1
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Gogar RK, Chhikara N, Vo M, Gilbert NC, Dunkle JA, Frantom PA. The structure of the SufS-SufE complex reveals interactions driving protected persulfide transfer in iron-sulfur cluster biogenesis. J Biol Chem 2024:107641. [PMID: 39122000 DOI: 10.1016/j.jbc.2024.107641] [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: 05/24/2024] [Revised: 07/11/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
Fe-S clusters are critical cofactors for redox chemistry in all organisms. The cysteine desulfurase, SufS, provides sulfur in the SUF Fe-S cluster bioassembly pathway. SufS is a dimeric, PLP-dependent enzyme that uses cysteine as a substrate to generate alanine and a covalent persulfide on an active site cysteine residue. SufS enzymes are activated by an accessory transpersulfurase protein, either SufE or SufU depending on the organism, which accepts the persulfide product and delivers it to downstream partners for Fe-S assembly. Here, using E. coli proteins, we present the first X-ray crystal structure of a SufS/SufE complex. There is a 1:1 stoichiometry with each monomeric unit of the EcSufS dimer bound to one EcSufE subunit, though one EcSufE is rotated ∼7° closer to the EcSufS active site. EcSufE makes clear interactions with the α16 helix of EcSufS and site-directed mutants of several α16 residues were deficient in EcSufE binding. Analysis of the EcSufE structure showed a loss of electron density at the EcSufS/EcSufE interface for a flexible loop containing the highly conserved residue R119. An R119A EcSufE variant binds EcSufS but is not active in cysteine desulfurase assays and fails to support Fe-S cluster bioassembly in vivo. 35S-transfer assays suggest that R119A EcSufE can receive a persulfide, suggesting the residue may function in a release mechanism. The structure of the EcSufS/EcSufE complex allows for comparison with other cysteine desulfurases to understand mechanisms of protected persulfide transfer across protein interfaces.
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Affiliation(s)
- Rajleen K Gogar
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Nidhi Chhikara
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Minh Vo
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Nathaniel C Gilbert
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Jack A Dunkle
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, AL, 35487, USA.
| | - Patrick A Frantom
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, AL, 35487, USA.
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2
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Kairis A, Neves BD, Couturier J, Remacle C, Rouhier N. Iron‑sulfur cluster synthesis in plastids by the SUF system: A mechanistic and structural perspective. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119797. [PMID: 39033932 DOI: 10.1016/j.bbamcr.2024.119797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 07/05/2024] [Accepted: 07/08/2024] [Indexed: 07/23/2024]
Abstract
About 50 proteins expressed in plastids of photosynthetic eukaryotes ligate iron‑sulfur (Fe-S) clusters and ensure vital functions in photosynthesis, sulfur and nitrogen assimilation, but also in the synthesis of pigments, vitamins and hormones. The synthesis of these Fe-S clusters, which are co- or post-translationally incorporated into these proteins, relies on several proteins belonging to the so-called sulfur mobilization (SUF) machinery. An Fe-S cluster is first de novo synthesized on a scaffold protein complex before additional late-acting maturation factors act in the specific transfer, possible conversion and insertion of this cluster into target recipient proteins. In this review, we will summarize what is known about the molecular mechanisms responsible for both the synthesis and transfer steps, focusing in particular on the structural aspects that allow the formation of the required protein complexes.
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Affiliation(s)
- Antoine Kairis
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France; Genetics and Physiology of Microalgae, InBios/Phytosystems Research Unit, University of Liège, 4000 Liège, Belgium
| | | | - Jérémy Couturier
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France; Institut Universitaire de France, F-75000 Paris, France
| | - Claire Remacle
- Genetics and Physiology of Microalgae, InBios/Phytosystems Research Unit, University of Liège, 4000 Liège, Belgium
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3
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Swindell J, Dos Santos PC. Interactions with sulfur acceptors modulate the reactivity of cysteine desulfurases and define their physiological functions. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119794. [PMID: 39033933 DOI: 10.1016/j.bbamcr.2024.119794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 06/21/2024] [Accepted: 07/11/2024] [Indexed: 07/23/2024]
Abstract
Sulfur-containing biomolecules such as [FeS] clusters, thiamin, biotin, molybdenum cofactor, and sulfur-containing tRNA nucleosides are essential for various biochemical reactions. The amino acid l-cysteine serves as the major sulfur source for the biosynthetic pathways of these sulfur-containing cofactors in prokaryotic and eukaryotic systems. The first reaction in the sulfur mobilization involves a class of pyridoxal-5'-phosphate (PLP) dependent enzymes catalyzing a Cys:sulfur acceptor sulfurtransferase reaction. The first half of the catalytic reaction involves a PLP-dependent CS bond cleavage, resulting in a persulfide enzyme intermediate. The second half of the reaction involves the subsequent transfer of the thiol group to a specific acceptor molecule, which is responsible for the physiological role of the enzyme. Structural and biochemical analysis of these Cys sulfurtransferase enzymes shows that specific protein-protein interactions with sulfur acceptors modulate their catalytic reactivity and restrict their biochemical functions.
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Affiliation(s)
- Jimmy Swindell
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, 27109, United States of America
| | - Patricia C Dos Santos
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, 27109, United States of America.
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4
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Gogar RK, Chhikara N, Vo M, Gilbert NC, Dunkle JA, Frantom PA. The structure of the SufS-SufE complex reveals interactions driving protected persulfide transfer in iron-sulfur cluster biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.595560. [PMID: 38826363 PMCID: PMC11142160 DOI: 10.1101/2024.05.23.595560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Fe-S clusters are critical cofactors for redox chemistry in all organisms. The cysteine desulfurase, SufS, provides sulfur in the SUF Fe-S cluster bioassembly pathway. SufS is a dimeric, PLP-dependent enzyme that uses cysteine as a substrate to generate alanine and a covalent persulfide on an active site cysteine residue. SufS enzymes are activated by an accessory transpersulfurase protein, either SufE or SufU depending on the organism, which accepts the persulfide product and delivers it to downstream partners for Fe-S assembly. Here, using E. coli proteins, we present the first X-ray crystal structure of a SufS/SufE complex. There is a 1:1 stoichiometry with each monomeric unit of the EcSufS dimer bound to one EcSufE subunit, though one EcSufE is rotated ~7° closer to the EcSufS active site. EcSufE makes clear interactions with the α16 helix of EcSufS and site-directed mutants of several α16 residues were deficient in EcSufE binding. Analysis of the EcSufE structure showed a loss of electron density at the EcSufS/EcSufE interface for a flexible loop containing the highly conserved residue R119. An R119A EcSufE variant binds EcSufS but is not active in cysteine desulfurase assays and fails to support Fe-S cluster bioassembly in vivo. 35S-transfer assays suggest that R119A EcSufE can receive a persulfide, suggesting the residue may function in a release mechanism. The structure of the EcSufS/EcSufE complex allows for comparison with other cysteine desulfurases to understand mechanisms of protected persulfide transfer across protein interfaces.
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Affiliation(s)
- Rajleen K. Gogar
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Nidhi Chhikara
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Minh Vo
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Nathaniel C. Gilbert
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Jack A. Dunkle
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Patrick A. Frantom
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, AL, 35487, USA
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5
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Benisch R, Andreas MP, Giessen TW. A widespread bacterial protein compartment sequesters and stores elemental sulfur. SCIENCE ADVANCES 2024; 10:eadk9345. [PMID: 38306423 PMCID: PMC10836720 DOI: 10.1126/sciadv.adk9345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Subcellular compartments often serve to store nutrients or sequester labile or toxic compounds. As bacteria mostly do not possess membrane-bound organelles, they often have to rely on protein-based compartments. Encapsulins are one of the most prevalent protein-based compartmentalization strategies found in prokaryotes. Here, we show that desulfurase encapsulins can sequester and store large amounts of crystalline elemental sulfur. We determine the 1.78-angstrom cryo-EM structure of a 24-nanometer desulfurase-loaded encapsulin. Elemental sulfur crystals can be formed inside the encapsulin shell in a desulfurase-dependent manner with l-cysteine as the sulfur donor. Sulfur accumulation can be influenced by the concentration and type of sulfur source in growth medium. The selectively permeable protein shell allows the storage of redox-labile elemental sulfur by excluding cellular reducing agents, while encapsulation substantially improves desulfurase activity and stability. These findings represent an example of a protein compartment able to accumulate and store elemental sulfur.
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Affiliation(s)
- Robert Benisch
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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6
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Elchennawi I, Carpentier P, Caux C, Ponge M, Ollagnier de Choudens S. Structural and Biochemical Characterization of Mycobacterium tuberculosis Zinc SufU-SufS Complex. Biomolecules 2023; 13:biom13050732. [PMID: 37238602 DOI: 10.3390/biom13050732] [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: 02/28/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 05/28/2023] Open
Abstract
Iron-sulfur (Fe-S) clusters are inorganic prosthetic groups in proteins composed exclusively of iron and inorganic sulfide. These cofactors are required in a wide range of critical cellular pathways. Iron-sulfur clusters do not form spontaneously in vivo; several proteins are required to mobilize sulfur and iron, assemble and traffic-nascent clusters. Bacteria have developed several Fe-S assembly systems, such as the ISC, NIF, and SUF systems. Interestingly, in Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), the SUF machinery is the primary Fe-S biogenesis system. This operon is essential for the viability of Mtb under normal growth conditions, and the genes it contains are known to be vulnerable, revealing the Mtb SUF system as an interesting target in the fight against tuberculosis. In the present study, two proteins of the Mtb SUF system were characterized for the first time: Rv1464(sufS) and Rv1465(sufU). The results presented reveal how these two proteins work together and thus provide insights into Fe-S biogenesis/metabolism by this pathogen. Combining biochemistry and structural approaches, we showed that Rv1464 is a type II cysteine-desulfurase enzyme and that Rv1465 is a zinc-dependent protein interacting with Rv1464. Endowed with a sulfurtransferase activity, Rv1465 significantly enhances the cysteine-desulfurase activity of Rv1464 by transferring the sulfur atom from persulfide on Rv1464 to its conserved Cys40 residue. The zinc ion is important for the sulfur transfer reaction between SufS and SufU, and His354 in SufS plays an essential role in this reaction. Finally, we showed that Mtb SufS-SufU is more resistant to oxidative stress than E. coli SufS-SufE and that the presence of zinc in SufU is likely responsible for this improved resistance. This study on Rv1464 and Rv1465 will help guide the design of future anti-tuberculosis agents.
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Affiliation(s)
- Ingie Elchennawi
- CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, 38000 Grenoble, France
| | - Philippe Carpentier
- CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, 38000 Grenoble, France
- European Synchrotron Radiation Facility, 38000 Grenoble, France
| | - Christelle Caux
- CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, 38000 Grenoble, France
| | - Marine Ponge
- CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, 38000 Grenoble, France
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7
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Gogar RK, Carroll F, Conte JV, Nasef M, Dunkle JA, Frantom PA. The β-latch structural element of the SufS cysteine desulfurase mediates active site accessibility and SufE transpersulfurase positioning. J Biol Chem 2023; 299:102966. [PMID: 36736428 PMCID: PMC10011822 DOI: 10.1016/j.jbc.2023.102966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Under oxidative stress and iron starvation conditions, Escherichia coli uses the Suf pathway to assemble iron-sulfur clusters. The Suf pathway mobilizes sulfur via SufS, a type II cysteine desulfurase. SufS is a pyridoxal-5'-phosphate-dependent enzyme that uses cysteine to generate alanine and an active-site persulfide (C364-S-S-). The SufS persulfide is protected from external oxidants/reductants and requires the transpersulfurase, SufE, to accept the persulfide to complete the SufS catalytic cycle. Recent reports on SufS identified a conserved "β-latch" structural element that includes the α6 helix, a glycine-rich loop, a β-hairpin, and a cis-proline residue. To identify a functional role for the β-latch, we used site-directed mutagenesis to obtain the N99D and N99A SufS variants. N99 is a conserved residue that connects the α6 helix to the backbone of the glycine-rich loop via hydrogen bonds. Our x-ray crystal structures for N99A and N99D SufS show a distorted beta-hairpin and glycine-rich loop, respectively, along with changes in the dimer geometry. The structural disruption of the N99 variants allowed the external reductant TCEP to react with the active-site C364-persulfide intermediate to complete the SufS catalytic cycle in the absence of SufE. The substitutions also appear to disrupt formation of a high-affinity, close approach SufS-SufE complex as measured with fluorescence polarization. Collectively, these findings demonstrate that the β-latch does not affect the chemistry of persulfide formation but does protect it from undesired reductants. The data also indicate the β-latch plays an unexpected role in forming a close approach SufS-SufE complex to promote persulfide transfer.
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Affiliation(s)
- Rajleen K Gogar
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, Alabama, USA
| | - Franki Carroll
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, Alabama, USA
| | - Juliana V Conte
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, Alabama, USA
| | - Mohamed Nasef
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, Alabama, USA
| | - Jack A Dunkle
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, Alabama, USA.
| | - Patrick A Frantom
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, Alabama, USA.
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8
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Hudspeth J, Boncella AE, Sabo ET, Andrews T, Boyd JM, Morrison CN. Structural and Biochemical Characterization of Staphylococcus aureus Cysteine Desulfurase Complex SufSU. ACS OMEGA 2022; 7:44124-44133. [PMID: 36506149 PMCID: PMC9730764 DOI: 10.1021/acsomega.2c05576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/09/2022] [Indexed: 06/01/2023]
Abstract
In this work, we provide the first in vitro characterization of two essential proteins from Staphylococcus aureus (S. aureus) involved in iron-sulfur (Fe-S) cluster biogenesis: the cysteine desulfurase SufS and the sulfurtransferase SufU. Together, these proteins form the transient SufSU complex and execute the first stage of Fe-S cluster biogenesis in the SUF-like pathway in Gram-positive bacteria. The proteins involved in the SUF-like pathway, such as SufS and SufU, are essential in Gram-positive bacteria since these bacteria tend to lack redundant Fe-S cluster biogenesis pathways. Most previous work characterizing the SUF-like pathway has focused on Bacillus subtilis (B. subtilis). We focus on the SUF-like pathway in S. aureus because of its potential to serve as a therapeutic target to treat S. aureus infections. Herein, we characterize S. aureus SufS (SaSufS) by X-ray crystallography and UV-vis spectroscopy, and we characterize S. aureus SufU (SaSufU) by a zinc binding fluorescence assay and small-angle X-ray scattering. We show that SaSufS is a type II cysteine desulfurase and that SaSufU is a Zn2+-containing sulfurtransferase. Additionally, we evaluated the cysteine desulfurase activity of the SaSufSU complex and compared its activity to that of B. subtilis SufSU. Subsequent cross-species activity analysis reveals a surprising result: SaSufS is significantly less stimulated by SufU than BsSufS. Our results set a basis for further characterization of SaSufSU as well as the development of new therapeutic strategies for treating infections caused by S. aureus by inhibiting the SUF-like pathway.
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Affiliation(s)
- Jesse
D. Hudspeth
- Department
of Chemistry, Colorado School of Mines, 1500 Illinois St, Golden, Colorado 80401, United States
| | - Amy E. Boncella
- Department
of Chemistry, Colorado School of Mines, 1500 Illinois St, Golden, Colorado 80401, United States
| | - Emily T. Sabo
- Department
of Chemistry, Colorado School of Mines, 1500 Illinois St, Golden, Colorado 80401, United States
| | - Taylor Andrews
- Department
of Biochemistry and Microbiology, Rutgers
University, 76 Lipman Dr., New Brunswick, New Jersey 08901, United States
| | - Jeffrey M. Boyd
- Department
of Biochemistry and Microbiology, Rutgers
University, 76 Lipman Dr., New Brunswick, New Jersey 08901, United States
| | - Christine N. Morrison
- Department
of Chemistry, Colorado School of Mines, 1500 Illinois St, Golden, Colorado 80401, United States
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9
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Cuevasanta E, Benchoam D, Semelak JA, Möller MN, Zeida A, Trujillo M, Alvarez B, Estrin DA. Possible molecular basis of the biochemical effects of cysteine-derived persulfides. Front Mol Biosci 2022; 9:975988. [PMID: 36213129 PMCID: PMC9538486 DOI: 10.3389/fmolb.2022.975988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/15/2022] [Indexed: 12/03/2022] Open
Abstract
Persulfides (RSSH/RSS−) are species closely related to thiols (RSH/RS−) and hydrogen sulfide (H2S/HS−), and can be formed in biological systems in both low and high molecular weight cysteine-containing compounds. They are key intermediates in catabolic and biosynthetic processes, and have been proposed to participate in the transduction of hydrogen sulfide effects. Persulfides are acidic, more acidic than thiols, and the persulfide anions are expected to be the predominant species at neutral pH. The persulfide anion has high nucleophilicity, due in part to the alpha effect, i.e., the increased reactivity of a nucleophile when the neighboring atom has high electron density. In addition, persulfides have electrophilic character, a property that is absent in both thiols and hydrogen sulfide. In this article, the biochemistry of persulfides is described, and the possible ways in which the formation of a persulfide could impact on the properties of the biomolecule involved are discussed.
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Affiliation(s)
- Ernesto Cuevasanta
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Unidad de Bioquímica Analítica, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Dayana Benchoam
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
- Graduate Program in Chemistry, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Jonathan A. Semelak
- Departamento de Química Inorgánica, Analítica y Química Física, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET, Buenos Aires, Argentina
| | - Matías N. Möller
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ari Zeida
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Madia Trujillo
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET, Buenos Aires, Argentina
- *Correspondence: Darío A. Estrin,
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10
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Fujishiro T, Nakamura R, Kunichika K, Takahashi Y. Structural diversity of cysteine desulfurases involved in iron-sulfur cluster biosynthesis. Biophys Physicobiol 2022; 19:1-18. [PMID: 35377584 PMCID: PMC8918507 DOI: 10.2142/biophysico.bppb-v19.0001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/02/2022] [Indexed: 12/04/2022] Open
Abstract
Cysteine desulfurases are pyridoxal-5'-phosphate (PLP)-dependent enzymes that mobilize sulfur derived from the l-cysteine substrate to the partner sulfur acceptor proteins. Three cysteine desulfurases, IscS, NifS, and SufS, have been identified in ISC, NIF, and SUF/SUF-like systems for iron-sulfur (Fe-S) cluster biosynthesis, respectively. These cysteine desulfurases have been investigated over decades, providing insights into shared/distinct catalytic processes based on two types of enzymes (type I: IscS and NifS, type II: SufS). This review summarizes the insights into the structural/functional varieties of bacterial and eukaryotic cysteine desulfurases involved in Fe-S cluster biosynthetic systems. In addition, an inactive cysteine desulfurase IscS paralog, which contains pyridoxamine-5'-phosphate (PMP), instead of PLP, is also described to account for its hypothetical function in Fe-S cluster biosynthesis involving this paralog. The structural basis for cysteine desulfurase functions will be a stepping stone towards understanding the diversity and evolution of Fe-S cluster biosynthesis.
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Affiliation(s)
- Takashi Fujishiro
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Ryosuke Nakamura
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Kouhei Kunichika
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Yasuhiro Takahashi
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
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11
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Abstract
Iron–sulfur (Fe–S) clusters are protein cofactors of a multitude of enzymes performing essential biological functions. Specialized multi-protein machineries present in all types of organisms support their biosynthesis. These machineries encompass a scaffold protein on which Fe–S clusters are assembled and a cysteine desulfurase that provides sulfur in the form of a persulfide. The sulfide ions are produced by reductive cleavage of the persulfide, which involves specific reductase systems. Several other components are required for Fe–S biosynthesis, including frataxin, a key protein of controversial function and accessory components for insertion of Fe–S clusters in client proteins. Fe–S cluster biosynthesis is thought to rely on concerted and carefully orchestrated processes. However, the elucidation of the mechanisms of their assembly has remained a challenging task due to the biochemical versatility of iron and sulfur and the relative instability of Fe–S clusters. Nonetheless, significant progresses have been achieved in the past years, using biochemical, spectroscopic and structural approaches with reconstituted system in vitro. In this paper, we review the most recent advances on the mechanism of assembly for the founding member of the Fe–S cluster family, the [2Fe2S] cluster that is the building block of all other Fe–S clusters. The aim is to provide a survey of the mechanisms of iron and sulfur insertion in the scaffold proteins by examining how these processes are coordinated, how sulfide is produced and how the dinuclear [2Fe2S] cluster is formed, keeping in mind the question of the physiological relevance of the reconstituted systems. We also cover the latest outcomes on the functional role of the controversial frataxin protein in Fe–S cluster biosynthesis.
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12
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Blahut M, Sanchez E, Fisher CE, Outten FW. Fe-S cluster biogenesis by the bacterial Suf pathway. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118829. [PMID: 32822728 DOI: 10.1016/j.bbamcr.2020.118829] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 01/01/2023]
Abstract
Biogenesis of iron-sulfur (FeS) clusters in an essential process in living organisms due to the critical role of FeS cluster proteins in myriad cell functions. During biogenesis of FeS clusters, multi-protein complexes are used to drive the mobilization and protection of reactive sulfur and iron intermediates, regulate assembly of various FeS clusters on an ATPase-dependent, multi-protein scaffold, and target nascent clusters to their downstream protein targets. The evolutionarily ancient sulfur formation (Suf) pathway for FeS cluster assembly is found in bacteria and archaea. In Escherichia coli, the Suf pathway functions as an emergency pathway under conditions of iron limitation or oxidative stress. In other pathogenic bacteria, such as Mycobacterium tuberculosis and Enterococcus faecalis, the Suf pathway is the sole source for FeS clusters and therefore is a potential target for the development of novel antibacterial compounds. Here we summarize the considerable progress that has been made in characterizing the first step of mobilization and protection of reactive sulfur carried out by the SufS-SufE or SufS-SufU complex, FeS cluster assembly on SufBC2D scaffold complexes, and the downstream trafficking of nascent FeS clusters to A-type carrier (ATC) proteins. Cell Biology of Metals III edited by Roland Lill and Mick Petris.
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Affiliation(s)
- Matthew Blahut
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - Enis Sanchez
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - Claire E Fisher
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - F Wayne Outten
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA.
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13
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Structural Analysis of an l-Cysteine Desulfurase from an Ssp DNA Phosphorothioation System. mBio 2020; 11:mBio.00488-20. [PMID: 32345643 PMCID: PMC7188994 DOI: 10.1128/mbio.00488-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Apart from its roles in Fe-S cluster assembly, tRNA thiolation, and sulfur-containing cofactor biosynthesis, cysteine desulfurase serves as a sulfur donor in the DNA PT modification, in which a sulfur atom substitutes a nonbridging oxygen in the DNA phosphodiester backbone. The initial sulfur mobilization from l-cysteine is catalyzed by the SspA cysteine desulfurase in the SspABCD-mediated DNA PT modification system. By determining the crystal structure of SspA, the study presents the molecular mechanism that SspA employs to recognize its cysteine substrate and PLP cofactor. To overcome the long distance (8.9 Å) between the catalytic Cys314 and the cysteine substrate, a conformational change occurs to bring Cys314 to the vicinity of the substrate, allowing for nucleophilic attack. DNA phosphorothioate (PT) modification, in which the nonbridging oxygen in the sugar-phosphate backbone is substituted by sulfur, is catalyzed by DndABCDE or SspABCD in a double-stranded or single-stranded manner, respectively. In Dnd and Ssp systems, mobilization of sulfur in PT formation starts with the activation of the sulfur atom of cysteine catalyzed by the DndA and SspA cysteine desulfurases, respectively. Despite playing the same biochemical role, SspA cannot be functionally replaced by DndA, indicating its unique physiological properties. In this study, we solved the crystal structure of Vibrio cyclitrophicus SspA in complex with its natural substrate, cysteine, and cofactor, pyridoxal phosphate (PLP), at a resolution of 1.80 Å. Our solved structure revealed the molecular mechanism that SspA employs to recognize its cysteine substrate and PLP cofactor, suggesting a common binding mode shared by cysteine desulfurases. In addition, although the distance between the catalytic Cys314 and the substrate cysteine is 8.9 Å, which is too far for direct interaction, our structural modeling and biochemical analysis revealed a conformational change in the active site region toward the cysteine substrate to move them close to each other to facilitate the nucleophilic attack. Finally, the pulldown analysis showed that SspA could form a complex with SspD, an ATP pyrophosphatase, suggesting that SspD might potentially accept the activated sulfur atom directly from SspA, providing further insights into the biochemical pathway of Ssp-mediated PT modification.
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14
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Dunkle JA, Bruno MR, Frantom PA. Structural evidence for a latch mechanism regulating access to the active site of SufS-family cysteine desulfurases. Acta Crystallogr D Struct Biol 2020; 76:291-301. [PMID: 32133993 PMCID: PMC7057215 DOI: 10.1107/s2059798320000790] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 01/22/2020] [Indexed: 11/10/2022] Open
Abstract
Cysteine serves as the sulfur source for the biosynthesis of Fe-S clusters and thio-cofactors, molecules that are required for core metabolic processes in all organisms. Therefore, cysteine desulfurases, which mobilize sulfur for its incorporation into thio-cofactors by cleaving the Cα-S bond of cysteine, are ubiquitous in nature. SufS, a type 2 cysteine desulfurase that is present in plants and microorganisms, mobilizes sulfur from cysteine to the transpersulfurase SufE to initiate Fe-S biosynthesis. Here, a 1.5 Å resolution X-ray crystal structure of the Escherichia coli SufS homodimer is reported which adopts a state in which the two monomers are rotated relative to their resting state, displacing a β-hairpin from its typical position blocking transpersulfurase access to the SufS active site. A global structure and sequence analysis of SufS family members indicates that the active-site β-hairpin is likely to require adjacent structural elements to function as a β-latch regulating access to the SufS active site.
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Affiliation(s)
- Jack A. Dunkle
- Department of Chemistry and Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL 35401, USA
| | - Michael R. Bruno
- Department of Chemistry and Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL 35401, USA
| | - Patrick A. Frantom
- Department of Chemistry and Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL 35401, USA
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15
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Persulfides, at the crossroads between hydrogen sulfide and thiols. Essays Biochem 2020; 64:155-168. [DOI: 10.1042/ebc20190049] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 12/14/2022]
Abstract
AbstractPersulfides (RSSH/RSS−) can be formed in protein and non-protein thiols (RSH) through several different pathways, some of which are dependent on hydrogen sulfide (H2S/HS−). In addition to their roles in biosynthetic processes, persulfides are possible transducers of physiological effects of H2S through the modification of critical cysteines. Persulfides have a very rich biological chemistry that is currently under investigation. They are more nucleophilic and acidic than thiols and, unlike thiols, they can also be electrophilic. They are especially good one-electron reductants. Methods to detect their formation are under continuous development. In this minireview we describe the pathways of formation of persulfides, their biochemical properties and the techniques available for their detection, and we discuss the possible implications of their formation in biological systems.
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16
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Nakamura R, Hikita M, Ogawa S, Takahashi Y, Fujishiro T. Snapshots of PLP‐substrate and PLP‐product external aldimines as intermediates in two types of cysteine desulfurase enzymes. FEBS J 2019; 287:1138-1154. [DOI: 10.1111/febs.15081] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/11/2019] [Accepted: 10/01/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Ryosuke Nakamura
- Department of Biochemistry and Molecular Biology Graduate School of Science and Engineering Saitama University Saitama Japan
| | - Masahide Hikita
- Structural Biology Research Center, Photon Factory Institute of Materials Structure Science High Energy Accelerator Research Organization Tsukuba Japan
| | - Shoko Ogawa
- Department of Biochemistry and Molecular Biology Graduate School of Science and Engineering Saitama University Saitama Japan
| | - Yasuhiro Takahashi
- Department of Biochemistry and Molecular Biology Graduate School of Science and Engineering Saitama University Saitama Japan
| | - Takashi Fujishiro
- Department of Biochemistry and Molecular Biology Graduate School of Science and Engineering Saitama University Saitama Japan
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17
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Blahut M, Wise CE, Bruno MR, Dong G, Makris TM, Frantom PA, Dunkle JA, Outten FW. Direct observation of intermediates in the SufS cysteine desulfurase reaction reveals functional roles of conserved active-site residues. J Biol Chem 2019; 294:12444-12458. [PMID: 31248989 DOI: 10.1074/jbc.ra119.009471] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/16/2019] [Indexed: 12/25/2022] Open
Abstract
Iron-sulfur (Fe-S) clusters are necessary for the proper functioning of numerous metalloproteins. Fe-S cluster (Isc) and sulfur utilization factor (Suf) pathways are the key biosynthetic routes responsible for generating these Fe-S cluster prosthetic groups in Escherichia coli Although Isc dominates under normal conditions, Suf takes over during periods of iron depletion and oxidative stress. Sulfur acquisition via these systems relies on the ability to remove sulfur from free cysteine using a cysteine desulfurase mechanism. In the Suf pathway, the dimeric SufS protein uses the cofactor pyridoxal 5'-phosphate (PLP) to abstract sulfur from free cysteine, resulting in the production of alanine and persulfide. Despite much progress, the stepwise mechanism by which this PLP-dependent enzyme operates remains unclear. Here, using rapid-mixing kinetics in conjunction with X-ray crystallography, we analyzed the pre-steady-state kinetics of this process while assigning early intermediates of the mechanism. We employed H123A and C364A SufS variants to trap Cys-aldimine and Cys-ketimine intermediates of the cysteine desulfurase reaction, enabling direct observations of these intermediates and associated conformational changes of the SufS active site. Of note, we propose that Cys-364 is essential for positioning the Cys-aldimine for Cα deprotonation, His-123 acts to protonate the Ala-enamine intermediate, and Arg-56 facilitates catalysis by hydrogen bonding with the sulfhydryl of Cys-aldimine. Our results, along with previous SufS structural findings, suggest a detailed model of the SufS-catalyzed reaction from Cys binding to C-S bond cleavage and indicate that Arg-56, His-123, and Cys-364 are critical SufS residues in this C-S bond cleavage pathway.
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Affiliation(s)
- Matthew Blahut
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Courtney E Wise
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Michael R Bruno
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487
| | - Guangchao Dong
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Thomas M Makris
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Patrick A Frantom
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487
| | - Jack A Dunkle
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487.
| | - F Wayne Outten
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208.
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18
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Benchoam D, Cuevasanta E, Möller MN, Alvarez B. Hydrogen Sulfide and Persulfides Oxidation by Biologically Relevant Oxidizing Species. Antioxidants (Basel) 2019; 8:antiox8020048. [PMID: 30813248 PMCID: PMC6406583 DOI: 10.3390/antiox8020048] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 12/12/2022] Open
Abstract
Hydrogen sulfide (H2S/HS–) can be formed in mammalian tissues and exert physiological effects. It can react with metal centers and oxidized thiol products such as disulfides (RSSR) and sulfenic acids (RSOH). Reactions with oxidized thiol products form persulfides (RSSH/RSS–). Persulfides have been proposed to transduce the signaling effects of H2S through the modification of critical cysteines. They are more nucleophilic and acidic than thiols and, contrary to thiols, also possess electrophilic character. In this review, we summarize the biochemistry of hydrogen sulfide and persulfides, focusing on redox aspects. We describe biologically relevant one- and two-electron oxidants and their reactions with H2S and persulfides, as well as the fates of the oxidation products. The biological implications are discussed.
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Affiliation(s)
- Dayana Benchoam
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay.
- Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo 11800, Uruguay.
| | - Ernesto Cuevasanta
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay.
- Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo 11800, Uruguay.
- Unidad de Bioquímica Analítica, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay.
| | - Matías N Möller
- Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo 11800, Uruguay.
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay.
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay.
- Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo 11800, Uruguay.
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19
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Dunkle JA, Bruno MR, Outten FW, Frantom PA. Structural Evidence for Dimer-Interface-Driven Regulation of the Type II Cysteine Desulfurase, SufS. Biochemistry 2019; 58:687-696. [PMID: 30571100 DOI: 10.1021/acs.biochem.8b01122] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
SufS is a type II cysteine desulfurase and acts as the initial step in the Suf Fe-S cluster assembly pathway. In Escherichia coli, this pathway is utilized under conditions of oxidative stress and is resistant to reactive oxygen species. Mechanistically, this means SufS must shift between protecting a covalent persulfide intermediate and making it available for transfer to the next protein partner in the pathway, SufE. Here, we report five X-ray crystal structures of SufS including a new structure of SufS containing an inward-facing persulfide intermediate on C364. Additional structures of SufS variants with substitutions at the dimer interface show changes in dimer geometry and suggest a conserved β-hairpin structure plays a role in mediating interactions with SufE. These new structures, along with previous HDX-MS and biochemical data, identify an interaction network capable of communication between active-sites of the SufS dimer coordinating the shift between desulfurase and transpersulfurase activities.
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Affiliation(s)
- Jack A Dunkle
- Department of Chemistry & Biochemistry , The University of Alabama , Tuscaloosa , Alabama 35487 , United States
| | - Michael R Bruno
- Department of Chemistry & Biochemistry , The University of Alabama , Tuscaloosa , Alabama 35487 , United States
| | - F Wayne Outten
- Department of Chemistry & Biochemistry , The University of South Carolina , Columbia , South Carolina 29208 , United States
| | - Patrick A Frantom
- Department of Chemistry & Biochemistry , The University of Alabama , Tuscaloosa , Alabama 35487 , United States
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20
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Metallocluster transactions: dynamic protein interactions guide the biosynthesis of Fe-S clusters in bacteria. Biochem Soc Trans 2018; 46:1593-1603. [PMID: 30381339 DOI: 10.1042/bst20180365] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/12/2018] [Accepted: 09/14/2018] [Indexed: 12/22/2022]
Abstract
Iron-sulfur (Fe-S) clusters are ubiquitous cofactors present in all domains of life. The chemistries catalyzed by these inorganic cofactors are diverse and their associated enzymes are involved in many cellular processes. Despite the wide range of structures reported for Fe-S clusters inserted into proteins, the biological synthesis of all Fe-S clusters starts with the assembly of simple units of 2Fe-2S and 4Fe-4S clusters. Several systems have been associated with the formation of Fe-S clusters in bacteria with varying phylogenetic origins and number of biosynthetic and regulatory components. All systems, however, construct Fe-S clusters through a similar biosynthetic scheme involving three main steps: (1) sulfur activation by a cysteine desulfurase, (2) cluster assembly by a scaffold protein, and (3) guided delivery of Fe-S units to either final acceptors or biosynthetic enzymes involved in the formation of complex metalloclusters. Another unifying feature on the biological formation of Fe-S clusters in bacteria is that these systems are tightly regulated by a network of protein interactions. Thus, the formation of transient protein complexes among biosynthetic components allows for the direct transfer of reactive sulfur and Fe-S intermediates preventing oxygen damage and reactions with non-physiological targets. Recent studies revealed the importance of reciprocal signature sequence motifs that enable specific protein-protein interactions and consequently guide the transactions between physiological donors and acceptors. Such findings provide insights into strategies used by bacteria to regulate the flow of reactive intermediates and provide protein barcodes to uncover yet-unidentified cellular components involved in Fe-S metabolism.
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21
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Dos Santos PC. B. subtilis as a Model for Studying the Assembly of Fe-S Clusters in Gram-Positive Bacteria. Methods Enzymol 2018; 595:185-212. [PMID: 28882201 DOI: 10.1016/bs.mie.2017.07.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Complexes of iron and sulfur (Fe-S clusters) are widely distributed in nature and participate in essential biochemical reactions. The biological formation of Fe-S clusters involves dedicated pathways responsible for the mobilization of sulfur, the assembly of Fe-S clusters, and the transfer of these clusters to target proteins. Genomic analysis of Bacillus subtilis and other Gram-positive bacteria indicated the presence of only one Fe-S cluster biosynthesis pathway, which is distinct in number of components and organization from previously studied systems. B. subtilis has been used as a model system for the characterization of cysteine desulfurases responsible for sulfur mobilization reactions in the biogenesis of Fe-S clusters and other sulfur-containing cofactors. Cysteine desulfurases catalyze the cleavage of the C-S bond from the amino acid cysteine and subsequent transfer of sulfur to acceptor molecules. These reactions can be monitored by the rate of alanine formation, the first product in the reaction, and sulfide formation, a byproduct of reactions performed under reducing conditions. The assembly of Fe-S clusters on protein scaffolds and the transfer of these clusters to target acceptors are determined through a combination of spectroscopic methods probing the rate of cluster assembly and transfer. This chapter provides a description of reactions promoting the assembly of Fe-S clusters in bacteria as well as methods used to study functions of each biosynthetic component and identify mechanistic differences employed by these enzymes across different pathways.
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22
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Kim D, Singh H, Dai Y, Dong G, Busenlehner LS, Outten FW, Frantom PA. Changes in Protein Dynamics in Escherichia coli SufS Reveal a Possible Conserved Regulatory Mechanism in Type II Cysteine Desulfurase Systems. Biochemistry 2018; 57:5210-5217. [PMID: 29589903 DOI: 10.1021/acs.biochem.7b01275] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the Suf Fe-S cluster assembly pathway, the activity of the cysteine desulfurase, SufS, is regulated by interactions with the accessory sulfotransferase protein, SufE. SufE has been shown to stimulate SufS activity, likely by inducing conformational changes in the SufS active site that promote the desulfurase step and by acting as an efficient persulfide acceptor in the transpersulfuration step. Previous results point toward an additional level of regulation through a "half-sites" mechanism that affects the stoichiometry and affinity for SufE as the dimeric SufS shifts between desulfurase and transpersulfuration activities. Investigation of the covalent persulfide intermediate of SufS by backbone amide hydrogen-deuterium exchange mass spectrometry identified two active site peptides (residues 225-236 and 356-366) and two peptides at the dimer interface of SufS (residues 88-100 and 243-255) that exhibit changes in deuterium uptake upon formation of the intermediate. Residues in these peptides are organized to form a conduit between the two active sites upon persulfide formation and include key cross-monomer interactions, suggesting they may play a role in the half-sites regulation. Three evolutionarily conserved residues at the dimer interface (R92, E96, and E250) were investigated by alanine scanning mutagenesis. Two of the substituted enzymes (E96A and E250A SufS) resulted in 6-fold increases in the value of KSufE, confirming a functional role. Re-examination of the dimer interface in reported crystal structures of SufS and the SufS homologue CsdA identified previously unnoticed residue mobility at the dimer interface. The identification of conformational changes at the dimer interface by hydrogen-deuterium exchange confirmed by mutagenesis and structural reports provides a physical mechanism for active site communication in the half-sites regulation of SufS activity. Given the conservation of the interface interactions, this mechanism may be broadly applicable to type II cysteine desulfurase systems.
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Affiliation(s)
- Dokyong Kim
- Department of Chemistry and Biochemistry , The University of Alabama , Tuscaloosa , Alabama 35487 , United States
| | - Harsimran Singh
- Department of Chemistry and Biochemistry , The University of Alabama , Tuscaloosa , Alabama 35487 , United States
| | - Yuyuan Dai
- Department of Chemistry and Biochemistry , The University of South Carolina , Columbia , South Carolina 29208 , United States
| | - Guangchao Dong
- Department of Chemistry and Biochemistry , The University of South Carolina , Columbia , South Carolina 29208 , United States
| | - Laura S Busenlehner
- Department of Chemistry and Biochemistry , The University of Alabama , Tuscaloosa , Alabama 35487 , United States
| | - F Wayne Outten
- Department of Chemistry and Biochemistry , The University of South Carolina , Columbia , South Carolina 29208 , United States
| | - Patrick A Frantom
- Department of Chemistry and Biochemistry , The University of Alabama , Tuscaloosa , Alabama 35487 , United States
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23
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Lu Y. Assembly and Transfer of Iron-Sulfur Clusters in the Plastid. FRONTIERS IN PLANT SCIENCE 2018; 9:336. [PMID: 29662496 PMCID: PMC5890173 DOI: 10.3389/fpls.2018.00336] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/28/2018] [Indexed: 05/09/2023]
Abstract
Iron-Sulfur (Fe-S) clusters and proteins are essential to many growth and developmental processes. In plants, they exist in the plastids, mitochondria, cytosol, and nucleus. Six types of Fe-S clusters are found in the plastid: classic 2Fe-2S, NEET-type 2Fe-2S, Rieske-type 2Fe-2S, 3Fe-4S, 4Fe-4S, and siroheme 4Fe-4S. Classic, NEET-type, and Rieske-type 2Fe-2S clusters have the same 2Fe-2S core; similarly, common and siroheme 4Fe-4S clusters have the same 4Fe-4S core. Plastidial Fe-S clusters are assembled by the sulfur mobilization (SUF) pathway, which contains cysteine desulfurase (EC 2.8.1.7), sulfur transferase (EC 2.8.1.3), Fe-S scaffold complex, and Fe-S carrier proteins. The plastidial cysteine desulfurase-sulfur transferase-Fe-S-scaffold complex system is responsible for de novo assembly of all plastidial Fe-S clusters. However, different types of Fe-S clusters are transferred to recipient proteins via respective Fe-S carrier proteins. This review focuses on recent discoveries on the molecular functions of different assembly and transfer factors involved in the plastidial SUF pathway. It also discusses potential points for regulation of the SUF pathway, relationships among the plastidial, mitochondrial, and cytosolic Fe-S assembly and transfer pathways, as well as several open questions about the carrier proteins for Rieske-type 2Fe-2S, NEET-type 2Fe-2S, and 3F-4S clusters.
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24
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Pérard J, Ollagnier de Choudens S. Iron-sulfur clusters biogenesis by the SUF machinery: close to the molecular mechanism understanding. J Biol Inorg Chem 2017; 23:581-596. [PMID: 29280002 PMCID: PMC6006206 DOI: 10.1007/s00775-017-1527-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 12/11/2017] [Indexed: 11/30/2022]
Abstract
Iron–sulfur clusters (Fe–S) are amongst the most ancient and versatile inorganic cofactors in nature which are used by proteins for fundamental biological processes. Multiprotein machineries (NIF, ISC, SUF) exist for Fe–S cluster biogenesis which are mainly conserved from bacteria to human. SUF system (sufABCDSE operon) plays a general role in many bacteria under conditions of iron limitation or oxidative stress. In this mini-review, we will summarize the current understanding of the molecular mechanism of Fe–S biogenesis by SUF. The advances in our understanding of the molecular aspects of SUF originate from biochemical, biophysical and recent structural studies. Combined with recent in vivo experiments, the understanding of the Fe–S biogenesis mechanism considerably moved forward.
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Affiliation(s)
- J Pérard
- Laboratoire de Chimie et Biologie des Métaux, Biocat, Université Grenoble Alpes, Grenoble, France.,Laboratoire de Chimie et Biologie des Métaux, CNRS, BioCat, UMR 5249, Grenoble, France.,CEA-Grenoble, DRF/BIG/CBM, Grenoble, France
| | - Sandrine Ollagnier de Choudens
- Laboratoire de Chimie et Biologie des Métaux, Biocat, Université Grenoble Alpes, Grenoble, France. .,Laboratoire de Chimie et Biologie des Métaux, CNRS, BioCat, UMR 5249, Grenoble, France. .,CEA-Grenoble, DRF/BIG/CBM, Grenoble, France.
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25
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Fujishiro T, Terahata T, Kunichika K, Yokoyama N, Maruyama C, Asai K, Takahashi Y. Zinc-Ligand Swapping Mediated Complex Formation and Sulfur Transfer between SufS and SufU for Iron–Sulfur Cluster Biogenesis in Bacillus subtilis. J Am Chem Soc 2017; 139:18464-18467. [DOI: 10.1021/jacs.7b11307] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Takashi Fujishiro
- Department
of Biochemistry and Molecular Biology, Graduate School of Science
and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Takuya Terahata
- Department
of Biochemistry and Molecular Biology, Graduate School of Science
and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Kouhei Kunichika
- Department
of Biochemistry and Molecular Biology, Graduate School of Science
and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Nao Yokoyama
- Department
of Biochemistry and Molecular Biology, Graduate School of Science
and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Chihiro Maruyama
- Department
of Biochemistry and Molecular Biology, Graduate School of Science
and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Kei Asai
- Department
of Bioscience, Graduate School of Agriculture, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yasuhiro Takahashi
- Department
of Biochemistry and Molecular Biology, Graduate School of Science
and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
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Peña-Soler E, Aranda J, López-Estepa M, Gómez S, Garces F, Coll M, Fernández FJ, Tuñon I, Vega MC. Insights into the inhibited form of the redox-sensitive SufE-like sulfur acceptor CsdE. PLoS One 2017; 12:e0186286. [PMID: 29045454 PMCID: PMC5646864 DOI: 10.1371/journal.pone.0186286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/28/2017] [Indexed: 11/18/2022] Open
Abstract
Sulfur trafficking in living organisms relies on transpersulfuration reactions consisting in the enzyme-catalyzed transfer of S atoms via activated persulfidic S across protein-protein interfaces. The recent elucidation of the mechanistic basis for transpersulfuration in the CsdA-CsdE model system has paved the way for a better understanding of its role under oxidative stress. Herein we present the crystal structure of the oxidized, inactivated CsdE dimer at 2.4 Å resolution. The structure sheds light into the activation of the Cys61 nucleophile on its way from a solvent-secluded position in free CsdE to a fully extended conformation in the persulfurated CsdA-CsdE complex. Molecular dynamics simulations of available CsdE structures allow to delineate the sequence of conformational changes underwent by CsdE and to pinpoint the key role played by the deprotonation of the Cys61 thiol. The low-energy subunit orientation in the disulfide-bridged CsdE dimer demonstrates the likely physiologic relevance of this oxidative dead-end form of CsdE, suggesting that CsdE could act as a redox sensor in vivo.
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Affiliation(s)
- Esther Peña-Soler
- Chemical and Physical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
- Institute for Biomedical Research (IRB Barcelona), Barcelona, Spain
| | - Juan Aranda
- Departamento de Química Física, Universitat de València, Burjassot, Spain
| | - Miguel López-Estepa
- Chemical and Physical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Sara Gómez
- Chemical and Physical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Fernando Garces
- The Scripps Research Institute, La Jolla, California, United States of America
| | - Miquel Coll
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
- Institute for Biomedical Research (IRB Barcelona), Barcelona, Spain
| | - Francisco J. Fernández
- Chemical and Physical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain
- Abvance Biotech srl, Madrid, Spain
| | - Iñaki Tuñon
- Departamento de Química Física, Universitat de València, Burjassot, Spain
- * E-mail: , (MCV); (IT)
| | - M. Cristina Vega
- Chemical and Physical Biology Department, Center for Biological Research (CIB-CSIC), Madrid, Spain
- * E-mail: , (MCV); (IT)
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27
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Catalytic Intermediate Crystal Structures of Cysteine Desulfurase from the Archaeon Thermococcus onnurineus NA1. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2017; 2017:5395293. [PMID: 28536498 PMCID: PMC5426080 DOI: 10.1155/2017/5395293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/19/2017] [Indexed: 11/24/2022]
Abstract
Thermococcus onnurineus NA1 is an anaerobic archaeon usually found in a deep-sea hydrothermal vent area, which can use elemental sulfur (S0) as a terminal electron acceptor for energy. Sulfur, essential to many biomolecules such as sulfur-containing amino acids and cofactors including iron-sulfur cluster, is usually mobilized from cysteine by the pyridoxal 5′-phosphate- (PLP-) dependent enzyme of cysteine desulfurase (CDS). We determined the crystal structures of CDS from Thermococcus onnurineus NA1 (ToCDS), which include native internal aldimine (NAT), gem-diamine (GD) with alanine, internal aldimine structure with existing alanine (IAA), and internal aldimine with persulfide-bound Cys356 (PSF) structures. The catalytic intermediate structures showed the dihedral angle rotation of Schiff-base linkage relative to the PLP pyridine ring. The ToCDS structures were compared with bacterial CDS structures, which will help us to understand the role and catalytic mechanism of ToCDS in the archaeon Thermococcus onnurineus NA1.
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28
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Biological chemistry of hydrogen sulfide and persulfides. Arch Biochem Biophys 2017; 617:9-25. [DOI: 10.1016/j.abb.2016.09.018] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/28/2016] [Accepted: 09/29/2016] [Indexed: 02/08/2023]
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Blauenburg B, Mielcarek A, Altegoer F, Fage CD, Linne U, Bange G, Marahiel MA. Crystal Structure of Bacillus subtilis Cysteine Desulfurase SufS and Its Dynamic Interaction with Frataxin and Scaffold Protein SufU. PLoS One 2016; 11:e0158749. [PMID: 27382962 PMCID: PMC4934914 DOI: 10.1371/journal.pone.0158749] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/21/2016] [Indexed: 12/31/2022] Open
Abstract
The biosynthesis of iron sulfur (Fe-S) clusters in Bacillus subtilis is mediated by a SUF-type gene cluster, consisting of the cysteine desulfurase SufS, the scaffold protein SufU, and the putative chaperone complex SufB/SufC/SufD. Here, we present the high-resolution crystal structure of the SufS homodimer in its product-bound state (i.e., in complex with pyrodoxal-5'-phosphate, alanine, Cys361-persulfide). By performing hydrogen/deuterium exchange (H/DX) experiments, we characterized the interaction of SufS with SufU and demonstrate that SufU induces an opening of the active site pocket of SufS. Recent data indicate that frataxin could be involved in Fe-S cluster biosynthesis by facilitating iron incorporation. H/DX experiments show that frataxin indeed interacts with the SufS/SufU complex at the active site. Our findings deepen the current understanding of Fe-S cluster biosynthesis, a complex yet essential process, in the model organism B. subtilis.
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Affiliation(s)
- Bastian Blauenburg
- Department of Chemistry, Biochemistry, Hans-Meerwein Str. 4, Philipps University Marburg, 35043 Marburg, Germany
| | - Andreas Mielcarek
- Department of Chemistry, Biochemistry, Hans-Meerwein Str. 4, Philipps University Marburg, 35043 Marburg, Germany
| | - Florian Altegoer
- LOEWE Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| | - Christopher D. Fage
- Department of Chemistry, Biochemistry, Hans-Meerwein Str. 4, Philipps University Marburg, 35043 Marburg, Germany
| | - Uwe Linne
- Department of Chemistry, Biochemistry, Hans-Meerwein Str. 4, Philipps University Marburg, 35043 Marburg, Germany
| | - Gert Bange
- Department of Chemistry, Biochemistry, Hans-Meerwein Str. 4, Philipps University Marburg, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| | - Mohamed A. Marahiel
- Department of Chemistry, Biochemistry, Hans-Meerwein Str. 4, Philipps University Marburg, 35043 Marburg, Germany
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30
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Fernández FJ, Ardá A, López-Estepa M, Aranda J, Peña-Soler E, Garces F, Round A, Campos-Olivas R, Bruix M, Coll M, Tuñón I, Jiménez-Barbero J, Vega MC. Mechanism of Sulfur Transfer Across Protein–Protein Interfaces: The Cysteine Desulfurase Model System. ACS Catal 2016. [DOI: 10.1021/acscatal.6b00360] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Francisco J. Fernández
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
| | - Ana Ardá
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
- CIC bioGUNE, Bizkaia Technology
Park, Building 801A, 48170 Derio, Spain
| | - Miguel López-Estepa
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
| | - Juan Aranda
- Departamento
de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Esther Peña-Soler
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
| | - Fernando Garces
- The Scripps Research Institute, La
Jolla, 92037 California, United States
| | - Adam Round
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France
- Unit for
Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 38042 Grenoble, France
| | | | - Marta Bruix
- Instituto de Química Física Rocasolano (IQFR-CSIC), 28006 Madrid, Spain
| | - Miquel Coll
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
- Institute for Biomedical Research (IRB Barcelona), 08028 Barcelona, Spain
| | - Iñaki Tuñón
- Departamento
de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Jesús Jiménez-Barbero
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
- CIC bioGUNE, Bizkaia Technology
Park, Building 801A, 48170 Derio, Spain
- Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 13, 48009 Bilbao, Spain
- Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, 48940 Leioa, Bizkaia, Spain
| | - M. Cristina Vega
- Chemical
and Physical Biology Department, Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain
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31
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Kenne AN, Kim S, Park S. The crystal structure of Escherichia coli CsdE. Int J Biol Macromol 2016; 87:317-21. [PMID: 26944665 DOI: 10.1016/j.ijbiomac.2016.02.071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 02/26/2016] [Accepted: 02/27/2016] [Indexed: 11/19/2022]
Abstract
Sulfur incorporations both in the biosynthesis of sulfur-containing cofactors and in the sulfur-modifications of certain tRNAs are all mediated by the sulfur initially delivered from the cysteine desulfurases. Sulfur generated as persulfide from cysteine is transferred to the sulfur acceptor protein to further allow delivery to the required steps within an enzymatic process. CsdA which is one of the three cysteine desulfurases identified in Escherichia coli transfers sulfur to the non Fe-S sulfur-acceptor CsdE, however, the consequence of CsdE accepted sulfur is mostly unknown. In this study, we report the 2.4Å structure of free CsdE determined using X-ray crystallography, and compare the structure with the CsdE structure determined using NMR and also CsdE within the crystal CsdA-CsdE complex. Further analysis suggests that the positive electrostatic potential surfaces of CsdE may mediate interaction with a yet unidentified protein or possibly tRNA to deliver sulfur.
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Affiliation(s)
- Adela N Kenne
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea
| | - Sunmin Kim
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea
| | - SangYoun Park
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea.
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32
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Dai Y, Kim D, Dong G, Busenlehner LS, Frantom PA, Outten FW. SufE D74R Substitution Alters Active Site Loop Dynamics To Further Enhance SufE Interaction with the SufS Cysteine Desulfurase. Biochemistry 2015; 54:4824-33. [PMID: 26171726 DOI: 10.1021/acs.biochem.5b00663] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many essential metalloproteins require iron-sulfur (Fe-S) cluster cofactors for their function. In vivo persulfide formation from l-cysteine is a key step in the biogenesis of Fe-S clusters in most organisms. In Escherichia coli, the SufS cysteine desulfurase mobilizes persulfide from l-cysteine via a PLP-dependent ping-pong reaction. SufS requires the SufE partner protein to transfer the persulfide to the SufB Fe-S cluster scaffold. Without SufE, the SufS enzyme fails to efficiently turn over and remains locked in the persulfide-bound state. Coordinated protein-protein interactions mediate sulfur transfer from SufS to SufE. Multiple studies have suggested that SufE must undergo a conformational change to extend its active site Cys loop during sulfur transfer from SufS. To test this putative model, we mutated SufE Asp74 to Arg (D74R) to increase the dynamics of the SufE Cys51 loop. Amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) analysis of SufE D74R revealed an increase in solvent accessibility and dynamics in the loop containing the active site Cys51 used to accept persulfide from SufS. Our results indicate that the mutant protein has a stronger binding affinity for SufS than that of wild-type SufE. In addition, SufE D74R can still enhance SufS desulfurase activity and did not show saturation at higher SufE D74R concentrations, unlike wild-type SufE. These results show that dynamic changes may shift SufE to a sulfur-acceptor state that interacts more strongly with SufS.
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Affiliation(s)
- Yuyuan Dai
- †Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Dokyong Kim
- ‡Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Guangchao Dong
- †Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Laura S Busenlehner
- ‡Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Patrick A Frantom
- ‡Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - F Wayne Outten
- †Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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33
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The Structure of Escherichia coli TcdA (Also Known As CsdL) Reveals a Novel Topology and Provides Insight into the tRNA Binding Surface Required for N(6)-Threonylcarbamoyladenosine Dehydratase Activity. J Mol Biol 2015; 427:3074-85. [PMID: 26101842 DOI: 10.1016/j.jmb.2015.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/01/2015] [Accepted: 06/15/2015] [Indexed: 11/22/2022]
Abstract
Escherichia coli TcdA (also known as CsdL) was previously shown to catalyze the ATP-dependent dehydration/cyclization of hypermodified tRNA N(6)-threonylcarbamoyladenosine into further cyclic N(6)-threonylcarbamoyladenosine. In this study, we report the X-ray crystal structures of E. coli TcdA with either AMP or ATP bound. The AMP/ATP-bound N-terminal sub-domain of TcdA resembles the ATP-binding Rossmann fold of E. coli ThiF and MoeB that are enzymes respectively taking part in the biosynthesis of thiamine and molybdopterin; however, the remaining C-terminal sub-domain of TcdA adopts a structure unrelated to any other known folds. In TcdA, the ATP-utilizing adenylation of tRNA N(6)-threonylcarbamoyladenosine and a subsequent thioester formation via an active cysteine, similar to the mechanisms in ThiF and MoeB, could take place for the dehydratase function. Analysis of the structure with sequence alignment suggests the disordered Cys234 of TcdA as the most likely catalytic residue. The structure further indicates that the C-terminal sub-domain can provide a binding interface for the tRNA substrate. Binding study using the surface mutants of TcdA and tRNA reveals that the positively charged regions of mainly the C-terminal sub-domain are important for the tRNA recognition.
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34
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A novel cysteine desulfurase influencing organosulfur compounds in Lentinula edodes. Sci Rep 2015; 5:10047. [PMID: 26054293 PMCID: PMC4460571 DOI: 10.1038/srep10047] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/25/2015] [Indexed: 11/08/2022] Open
Abstract
Organosulfur compounds are the basis for the unique aroma of Lentinula edodes, and cysteine sulfoxide lyase (C-S lyase) is the key enzyme in this trait. The enzyme from Alliium sativum has been crystallized and well-characterized; however, there have been no reports of the characterization of fungi C-S lyase at the molecular level. We identified a L. edodes C-S lyase (Lecsl), cloned a gene of Csl encoded Lecsl and then combined modeling, simulations, and experiments to understand the molecular basis of the function of Lecsl. Our analysis revealed Lecsl to be a novel cysteine desulfurase and not a type of cysteine sulfoxide lyase. The pyridoxal-5-phosphate (PLP) molecule bonded tightly to Lecsl to form a Lecsl-PLP complex. Moreover, the Lecsl had one active center that served to bind two kinds of substrates, S-methyl-L-cysteine sulfoxide and L-cysteine, and had both cysteine sulfoxide lyase and cysteine desulfurase activity. We found that the amino acid residue Asn393 was essential for the catalytic activity of Lecsl and that the gene Csl encoded a novel cysteine desulfurase to influence organosulfur compounds in L. edodes. Our results provide a new insight into understanding the formation of the unique aroma of L. edodes.
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35
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The crystal structure and small-angle X-ray analysis of CsdL/TcdA reveal a new tRNA binding motif in the MoeB/E1 superfamily. PLoS One 2015; 10:e0118606. [PMID: 25897750 PMCID: PMC4405576 DOI: 10.1371/journal.pone.0118606] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 01/21/2015] [Indexed: 11/19/2022] Open
Abstract
Cyclic N6-threonylcarbamoyladenosine ('cyclic t6A', ct(6)A) is a non-thiolated hypermodification found in transfer RNAs (tRNAs) in bacteria, protists, fungi and plants. In bacteria and yeast cells ct(6)A has been shown to enhance translation fidelity and efficiency of ANN codons by improving the faithful discrimination of aminoacylated tRNAs by the ribosome. To further the understanding of ct(6)A biology we have determined the high-resolution crystal structures of CsdL/TcdA in complex with AMP and ATP, an E1-like activating enzyme from Escherichia coli, which catalyzes the ATP-dependent dehydration of t6A to form ct(6)A. CsdL/TcdA is a dimer whose structural integrity and dimer interface depend critically on strongly bound K+ and Na+ cations. By using biochemical assays and small-angle X-ray scattering we show that CsdL/TcdA can associate with tRNA with a 1:1 stoichiometry and with the proper position and orientation for the cyclization of t6A. Furthermore, we show by nuclear magnetic resonance that CsdL/TcdA engages in transient interactions with CsdA and CsdE, which, in the latter case, involve catalytically important residues. These short-lived interactions may underpin the precise channeling of sulfur atoms from cysteine to CsdL/TcdA as previously characterized. In summary, the combination of structural, biophysical and biochemical methods applied to CsdL/TcdA has afforded a more thorough understanding of how the structure of this E1-like enzyme has been fine tuned to accomplish ct(6)A synthesis on tRNAs while providing support for the notion that CsdA and CsdE are able to functionally interact with CsdL/TcdA.
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36
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Outten FW. Recent advances in the Suf Fe-S cluster biogenesis pathway: Beyond the Proteobacteria. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1464-9. [PMID: 25447545 DOI: 10.1016/j.bbamcr.2014.11.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 10/31/2014] [Accepted: 11/03/2014] [Indexed: 01/21/2023]
Abstract
Fe-S clusters play critical roles in cellular function throughout all three kingdoms of life. Consequently, Fe-S cluster biogenesis systems are present in most organisms. The Suf (sulfur formation) system is the most ancient of the three characterized Fe-S cluster biogenesis pathways, which also include the Isc and Nif systems. Much of the first work on the Suf system took place in Gram-negative Proteobacteria used as model organisms. These early studies led to a wealth of biochemical, genetic, and physiological information on Suf function. From those studies we have learned that SufB functions as an Fe-S scaffold in conjunction with SufC (and in some cases SufD). SufS and SufE together mobilize sulfur for cluster assembly and SufA traffics the complete Fe-S cluster from SufB to target apo-proteins. However, recent progress on the Suf system in other organisms has opened up new avenues of research and new hypotheses about Suf function. This review focuses primarily on the most recent discoveries about the Suf pathway and where those new models may lead the field. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- F Wayne Outten
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, SC 29208, USA.
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37
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Shared-intermediates in the biosynthesis of thio-cofactors: Mechanism and functions of cysteine desulfurases and sulfur acceptors. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1470-80. [PMID: 25447671 DOI: 10.1016/j.bbamcr.2014.10.018] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 10/07/2014] [Accepted: 10/19/2014] [Indexed: 12/20/2022]
Abstract
Cysteine desulfurases utilize a PLP-dependent mechanism to catalyze the first step of sulfur mobilization in the biosynthesis of sulfur-containing cofactors. Sulfur activation and integration into thiocofactors involve complex mechanisms and intricate biosynthetic schemes. Cysteine desulfurases catalyze sulfur-transfer reactions from l-cysteine to sulfur acceptor molecules participating in the biosynthesis of thio-cofactors, including Fe-S clusters, thionucleosides, thiamin, biotin, and molybdenum cofactor. The proposed mechanism of cysteine desulfurases involves the PLP-dependent cleavage of the C-S bond from l-cysteine via the formation of a persulfide enzyme intermediate, which is considered the hallmark step in sulfur mobilization. The subsequent sulfur transfer reaction varies with the class of cysteine desulfurase and sulfur acceptor. IscS serves as a mecca for sulfur incorporation into a network of intertwined pathways for the biosynthesis of thio-cofactors. The involvement of a single enzyme interacting with multiple acceptors, the recruitment of shared-intermediates partaking roles in multiple pathways, and the participation of Fe-S enzymes denote the interconnectivity of pathways involving sulfur trafficking. In Bacillus subtilis, the occurrence of multiple cysteine desulfurases partnering with dedicated sulfur acceptors partially deconvolutes the routes of sulfur trafficking and assigns specific roles for these enzymes. Understanding the roles of promiscuous vs. dedicated cysteine desulfurases and their partnership with shared-intermediates in the biosynthesis of thio-cofactors will help to map sulfur transfer events across interconnected pathways and to provide insight into the hierarchy of sulfur incorporation into biomolecules. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Roret T, Pégeot H, Couturier J, Mulliert G, Rouhier N, Didierjean C. X-ray structures of Nfs2, the plastidial cysteine desulfurase from Arabidopsis thaliana. Acta Crystallogr F Struct Biol Commun 2014; 70:1180-5. [PMID: 25195888 PMCID: PMC4157415 DOI: 10.1107/s2053230x14017026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 07/23/2014] [Indexed: 11/10/2022] Open
Abstract
The chloroplastic Arabidopsis thaliana Nfs2 (AtNfs2) is a group II pyridoxal 5'-phosphate-dependent cysteine desulfurase that is involved in the initial steps of iron-sulfur cluster biogenesis. The group II cysteine desulfurases require the presence of sulfurtransferases such as SufE proteins for optimal activity. Compared with group I cysteine desulfurases, proteins of this group contains a smaller extended lobe harbouring the catalytic cysteine and have a β-hairpin constraining the active site. Here, two crystal structures of AtNfs2 are reported: a wild-type form with the catalytic cysteine in a persulfide-intermediate state and a C384S variant mimicking the resting state of the enzyme. In both structures the well conserved Lys241 covalently binds pyridoxal 5'-phosphate, forming an internal aldimine. Based on available homologous bacterial complexes, a model of a complex between AtNfs2 and the SufE domain of its biological partner AtSufE1 is proposed, revealing the nature of the binding sites.
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Affiliation(s)
- Thomas Roret
- Université de Lorraine, UMR 7036 CRM2, BioMod Group, BP 70239, 54506 Vandoeuvre-lès-Nancy, France
- CNRS, UMR 7036 CRM2, BioMod Group, BP 70239, 54506 Vandoeuvre-lès-Nancy, France
| | - Henri Pégeot
- Université de Lorraine, UMR 1136 Interactions Arbres Microorganismes, 54500 Vandoeuvre-lès-Nancy, France
- INRA, UMR 1136 Interactions Arbres Microorganismes, 54280 Champenoux, France
| | - Jérémy Couturier
- Université de Lorraine, UMR 1136 Interactions Arbres Microorganismes, 54500 Vandoeuvre-lès-Nancy, France
- INRA, UMR 1136 Interactions Arbres Microorganismes, 54280 Champenoux, France
| | - Guillermo Mulliert
- Université de Lorraine, UMR 7036 CRM2, BioMod Group, BP 70239, 54506 Vandoeuvre-lès-Nancy, France
- CNRS, UMR 7036 CRM2, BioMod Group, BP 70239, 54506 Vandoeuvre-lès-Nancy, France
| | - Nicolas Rouhier
- Université de Lorraine, UMR 1136 Interactions Arbres Microorganismes, 54500 Vandoeuvre-lès-Nancy, France
- INRA, UMR 1136 Interactions Arbres Microorganismes, 54280 Champenoux, France
| | - Claude Didierjean
- Université de Lorraine, UMR 7036 CRM2, BioMod Group, BP 70239, 54506 Vandoeuvre-lès-Nancy, France
- CNRS, UMR 7036 CRM2, BioMod Group, BP 70239, 54506 Vandoeuvre-lès-Nancy, France
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39
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Singh H, Dai Y, Outten FW, Busenlehner LS. Escherichia coli SufE sulfur transfer protein modulates the SufS cysteine desulfurase through allosteric conformational dynamics. J Biol Chem 2013; 288:36189-200. [PMID: 24196966 PMCID: PMC3868733 DOI: 10.1074/jbc.m113.525709] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 11/05/2013] [Indexed: 11/06/2022] Open
Abstract
Fe-S clusters are critical metallocofactors required for cell function. Fe-S cluster biogenesis is carried out by assembly machinery consisting of multiple proteins. Fe-S cluster biogenesis proteins work together to mobilize sulfide and iron, form the nascent cluster, traffic the cluster to target metalloproteins, and regulate the assembly machinery in response to cellular Fe-S cluster demand. A complex series of protein-protein interactions is required for the assembly machinery to function properly. Despite considerable progress in obtaining static three-dimensional structures of the assembly proteins, little is known about transient protein-protein interactions during cluster assembly or the role of protein dynamics in the cluster assembly process. The Escherichia coli cysteine desulfurase SufS (EC 2.8.1.7) and its accessory protein SufE work together to mobilize persulfide from L-cysteine, which is then donated to the SufB Fe-S cluster scaffold. Here we use amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) to characterize SufS-SufE interactions and protein dynamics in solution. HDX-MS analysis shows that SufE binds near the SufS active site to accept persulfide from Cys-364. Furthermore, SufE binding initiates allosteric changes in other parts of the SufS structure that likely affect SufS catalysis and alter SufS monomer-monomer interactions. SufE enhances the initial l-cysteine substrate binding to SufS and formation of the external aldimine with pyridoxal phosphate required for early steps in SufS catalysis. Together, these results provide a new picture of the SufS-SufE sulfur transferase pathway and suggest a more active role for SufE in promoting the SufS cysteine desulfurase reaction for Fe-S cluster assembly.
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Affiliation(s)
- Harsimran Singh
- From the Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487 and
| | - Yuyuan Dai
- the Department of Chemistry and Biochemistry, The University of South Carolina, Columbia, South Carolina 29208
| | - F. Wayne Outten
- the Department of Chemistry and Biochemistry, The University of South Carolina, Columbia, South Carolina 29208
| | - Laura S. Busenlehner
- From the Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487 and
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