplification from the bacterial genomic DNA, and heterologous gene expression of a histidine-tagged polypeptide was obtained in a molybdopterin-overproducing strain of Escherichia coli. The recombinant protein was purified to homogeneity by nickel chelating affinity chromatography, and its main kinetic and chemical physical parameters were determined. Northern blot and enzyme activity analyses indicated that draSO gene expression is constitutive in D. radiodurans and that there is no increase upon exposure to thiosulfate and/or molybdenum(II).
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Affiliation(s)
- Giovanni D'Errico
- Istituto di Biochimica delle Proteine, CNR, via Pietro Castellino 111, 80131 Naples, Italy
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