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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 Crystallogr D Struct Biol 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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/04/2022] [Indexed: 11/23/2022] Open
Abstract
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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Affiliation(s)
- Jose Antonio Gavira
- Laboratorio de Estudios Cristalográficos, CSIC, Armilla, 18100 Granada, Spain
| | - Ana Cámara-Artigas
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence (ceiA3), Research Centre for Agricultural and Food Biotechnology (BITAL), Carretera de Sacramento s/n, Almería, 04120, Spain
| | - Jose Luis Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR–CSIC–BIFI and GBsC–CSIC–BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Jesús M. Torres de Pinedo
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Universidad de Granada, 18071 Granada, Spain
| | - Pilar Sánchez
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Universidad de Granada, 18071 Granada, Spain
| | - Esperanza Ortega
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Universidad de Granada, 18071 Granada, Spain
| | - Sergio Martinez-Rodríguez
- Laboratorio de Estudios Cristalográficos, CSIC, Armilla, 18100 Granada, Spain
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Universidad de Granada, 18071 Granada, Spain
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Rodríguez-Andrade O, Corral-Lugo A, Morales-García YE, Quintero-Hernández V, Rivera-Urbalejo AP, Molina-Romero D, Martínez-Contreras RD, Bernal P, Muñoz-Rojas J. Identification of Klebsiella Variicola T29A Genes Involved In Tolerance To Desiccation. Open Microbiol J 2019. [DOI: 10.2174/1874285801913010256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Introduction:Several plant-beneficial bacteria have the capability to promote the growth of plants through different mechanisms. The survival of such bacteria could be affected by environmental abiotic factors compromising their capabilities of phytostimulation. One of the limiting abiotic factors is low water availability.Materials and Methods:In extreme cases, bacterial cells can suffer desiccation, which triggers harmful effects on cells. Bacteria tolerant to desiccation have developed different strategies to cope with these conditions; however, the genes involved in these processes have not been sufficiently explored.Klebsiella variicolaT29A is a beneficial bacterial strain that promotes the growth of corn plants and is highly tolerant to desiccation. In the present work, we investigated genes involved in desiccation tolerance.Results & Discussion:As a result, a library of 8974 mutants of this bacterial strain was generated by random mutagenesis with mini-Tn5 transposon, and mutants that lost the capability to tolerate desiccation were selected. We found 14 sensitive mutants; those with the lowest bacterial survival rate contained mini-Tn5 transposon inserted into genes encoding a protein domain related to BetR, putative secretion ATPase and dihydroorotase. The mutant in the betR gene had the lowest survival; therefore, the mutagenized gene was validated using specific amplification and sequencing.Conclusion:Trans complementation with the wild-type gene improved the survival of the mutant under desiccation conditions, showing that this gene is a determinant for the survival ofK. variicolaT29A under desiccation conditions.
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van Loo B, Schober M, Valkov E, Heberlein M, Bornberg-Bauer E, Faber K, Hyvönen M, Hollfelder F. Structural and Mechanistic Analysis of the Choline Sulfatase from Sinorhizobium melliloti: A Class I Sulfatase Specific for an Alkyl Sulfate Ester. J Mol Biol 2018; 430:1004-1023. [PMID: 29458126 PMCID: PMC5870055 DOI: 10.1016/j.jmb.2018.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/09/2018] [Accepted: 02/13/2018] [Indexed: 12/23/2022]
Abstract
Hydrolysis of organic sulfate esters proceeds by two distinct mechanisms, water attacking at either sulfur (S-O bond cleavage) or carbon (C-O bond cleavage). In primary and secondary alkyl sulfates, attack at carbon is favored, whereas in aromatic sulfates and sulfated sugars, attack at sulfur is preferred. This mechanistic distinction is mirrored in the classification of enzymes that catalyze sulfate ester hydrolysis: arylsulfatases (ASs) catalyze S-O cleavage in sulfate sugars and arylsulfates, and alkyl sulfatases break the C-O bond of alkyl sulfates. Sinorhizobium meliloti choline sulfatase (SmCS) efficiently catalyzes the hydrolysis of alkyl sulfate choline-O-sulfate (kcat/KM=4.8×103s-1M-1) as well as arylsulfate 4-nitrophenyl sulfate (kcat/KM=12s-1M-1). Its 2.8-Å resolution X-ray structure shows a buried, largely hydrophobic active site in which a conserved glutamate (Glu386) plays a role in recognition of the quaternary ammonium group of the choline substrate. SmCS structurally resembles members of the alkaline phosphatase superfamily, being most closely related to dimeric ASs and tetrameric phosphonate monoester hydrolases. Although >70% of the amino acids between protomers align structurally (RMSDs 1.79-1.99Å), the oligomeric structures show distinctly different packing and protomer-protomer interfaces. The latter also play an important role in active site formation. Mutagenesis of the conserved active site residues typical for ASs, H218O-labeling studies and the observation of catalytically promiscuous behavior toward phosphoesters confirm the close relation to alkaline phosphatase superfamily members and suggest that SmCS is an AS that catalyzes S-O cleavage in alkyl sulfate esters with extreme catalytic proficiency.
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Affiliation(s)
- Bert van Loo
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom; Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, D-48149 Münster, Germany
| | - Markus Schober
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom; Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
| | - Eugene Valkov
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Magdalena Heberlein
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, D-48149 Münster, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, D-48149 Münster, Germany
| | - Kurt Faber
- Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.
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Rebello S, Joseph BV, Joseph SV, Jose L, Mundayoor S, Jisha MS. Bioconversion of sodium dodecyl sulphate to rhamnolipids by transformed Escherichia coli DH5α cells-a novel strategy for rhamnolipid synthesis. J Appl Microbiol 2015; 120:638-46. [PMID: 26677807 DOI: 10.1111/jam.13032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 11/28/2015] [Accepted: 12/13/2015] [Indexed: 11/29/2022]
Abstract
AIMS Biological synthesis of rhamnolipids from SDS by Pseudomonas aeruginosa S15 is found to be a cost effective mode of rhamnolipid synthesis. This study aimed to attempt rhamnolipid synthesis by transformant Escherichia coli DH5α cells. METHODS AND RESULTS Molecular analysis by curing experiments revealed that the properties of SDS based rhamnolipid synthesis were plasmid borne. Transformation of 10 kb plasmid to E. coli DH5α cells conferred rhamnolipid synthetic ability to transformant. Various genetic elements involved in SDS based rhamnolipid synthesis were analyzed using PCR based and restriction digestion based approaches. PCR amplification using primers specific for sdsA gene encoding alkylsulfatases yielded two significant amplicons viz, 1·2 kb fragment and 422 bp fragment, coding for putative dehydratase and ABC transporter respectively. Amplicon of sdsB gene lacked ability of SDS degradation and rhamnolipid synthesis. Rhamnolipid biosynthesis by transformant E. coli DH5α containing the whole of the 10 kb plasmid, was optimized to yield of 3·38 g l(-1) in 5 days of incubation. CONCLUSIONS Plasmid encoded rhamnolipid synthesis from recombinant E. coli cells is novel and could serve as yet another promising approach among various steps adopted for safe and effective rhamnolipid synthesis. SIGNIFICANCE AND IMPACT OF THE STUDY SDS based rhamnolipid synthesis by S15 attained a high substrate (SDS) to product (Rhamnolipid) conversion ratio. However, the use of Pseudomonas strains is always discouraged as they are opportunistic pathogens and could sometimes turn infectious. Thus, transformation of genetic elements coding SDS based rhamnolipid synthesis to nonpathogenic strains could be promising.
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Affiliation(s)
- S Rebello
- School of Biosciences, Mahatma Gandhi University, Kottayam, India.,UniBiosys Biotech Research Labs, Kalamaserry, India
| | - B V Joseph
- Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - S V Joseph
- Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - L Jose
- Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - S Mundayoor
- Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - M S Jisha
- School of Biosciences, Mahatma Gandhi University, Kottayam, India
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Sánchez-Romero JJ, Olguin LF. Choline sulfatase from Ensifer ( Sinorhizobium) meliloti: Characterization of the unmodified enzyme. Biochem Biophys Rep 2015; 3:161-168. [PMID: 30338300 PMCID: PMC6189696 DOI: 10.1016/j.bbrep.2015.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 08/03/2015] [Accepted: 08/04/2015] [Indexed: 11/28/2022] Open
Abstract
Ensifer (Sinorhizobium) meliloti is a nitrogen-fixing α-proteobacterium able to biosynthesize the osmoprotectant glycine betaine from choline sulfate through a metabolic pathway that starts with the enzyme choline-O-sulfatase. This protein seems to be widely distributed in microorganisms and thought to play an important role in their sulfur metabolism. However, only crude extracts with choline sulfatase activity have been studied. In this work, Ensifer (Sinorhizobium) meliloti choline-O-sulfatase was obtained in a high degree of purity after expression in Escherichia coli. Gel filtration and dynamic light scattering experiments showed that the recombinant enzyme exists as a dimer in solution. Using calorimetry, its catalytic activity against its natural substrate, choline-O-sulfate, gave a kcat=2.7×10−1 s−1 and a KM=11.1 mM. For the synthetic substrates p-nitrophenyl sulfate and methylumbelliferyl sulfate, the kcat values were 3.5×10−2 s−1 and 4.3×10−2 s−1, with KM values of 75.8 and 11.8 mM respectively. The low catalytic activity of the recombinant sulfatase was due to the absence of the formylglycine post-translational modification in its active-site cysteine 54. Nevertheless, unmodified Ensifer (Sinorhizobium) meliloti choline-O-sulfatase is a multiple-turnover enzyme with remarkable catalytic efficiency. First biochemical characterization of a recombinant choline-O-sulfatase. Recombinant enzyme has no post-translational modification in its active site cysteine. The unmodified enzyme exhibits multiple catalytic cycles. Despite a low kcat the enzyme accelerate 1020-fold the uncatalyzed reaction.
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Key Words
- COS, E. meliloti choline-O-sulfatase
- Catalytic efficiency
- Choline-O-sulfatase
- Choline-O-sulfate
- DLS, dynamic light scattering
- DTNB, 5,5′-Dithiobis(2-nitrobenzoic acid)
- DTT, DL-Dithiothreitol
- FGE, α-formylglycine-generating enzyme
- FGly, α-formylglycine
- Formylglycine post-translational modification
- ITC, isothermal titration calorimetry
- MALDI-TOF, matrix assisted laser desorption ionization time-of-flight
- MUS, 4-methylumbelliferyl sulfate
- TCEP, Tris(2-carboxyethyl)phosphine hydrochloride
- Type I sulfatase
- UPLC-ESI-Q-TOF-MS, Ultra-performance liquid chromatography-electrospray ionization-quadrupole time-of-flight-mass spectrometry
- anSME, anaerobic sulfatase maturing enzyme
- pNPS, p-nitrophenyl sulfate
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Affiliation(s)
- Juan José Sánchez-Romero
- Laboratorio de Biofisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México D. F. 04510, México
| | - Luis F Olguin
- Laboratorio de Biofisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México D. F. 04510, México
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