1
|
Liew JJM, Wicht DK, Gonzalez R, Dowling DP, Ellis HR. Current understanding of enzyme structure and function in bacterial two-component flavin-dependent desulfonases: Cleaving C-S bonds of organosulfur compounds. Arch Biochem Biophys 2024; 758:110048. [PMID: 38848996 DOI: 10.1016/j.abb.2024.110048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
The inherent structural properties of enzymes are critical in defining catalytic function. Often, studies to evaluate the relationship between structure and function are limited to only one defined structural element. The two-component flavin-dependent desulfonase family of enzymes involved in bacterial sulfur acquisition utilize a comprehensive range of structural features to carry out the desulfonation of organosulfur compounds. These metabolically essential two-component FMN-dependent desulfonase systems have been proposed to utilize oligomeric changes, protein-protein interactions for flavin transfer, and common mechanistic steps for carbon-sulfur bond cleavage. This review is focused on our current functional and structural understanding of two-component FMN-dependent desulfonase systems from multiple bacterial sources. Mechanistic and structural comparisons from recent independent studies provide fresh insights into the overall functional properties of these systems and note areas in need of further investigation. The review acknowledges current studies focused on evaluating the structural properties of these enzymes in relationship to their distinct catalytic function. The role of these enzymes in maintaining adequate sulfur levels, coupled with the conserved nature of these enzymes in diverse bacteria, underscore the importance in understanding the functional and structural nuances of these systems.
Collapse
Affiliation(s)
- Jeremy J M Liew
- Department of Chemistry, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Denyce K Wicht
- Department of Biochemistry, Chemistry, Environment, and Physics, Suffolk University, Boston, MA, 02108, USA
| | - Reyaz Gonzalez
- Department of Chemistry, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Daniel P Dowling
- Department of Chemistry, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Holly R Ellis
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, NC, 27834, USA.
| |
Collapse
|
2
|
Somai S, Yue K, Acevedo O, Ellis HR. Shorter Alkanesulfonate Carbon Chains Destabilize the Active Site Architecture of SsuD for Desulfonation. Biochemistry 2023; 62:85-94. [PMID: 36534405 DOI: 10.1021/acs.biochem.2c00586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Bacteria have evolved to utilize alternative organosulfur sources when sulfur is limiting. The SsuE/SsuD and MsuE/MsuD enzymes expressed when sulfur sources are restricted, are responsible for providing specific bacteria with sulfur in the form of alkanesulfonates. In this study, we evaluated why two structurally and functionally similar FMNH2-dependent monooxygenase enzymes (MsuD and SsuD) are needed for the acquisition of alkanesulfonates in some bacteria. In desulfonation assays, MsuD was able to utilize the entire range of alkanesulfonates (C1-C10). However, SsuD was not able to utilize smaller alkanesulfonate substrates. Interestingly, SsuD had a similar binding affinity for methanesulfonate (MES) (15 ± 1 μM) as MsuD (12 ± 1 μM) even though SsuD was not able to catalyze the desulfonation of the MES substrate. SsuD and MsuD showed decreased proteolytic susceptibility in the presence of FMNH2 with MES and octanesulfonate (OCS). Tighter loop closure was observed for the MsuD/FMNH2 complex with MES and OCS compared to SsuD under comparable conditions. Analysis of the SsuD/FMNH2/MES structure using accelerated molecular dynamics simulations found three different conformations for MES, demonstrating the instability of the bound structure. Even when MES was bound in a similar fashion to OCS within the active site, the smaller alkane chain resulted in a shift of FMNH2 so that it was no longer in a position to catalyze the desulfonation of MES. The active site of SsuD requires a longer alkane chain to maintain the appropriate architecture for desulfonation.
Collapse
Affiliation(s)
- Shruti Somai
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, North Carolina27834, United States
| | - Kun Yue
- Department of Chemistry, University of Miami, Coral Gables, Florida33146, United States
| | - Orlando Acevedo
- Department of Chemistry, University of Miami, Coral Gables, Florida33146, United States
| | - Holly R Ellis
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, North Carolina27834, United States
| |
Collapse
|
3
|
Snow AJD, Burchill L, Sharma M, Davies GJ, Williams SJ. Sulfoglycolysis: catabolic pathways for metabolism of sulfoquinovose. Chem Soc Rev 2021; 50:13628-13645. [PMID: 34816844 DOI: 10.1039/d1cs00846c] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Sulfoquinovose (SQ), a derivative of glucose with a C6-sulfonate, is produced by photosynthetic organisms and is the headgroup of the sulfolipid sulfoquinovosyl diacylglycerol. The degradation of SQ allows recycling of its elemental constituents and is important in the global sulfur and carbon biogeochemical cycles. Degradation of SQ by bacteria is achieved through a range of pathways that fall into two main groups. One group involves scission of the 6-carbon skeleton of SQ into two fragments with metabolic utilization of carbons 1-3 and excretion of carbons 4-6 as dihydroxypropanesulfonate or sulfolactate that is biomineralized to sulfite/sulfate by other members of the microbial community. The other involves the complete metabolism of SQ by desulfonylation involving cleavage of the C-S bond to release sulfite and glucose, the latter of which can enter glycolysis. The discovery of sulfoglycolytic pathways has revealed a wide range of novel enzymes and SQ binding proteins. Biochemical and structural characterization of the proteins and enzymes in these pathways have illuminated how the sulfonate group is recognized by Nature's catalysts, supporting bioinformatic annotation of sulfoglycolytic enzymes, and has identified functional and structural relationships with the pathways of glycolysis.
Collapse
Affiliation(s)
- Alexander J D Snow
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, UK.
| | - Laura Burchill
- School of Chemistry, University of Melbourne, Parkville, Victoria 3010, Australia. .,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mahima Sharma
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, UK.
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, UK.
| | - Spencer J Williams
- School of Chemistry, University of Melbourne, Parkville, Victoria 3010, Australia. .,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| |
Collapse
|
4
|
Matthews A, Schönfelder J, Lagies S, Schleicher E, Kammerer B, Ellis HR, Stull F, Teufel R. Bacterial flavoprotein monooxygenase YxeK salvages toxic S-(2-succino)-adducts via oxygenolytic C-S bond cleavage. FEBS J 2021; 289:787-807. [PMID: 34510734 DOI: 10.1111/febs.16193] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/18/2021] [Accepted: 09/09/2021] [Indexed: 01/23/2023]
Abstract
Thiol-containing nucleophiles such as cysteine react spontaneously with the citric acid cycle intermediate fumarate to form S-(2-succino)-adducts. In Bacillus subtilis, a salvaging pathway encoded by the yxe operon has recently been identified for the detoxification and exploitation of these compounds as sulfur sources. This route involves acetylation of S-(2-succino)cysteine to N-acetyl-2-succinocysteine, which is presumably converted to oxaloacetate and N-acetylcysteine, before a final deacetylation step affords cysteine. The critical oxidative cleavage of the C-S bond of N-acetyl-S-(2-succino)cysteine was proposed to depend on the predicted flavoprotein monooxygenase YxeK. Here, we characterize YxeK and verify its role in S-(2-succino)-adduct detoxification and sulfur metabolism. Detailed biochemical and mechanistic investigation of YxeK including 18 O-isotope-labeling experiments, homology modeling, substrate specificity tests, site-directed mutagenesis, and (pre-)steady-state kinetics provides insight into the enzyme's mechanism of action, which may involve a noncanonical flavin-N5-peroxide species for C-S bond oxygenolysis.
Collapse
Affiliation(s)
| | | | - Simon Lagies
- Institute of Organic Chemistry, University of Freiburg, Germany
| | - Erik Schleicher
- Institute of Physical Chemistry, University of Freiburg, Germany
| | - Bernd Kammerer
- Institute of Organic Chemistry, University of Freiburg, Germany.,BIOSS Center for Biological Signaling Studies, University of Freiburg, Germany
| | - Holly R Ellis
- Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Frederick Stull
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | - Robin Teufel
- Faculty of Biology, University of Freiburg, Germany
| |
Collapse
|
5
|
Liew JJM, El Saudi IM, Nguyen SV, Wicht DK, Dowling DP. Structures of the alkanesulfonate monooxygenase MsuD provide insight into C-S bond cleavage, substrate scope, and an unexpected role for the tetramer. J Biol Chem 2021; 297:100823. [PMID: 34029591 PMCID: PMC8234197 DOI: 10.1016/j.jbc.2021.100823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 02/01/2023] Open
Abstract
Bacterial two-component flavin-dependent monooxygenases cleave the stable C-S bond of environmental and anthropogenic organosulfur compounds. The monooxygenase MsuD converts methanesulfonate (MS-) to sulfite, completing the sulfur assimilation process during sulfate starvation, but the mechanism of this conversion remains unclear. To explore the mechanism of C-S bond cleavage, we report a series of crystal structures of MsuD from Pseudomonas fluorescens in different liganded states. This report provides the first crystal structures of an alkanesulfonate monooxygenase with a bound flavin and alkanesulfonate, elucidating the roles of the active site lid, the protein C terminus, and an active site loop in flavin and/or alkanesulfonate binding. These structures position MS- closest to the flavin N5 position, consistent with an N5-(hydro)peroxyflavin mechanism rather than a classical C4a-(hydro)peroxyflavin mechanism. A fully enclosed active site is observed in the ternary complex, mediated by interchain interaction of the C terminus at the tetramer interface. These structures identify an unexpected function of the protein C terminus in this protein family in stabilizing tetramer formation and the alkanesulfonate-binding site. Spurred by interest from the crystal structures, we conducted biochemical assays and molecular docking that redefine MsuD as a small- to medium-chain alkanesulfonate monooxygenase. Functional mutations verify the sulfonate-binding site and reveal the critical importance of the protein C terminus for monooxygenase function. These findings reveal a deeper understanding of MsuD's functionality at the molecular level and consequently how it operates within its role as part of the sulfur assimilation pathway.
Collapse
Affiliation(s)
- Jeremy J M Liew
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Israa M El Saudi
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Son V Nguyen
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Denyce K Wicht
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Daniel P Dowling
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA.
| |
Collapse
|
6
|
Thakur A, Somai S, Yue K, Ippolito N, Pagan D, Xiong J, Ellis HR, Acevedo O. Substrate-Dependent Mobile Loop Conformational Changes in Alkanesulfonate Monooxygenase from Accelerated Molecular Dynamics. Biochemistry 2020; 59:3582-3593. [PMID: 32881481 DOI: 10.1021/acs.biochem.0c00633] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Abhishek Thakur
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Shruti Somai
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Kun Yue
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Nicole Ippolito
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Dianne Pagan
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Jingyuan Xiong
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - Holly R. Ellis
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Orlando Acevedo
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| |
Collapse
|
7
|
Dayal PV, Singh H, Busenlehner LS, Ellis HR. Exposing the Alkanesulfonate Monooxygenase Protein–Protein Interaction Sites. Biochemistry 2015; 54:7531-8. [DOI: 10.1021/acs.biochem.5b00935] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paritosh V. Dayal
- Department
of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Harsimran Singh
- Department
of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Laura S. Busenlehner
- Department
of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Holly R. Ellis
- Department
of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| |
Collapse
|
8
|
Driggers CM, Dayal PV, Ellis HR, Karplus PA. Crystal Structure of Escherichia coli SsuE: Defining a General Catalytic Cycle for FMN Reductases of the Flavodoxin-like Superfamily. Biochemistry 2014; 53:3509-19. [DOI: 10.1021/bi500314f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Camden M. Driggers
- Department
of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural
and Life Sciences Building, Corvallis, Oregon 97331, United States
| | - Paritosh V. Dayal
- Department
of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
| | - Holly R. Ellis
- Department
of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
| | - P. Andrew Karplus
- Department
of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural
and Life Sciences Building, Corvallis, Oregon 97331, United States
| |
Collapse
|
9
|
Armacost K, Musila J, Gathiaka S, Ellis HR, Acevedo O. Exploring the Catalytic Mechanism of Alkanesulfonate Monooxygenase Using Molecular Dynamics. Biochemistry 2014; 53:3308-17. [DOI: 10.1021/bi5002085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kira Armacost
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Jonathan Musila
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Symon Gathiaka
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Holly R. Ellis
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Orlando Acevedo
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| |
Collapse
|
10
|
Identification of critical steps governing the two-component alkanesulfonate monooxygenase catalytic mechanism. Biochemistry 2012; 51:6378-87. [PMID: 22775358 DOI: 10.1021/bi300138d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The alkanesulfonate monooxygenase enzyme (SsuD) catalyzes the oxygenolytic cleavage of a carbon-sulfur bond from sulfonated substrates. A mechanism involving acid-base catalysis has been proposed for the desulfonation mechanism by SsuD. In the proposed mechanism, base catalysis is involved in abstracting a proton from the alkane peroxyflavin intermediate, while acid catalysis is needed for the protonation of the FMNO(-) intermediate. The pH profiles of k(cat) indicate that catalysis by SsuD requires a group with a pK(a) of 6.6 ± 0.2 to be deprotonated and a second group with a pK(a) of 9.5 ± 0.1 to be protonated. The upper pK(a) value was not present in the pH profiles of k(cat)/K(m). Several conserved amino acid residues (His228, His11, His333, Cys54, and Arg226) have been identified as having potential catalytic importance due to the similar spatial arrangements with close structural and functional relatives of SsuD. Substitutions to these amino acid residues were generated, and the pH dependencies were evaluated and compared to wild-type SsuD. Although a histidine residue was previously proposed to be the active site base, the His variants possessed similar steady-state kinetic parameters as wild-type SsuD. Interestingly, R226A and R226K SsuD variants possessed undetectable activity, and there was no detectable formation of the C4a-(hydro)peroxyflavin intermediate for the Arg226 SsuD variants. Guanidinium rescue with the R226A SsuD variant resulted in the recovery of 1.5% of the wild-type SsuD k(cat) value. These results implicate Arg226 playing a critical role in catalysis and provide essential insights into the mechanistic steps that guide the SsuD desulfonation process.
Collapse
|