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Gavira JA, Cámara-Artigas A, Neira JL, Torres de Pinedo JM, Sánchez P, Ortega E, Martinez-Rodríguez S. Structural insights into choline- O-sulfatase reveal the molecular determinants for ligand binding. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:669-682. [PMID: 35503214 PMCID: PMC9063841 DOI: 10.1107/s2059798322003709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/04/2022] [Indexed: 11/23/2022]
Abstract
The first structures of a choline-O-sulfatase bound to different ligands are reported. Choline-O-sulfatase (COSe; EC 3.1.6.6) is a member of the alkaline phosphatase (AP) superfamily, and its natural function is to hydrolyze choline-O-sulfate into choline and sulfate. Despite its natural function, the major interest in this enzyme resides in the landmark catalytic/substrate promiscuity of sulfatases, which has led to attention in the biotechnological field due to their potential in protein engineering. In this work, an in-depth structural analysis of wild-type Sinorhizobium (Ensifer) meliloti COSe (SmeCOSe) and its C54S active-site mutant is reported. The binding mode of this AP superfamily member to both products of the reaction (sulfate and choline) and to a substrate-like compound are shown for the first time. The structures further confirm the importance of the C-terminal extension of the enzyme in becoming part of the active site and participating in enzyme activity through dynamic intra-subunit and inter-subunit hydrogen bonds (Asn146A–Asp500B–Asn498B). These residues act as the ‘gatekeeper’ responsible for the open/closed conformations of the enzyme, in addition to assisting in ligand binding through the rearrangement of Leu499 (with a movement of approximately 5 Å). Trp129 and His145 clamp the quaternary ammonium moiety of choline and also connect the catalytic cleft to the C-terminus of an adjacent protomer. The structural information reported here contrasts with the proposed role of conformational dynamics in promoting the enzymatic catalytic proficiency of an enzyme.
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2
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Li CC, Tang XY, Zhu YB, Song YJ, Zhao NL, Huang Q, Mou XY, Luo GH, Liu TG, Tong AP, Tang H, Bao R. Structural analysis of the sulfatase AmAS from Akkermansia muciniphila. Acta Crystallogr D Struct Biol 2021; 77:1614-1623. [DOI: 10.1107/s2059798321010317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 10/05/2021] [Indexed: 11/11/2022] Open
Abstract
Akkermansia muciniphila, an anaerobic Gram-negative bacterium, is a major intestinal commensal bacterium that can modulate the host immune response. It colonizes the mucosal layer and produces nutrients for the gut mucosa and other commensal bacteria. It is believed that mucin desulfation is the rate-limiting step in the mucin-degradation process, and bacterial sulfatases that carry out mucin desulfation have been well studied. However, little is known about the structural characteristics of A. muciniphila sulfatases. Here, the crystal structure of the premature form of the A. muciniphila sulfatase AmAS was determined. Structural analysis combined with docking experiments defined the critical active-site residues that are responsible for catalysis. The loop regions I–V were proposed to be essential for substrate binding. Structure-based sequence alignment and structural superposition allow further elucidation of how different subclasses of formylglycine-dependent sulfatases (FGly sulfatases) adopt the same catalytic mechanism but exhibit diverse substrate specificities. These results advance the understanding of the substrate-recognition mechanisms of A. muciniphila FGly-type sulfatases. Structural variations around the active sites account for the different substrate-binding properties. These results will enhance the understanding of the roles of bacterial sulfatases in the metabolism of glycans and host–microbe interactions in the human gut environment.
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3
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Buchholz PCF, van Loo B, Eenink BDG, Bornberg-Bauer E, Pleiss J. Ancestral sequences of a large promiscuous enzyme family correspond to bridges in sequence space in a network representation. J R Soc Interface 2021; 18:20210389. [PMID: 34727710 DOI: 10.1098/rsif.2021.0389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Evolutionary relationships of protein families can be characterized either by networks or by trees. Whereas trees allow for hierarchical grouping and reconstruction of the most likely ancestral sequences, networks lack a time axis but allow for thresholds of pairwise sequence identity to be chosen and, therefore, the clustering of family members with presumably more similar functions. Here, we use the large family of arylsulfatases and phosphonate monoester hydrolases to investigate similarities, strengths and weaknesses in tree and network representations. For varying thresholds of pairwise sequence identity, values of betweenness centrality and clustering coefficients were derived for nodes of the reconstructed ancestors to measure the propensity to act as a bridge in a network. Based on these properties, ancestral protein sequences emerge as bridges in protein sequence networks. Interestingly, many ancestral protein sequences appear close to extant sequences. Therefore, reconstructed ancestor sequences might also be interpreted as yet-to-be-identified homologues. The concept of ancestor reconstruction is compared to consensus sequences, too. It was found that hub sequences in a network, e.g. reconstructed ancestral sequences that are connected to many neighbouring sequences, share closer similarity with derived consensus sequences. Therefore, some reconstructed ancestor sequences can also be interpreted as consensus sequences.
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Affiliation(s)
- Patrick C F Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart 70569, Germany
| | - Bert van Loo
- Department of Applied Sciences, Northumbria University, Newcastle-upon-Tyne NE1 8ST, UK.,Institute for Evolution and Biodiversity, University of Münster, Hüfferstraße 1, Münster 48149, Germany
| | - Bernard D G Eenink
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstraße 1, Münster 48149, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstraße 1, Münster 48149, Germany.,Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen 72076, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart 70569, Germany
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Kolchina NV, Rychkov GN, Kulminskaya AA, Ibatullin FM, Petukhov MG, Bobrov KS. Structural Organization of the Active Center of Unmodified Recombinant Sulfatase from the Mycelial Fungi Fusarium proliferatum LE1. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020040081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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van Loo B, Heberlein M, Mair P, Zinchenko A, Schüürmann J, Eenink BDG, Holstein JM, Dilkaute C, Jose J, Hollfelder F, Bornberg-Bauer E. High-Throughput, Lysis-Free Screening for Sulfatase Activity Using Escherichia coli Autodisplay in Microdroplets. ACS Synth Biol 2019; 8:2690-2700. [PMID: 31738524 DOI: 10.1021/acssynbio.9b00274] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Directed evolution of enzymes toward improved catalytic performance has become a powerful tool in protein engineering. To be effective, a directed evolution campaign requires the use of high-throughput screening. In this study we describe the development of an ultra high-throughput lysis-free procedure to screen for improved sulfatase activity by combining microdroplet-based single-variant activity sorting with E. coli autodisplay. For the first step in a 4-step screening procedure, we quantitatively screened >105 variants of the homodimeric arylsulfatase from Silicibacter pomeroyi (SpAS1), displayed on the E. coli cell surface, for improved sulfatase activity using fluorescence activated droplet sorting. Compartmentalization of the fluorescent reaction product with living E. coli cells autodisplaying the sulfatase variants ensured the continuous linkage of genotype and phenotype during droplet sorting and allowed for direct recovery by simple regrowth of the sorted cells. The use of autodisplay on living cells simplified and reduced the degree of liquid handling during all steps in the screening procedure to the single event of simply mixing substrate and cells. The percentage of apparent improved variants was enriched >10-fold as a result of droplet sorting. We ultimately identified 25 SpAS1 variants with improved performance toward 4-nitrophenyl sulfate (up to 6.2-fold) and/or fluorescein disulfate (up to 30-fold). In SpAS1 variants with improved performance toward the bulky fluorescein disulfate, many of the beneficial mutations occur in residues that form hydrogen bonds between α-helices in the C-terminal oligomerization region, suggesting a previously unknown role for the dimer interface in shaping the substrate binding site of SpAS1.
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Affiliation(s)
- Bert van Loo
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Magdalena Heberlein
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Philip Mair
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Anastasia Zinchenko
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Jan Schüürmann
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, 48149 Münster, Germany
| | - Bernard D. G. Eenink
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Josephin M. Holstein
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Carina Dilkaute
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, 48149 Münster, Germany
| | - Joachim Jose
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, 48149 Münster, Germany
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
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Kleinsteuber S, Rohwerder T, Lohse U, Seiwert B, Reemtsma T. Sated by a Zero-Calorie Sweetener: Wastewater Bacteria Can Feed on Acesulfame. Front Microbiol 2019; 10:2606. [PMID: 31824446 PMCID: PMC6879467 DOI: 10.3389/fmicb.2019.02606] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/28/2019] [Indexed: 01/05/2023] Open
Abstract
The widely used artificial sweetener acesulfame K has long been considered recalcitrant in biological wastewater treatment. Due to its persistence and mobility in the aquatic environment, acesulfame has been used as marker substance for wastewater input in surface water and groundwater. However, recent studies indicated that the potential to remove this xenobiotic compound is emerging in wastewater treatment plants worldwide, leading to decreasing mass loads in receiving waters despite unchanged human consumption patterns. Here we show evidence that acesulfame can be mineralized in a catabolic process and used as sole carbon source by bacterial pure strains isolated from activated sludge and identified as Bosea sp. and Chelatococcus sp. The strains mineralize 1 g/L acesulfame K within 8–9 days. We discuss the potential degradation pathway and how this novel catabolic trait confirms the “principle of microbial infallibility.” Once the enzymes involved in acesulfame degradation and their genes are identified, it will be possible to survey diverse environments and trace back the evolutionary origin as well as the mechanisms of global distribution and establishment of such a new catabolic trait.
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Affiliation(s)
- Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Thore Rohwerder
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Ute Lohse
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Bettina Seiwert
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Thorsten Reemtsma
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Institute for Analytical Chemistry, University of Leipzig, Leipzig, Germany
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van Loo B, Berry R, Boonyuen U, Mohamed MF, Golicnik M, Hengge AC, Hollfelder F. Transition-State Interactions in a Promiscuous Enzyme: Sulfate and Phosphate Monoester Hydrolysis by Pseudomonas aeruginosa Arylsulfatase. Biochemistry 2019; 58:1363-1378. [PMID: 30810299 PMCID: PMC11098524 DOI: 10.1021/acs.biochem.8b00996] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pseudomonas aeruginosa arylsulfatase (PAS) hydrolyzes sulfate and, promiscuously, phosphate monoesters. Enzyme-catalyzed sulfate transfer is crucial to a wide variety of biological processes, but detailed studies of the mechanistic contributions to its catalysis are lacking. We present linear free energy relationships (LFERs) and kinetic isotope effects (KIEs) of PAS and analyses of active site mutants that suggest a key role for leaving group (LG) stabilization. In LFERs PASWT has a much less negative Brønsted coefficient (βleaving groupobs-Enz = -0.33) than the uncatalyzed reaction (βleaving groupobs = -1.81). This situation is diminished when cationic active site groups are exchanged for alanine. The considerable degree of bond breaking during the transition state (TS) is evidenced by an 18Obridge KIE of 1.0088. LFER and KIE data for several active site mutants point to leaving group stabilization by active site K375, in cooperation with H211. 15N KIEs and the increased sensitivity to leaving group ability of the sulfatase activity in neat D2O (Δβleaving groupH-D = +0.06) suggest that the mechanism for S-Obridge bond fission shifts, with decreasing leaving group ability, from charge compensation via Lewis acid interactions toward direct proton donation. 18Ononbridge KIEs indicate that the TS for PAS-catalyzed sulfate monoester hydrolysis has a significantly more associative character compared to the uncatalyzed reaction, while PAS-catalyzed phosphate monoester hydrolysis does not show this shift. This difference in enzyme-catalyzed TSs appears to be the major factor favoring specificity toward sulfate over phosphate esters by this promiscuous hydrolase, since other features are either too similar (uncatalyzed TS) or inherently favor phosphate (charge).
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Affiliation(s)
- Bert van Loo
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Ryan Berry
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Usa Boonyuen
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Mark F. Mohamed
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Marko Golicnik
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alvan C. Hengge
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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8
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van Loo B, Bayer CD, Fischer G, Jonas S, Valkov E, Mohamed MF, Vorobieva A, Dutruel C, Hyvönen M, Hollfelder F. Balancing Specificity and Promiscuity in Enzyme Evolution: Multidimensional Activity Transitions in the Alkaline Phosphatase Superfamily. J Am Chem Soc 2018; 141:370-387. [PMID: 30497259 DOI: 10.1021/jacs.8b10290] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Highly proficient, promiscuous enzymes can be springboards for functional evolution, able to avoid loss of function during adaptation by their capacity to promote multiple reactions. We employ a systematic comparative study of structure, sequence, and substrate specificity to track the evolution of specificity and reactivity between promiscuous members of clades of the alkaline phosphatase (AP) superfamily. Construction of a phylogenetic tree of protein sequences maps out the likely transition zone between arylsulfatases (ASs) and phosphonate monoester hydrolases (PMHs). Kinetic analysis shows that all enzymes characterized have four chemically distinct phospho- and sulfoesterase activities, with rate accelerations ranging from 1011- to 1017-fold for their primary and 109- to 1012-fold for their promiscuous reactions, suggesting that catalytic promiscuity is widespread in the AP-superfamily. This functional characterization and crystallography reveal a novel class of ASs that is so similar in sequence to known PMHs that it had not been recognized as having diverged in function. Based on analysis of snapshots of catalytic promiscuity "in transition", we develop possible models that would allow functional evolution and determine scenarios for trade-off between multiple activities. For the new ASs, we observe largely invariant substrate specificity that would facilitate the transition from ASs to PMHs via trade-off-free molecular exaptation, that is, evolution without initial loss of primary activity and specificity toward the original substrate. This ability to bypass low activity generalists provides a molecular solution to avoid adaptive conflict.
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Affiliation(s)
- Bert van Loo
- Department of Biochemistry , University of Cambridge , Cambridge CB2 1GA , United Kingdom
| | - Christopher D Bayer
- Department of Biochemistry , University of Cambridge , Cambridge CB2 1GA , United Kingdom
| | - Gerhard Fischer
- Department of Biochemistry , University of Cambridge , Cambridge CB2 1GA , United Kingdom
| | - Stefanie Jonas
- Department of Biochemistry , University of Cambridge , Cambridge CB2 1GA , United Kingdom
| | - Eugene Valkov
- Department of Biochemistry , University of Cambridge , Cambridge CB2 1GA , United Kingdom
| | - Mark F Mohamed
- Department of Biochemistry , University of Cambridge , Cambridge CB2 1GA , United Kingdom
| | - Anastassia Vorobieva
- Department of Biochemistry , University of Cambridge , Cambridge CB2 1GA , United Kingdom
| | - Celine Dutruel
- Department of Biochemistry , University of Cambridge , Cambridge CB2 1GA , United Kingdom
| | - Marko Hyvönen
- Department of Biochemistry , University of Cambridge , Cambridge CB2 1GA , United Kingdom
| | - Florian Hollfelder
- Department of Biochemistry , University of Cambridge , Cambridge CB2 1GA , United Kingdom
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9
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Uduwela DR, Pabis A, Stevenson BJ, Kamerlin SCL, McLeod MD. Enhancing the Steroid Sulfatase Activity of the Arylsulfatase from Pseudomonas aeruginosa. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02905] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dimanthi R. Uduwela
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Anna Pabis
- Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
| | - Bradley J. Stevenson
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Shina C. L. Kamerlin
- Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
| | - Malcolm D. McLeod
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
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10
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High resolution crystal structure of the catalytic domain of MCR-1. Sci Rep 2016; 6:39540. [PMID: 28000749 PMCID: PMC5175174 DOI: 10.1038/srep39540] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/24/2016] [Indexed: 01/07/2023] Open
Abstract
The newly identified mobile colistin resistant gene (mcr-1) rapidly spread among different bacterial strains and confers colistin resistance to its host, which has become a global concern. Based on sequence alignment, MCR-1 should be a phosphoethanolamine transferase, members of the YhjW/YjdB/YijP superfamily and catalyze the addition of phosphoethanolamine to lipid A, which needs to be validated experimentally. Here we report the first high-resolution crystal structure of the C-terminal catalytic domain of MCR-1 (MCR-1C) in its native state. The active pocket of native MCR-1C depicts unphosphorylated nucleophilic residue Thr285 in coordination with two Zinc ions and water molecules. A flexible adjacent active site loop (aa: Lys348-365) pose an open conformation compared to its structural homologues, suggesting of an open substrate entry channel. Taken together, this structure sets ground for further study of substrate binding and MCR-1 catalytic mechanism in development of potential therapeutic agents.
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