1
|
Carugo O, Resnati G, Metrangolo P. Chalcogen Bonds Involving Selenium in Protein Structures. ACS Chem Biol 2021; 16:1622-1627. [PMID: 34477364 PMCID: PMC8453483 DOI: 10.1021/acschembio.1c00441] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Indexed: 12/11/2022]
Abstract
Chalcogen bonds are the specific interactions involving group 16 elements as electrophilic sites. The role of chalcogen atoms as sticky sites in biomolecules is underappreciated, and the few available studies have mostly focused on S. Here, we carried out a statistical analysis over 3562 protein structures in the Protein Data Bank (PDB) containing 18 266 selenomethionines and found that Se···O chalcogen bonds are commonplace. These findings may help the future design of functional peptides and contribute to understanding the role of Se in nature.
Collapse
Affiliation(s)
- Oliviero Carugo
- Department
of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Giuseppe Resnati
- Department
of Chemistry, Materials, and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, 20131 Milano, Italy
| | - Pierangelo Metrangolo
- Department
of Chemistry, Materials, and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, 20131 Milano, Italy
| |
Collapse
|
2
|
Johnstone MA, Nelson SJ, O'Leary C, Self WT. Exploring the selenium-over-sulfur substrate specificity and kinetics of a bacterial selenocysteine lyase. Biochimie 2021; 182:166-176. [PMID: 33444662 DOI: 10.1016/j.biochi.2021.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/28/2020] [Accepted: 01/04/2021] [Indexed: 11/15/2022]
Abstract
Selenium is a vital micronutrient in many organisms. While traces are required for microbial utilization, excess amounts are toxic; thus, selenium can be regarded as a biological double-edged sword. Selenium is chemically similar to the essential element sulfur, but curiously, evolution has selected the former over the latter for a subset of oxidoreductases. Enzymes involved in sulfur metabolism are less discriminate in terms of preventing selenium incorporation; however, its specific incorporation into selenoproteins reveals a highly discriminate process that is not completely understood. We have identified SclA, a NifS-like protein in the nosocomial pathogen, Enterococcus faecalis, and characterized its enzymatic activity and specificity for l-selenocysteine over l-cysteine. It is known that Asp-146 is required for selenocysteine specificity in the human selenocysteine lyase. Thus, using computational biology, we compared the bacterial and mammalian enzymes and identified His-100, an Asp-146 ortholog in SclA, and generated site-directed mutants in order to study the residue's potential role in the l-selenocysteine discrimination mechanism. The proteins were overexpressed, purified, and characterized for their biochemical properties. All mutants exhibited varying Michaelis-Menten behavior towards l-selenocysteine, but His-100 was not found to be essential for this activity. Additionally, l-cysteine acted as a competitive inhibitor of all enzymes with higher affinity than l-selenocysteine. Finally, we discovered that SclA exhibited low activity with l-cysteine as a poor substrate regardless of mutations. We conclude that His-100 is not required for l-selenocysteine specificity, underscoring the inherent differences in discriminatory mechanisms between bacterial NifS-like proteins and mammalian selenocysteine lyases.
Collapse
Affiliation(s)
- Michael A Johnstone
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA
| | - Samantha J Nelson
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA
| | - Christine O'Leary
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA
| | - William T Self
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA.
| |
Collapse
|
3
|
Selenocysteine β-Lyase: Biochemistry, Regulation and Physiological Role of the Selenocysteine Decomposition Enzyme. Antioxidants (Basel) 2019; 8:antiox8090357. [PMID: 31480609 PMCID: PMC6770646 DOI: 10.3390/antiox8090357] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 08/23/2019] [Accepted: 08/27/2019] [Indexed: 12/19/2022] Open
Abstract
The enzyme selenocysteine β-lyase (SCLY) was first isolated in 1982 from pig livers, followed by its identification in bacteria. SCLY works as a homodimer, utilizing pyridoxal 5'-phosphate as a cofactor, and catalyzing the specific decomposition of the amino acid selenocysteine into alanine and selenide. The enzyme is thought to deliver its selenide as a substrate for selenophosphate synthetases, which will ultimately be reutilized in selenoprotein synthesis. SCLY subcellular localization is unresolved, as it has been observed both in the cytosol and in the nucleus depending on the technical approach used. The highest SCLY expression and activity in mammals is found in the liver and kidneys. Disruption of the Scly gene in mice led to obesity, hyperinsulinemia, glucose intolerance, and hepatic steatosis, with SCLY being suggested as a participant in the regulation of energy metabolism in a sex-dependent manner. With the physiological role of SCLY still not fully understood, this review attempts to discuss the available literature regarding SCLY in animals and provides avenues for possible future investigation.
Collapse
|
4
|
Cupp-Sutton KA, Ashby MT. Biological Chemistry of Hydrogen Selenide. Antioxidants (Basel) 2016; 5:E42. [PMID: 27879667 PMCID: PMC5187540 DOI: 10.3390/antiox5040042] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 11/04/2016] [Accepted: 11/08/2016] [Indexed: 12/13/2022] Open
Abstract
There are no two main-group elements that exhibit more similar physical and chemical properties than sulfur and selenium. Nonetheless, Nature has deemed both essential for life and has found a way to exploit the subtle unique properties of selenium to include it in biochemistry despite its congener sulfur being 10,000 times more abundant. Selenium is more easily oxidized and it is kinetically more labile, so all selenium compounds could be considered to be "Reactive Selenium Compounds" relative to their sulfur analogues. What is furthermore remarkable is that one of the most reactive forms of selenium, hydrogen selenide (HSe- at physiologic pH), is proposed to be the starting point for the biosynthesis of selenium-containing molecules. This review contrasts the chemical properties of sulfur and selenium and critically assesses the role of hydrogen selenide in biological chemistry.
Collapse
Affiliation(s)
- Kellye A Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA.
| | - Michael T Ashby
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA.
| |
Collapse
|
5
|
Danchin A, Sekowska A. The logic of metabolism and its fuzzy consequences. Environ Microbiol 2013; 16:19-28. [PMID: 24387040 DOI: 10.1111/1462-2920.12270] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 08/02/2013] [Accepted: 08/26/2013] [Indexed: 12/26/2022]
Abstract
Intermediary metabolism molecules are orchestrated into logical pathways stemming from history (L-amino acids, D-sugars) and dynamic constraints (hydrolysis of pyrophosphate or amide groups is the driving force of anabolism). Beside essential metabolites, numerous variants derive from programmed or accidental changes. Broken down, variants enter standard pathways, producing further variants. Macromolecule modification alters enzyme reactions specificity. Metabolism conform thermodynamic laws, precluding strict accuracy. Hence, for each regular pathway, a wealth of variants inputs and produces metabolites that are similar to but not the exact replicas of core metabolites. As corollary, a shadow, paralogous metabolism, is associated to standard metabolism. We focus on a logic of paralogous metabolism based on diversion of the core metabolic mimics into pathways where they are modified to minimize their input in the core pathways where they create havoc. We propose that a significant proportion of paralogues of well-characterized enzymes have evolved as the natural way to cope with paralogous metabolites. A second type of denouement uses a process where protecting/deprotecting unwanted metabolites - conceptually similar to the procedure used in the laboratory of an organic chemist - is used to enter a completely new catabolic pathway.
Collapse
Affiliation(s)
- Antoine Danchin
- Building G1, AMAbiotics SAS, 2 rue Gaston Crémieux, Evry, 91000, France
| | | |
Collapse
|
6
|
Collins R, Johansson AL, Karlberg T, Markova N, van den Berg S, Olesen K, Hammarström M, Flores A, Schüler H, Schiavone LH, Brzezinski P, Arnér ESJ, Högbom M. Biochemical discrimination between selenium and sulfur 1: a single residue provides selenium specificity to human selenocysteine lyase. PLoS One 2012; 7:e30581. [PMID: 22295093 PMCID: PMC3266270 DOI: 10.1371/journal.pone.0030581] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 12/19/2011] [Indexed: 11/24/2022] Open
Abstract
Selenium and sulfur are two closely related basic elements utilized in nature for a vast array of biochemical reactions. While toxic at higher concentrations, selenium is an essential trace element incorporated into selenoproteins as selenocysteine (Sec), the selenium analogue of cysteine (Cys). Sec lyases (SCLs) and Cys desulfurases (CDs) catalyze the removal of selenium or sulfur from Sec or Cys and generally act on both substrates. In contrast, human SCL (hSCL) is specific for Sec although the only difference between Sec and Cys is the identity of a single atom. The chemical basis of this selenium-over-sulfur discrimination is not understood. Here we describe the X-ray crystal structure of hSCL and identify Asp146 as the key residue that provides the Sec specificity. A D146K variant resulted in loss of Sec specificity and appearance of CD activity. A dynamic active site segment also provides the structural prerequisites for direct product delivery of selenide produced by Sec cleavage, thus avoiding release of reactive selenide species into the cell. We thus here define a molecular determinant for enzymatic specificity discrimination between a single selenium versus sulfur atom, elements with very similar chemical properties. Our findings thus provide molecular insights into a key level of control in human selenium and selenoprotein turnover and metabolism.
Collapse
Affiliation(s)
- Ruairi Collins
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Ann-Louise Johansson
- Stockholm Center for Biomembrane Research, Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences C4, Stockholm University, Stockholm, Sweden
| | - Tobias Karlberg
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Natalia Markova
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Susanne van den Berg
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Kenneth Olesen
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Martin Hammarström
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Alex Flores
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Herwig Schüler
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Lovisa Holmberg Schiavone
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Peter Brzezinski
- Stockholm Center for Biomembrane Research, Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences C4, Stockholm University, Stockholm, Sweden
| | - Elias S. J. Arnér
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Martin Högbom
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
- Stockholm Center for Biomembrane Research, Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences C4, Stockholm University, Stockholm, Sweden
- * E-mail:
| |
Collapse
|