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Filić Ž, Bielen A, Šarić E, Ćehić M, Crnolatac I, Tomić S, Vujaklija D, Abramić M. Evaluation of the Structure-Function Relationship of SGNH Lipase from Streptomyces rimosus by Site-Directed Mutagenesis and Computational Approach. Int J Mol Sci 2024; 25:595. [PMID: 38203766 PMCID: PMC10779480 DOI: 10.3390/ijms25010595] [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: 11/03/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Streptomyces rimosus extracellular lipase (SrL) is a multifunctional hydrolase belonging to the SGNH family. Here site-directed mutagenesis (SDM) was used for the first time to investigate the functional significance of the conserved amino acid residues Ser10, Gly54, Asn82, Asn213, and His216 in the active site of SrL. The hydrolytic activity of SrL variants was determined using para-nitrophenyl (pNP) esters with C4, C8, and C16 fatty acid chains. Mutation of Ser10, Asn82, or His216, but not Gly54, to Ala abolished lipase activity for all substrates. In contrast, the Asn213Ala variant showed increased enzymatic activity for C8 and C16 pNP esters. Molecular dynamics (MD) simulations showed that the interactions between the long alkyl chain substrate (C16) and Ser10 and Asn82 were strongest in Asn213Ala SrL. In addition to Asn82, Gly54, and Ser10, several new constituents of the substrate binding site were recognized (Lys28, Ser53, Thr89, and Glu212), as well as strong electrostatic interactions between Lys28 and Glu212. In addition to the H bonds Ser10-His216 and His216-Ser214, Tyr11 interacted strongly with Ser10 and His216 in all complexes with an active enzyme form. A previously unknown strong H bond between the catalytically important Asn82 and Gly54 was uncovered, which stabilizes the substrate in an orientation suitable for the enzyme reaction.
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Affiliation(s)
- Želimira Filić
- Division of Physical Chemistry, Institute Ruđer Bošković, 10000 Zagreb, Croatia; (Ž.F.); (E.Š.); (M.Ć.)
| | - Ana Bielen
- Faculty of Food Technology and Biotechnology, University of Zagreb, 10000 Zagreb, Croatia;
| | - Ela Šarić
- Division of Physical Chemistry, Institute Ruđer Bošković, 10000 Zagreb, Croatia; (Ž.F.); (E.Š.); (M.Ć.)
| | - Mirsada Ćehić
- Division of Physical Chemistry, Institute Ruđer Bošković, 10000 Zagreb, Croatia; (Ž.F.); (E.Š.); (M.Ć.)
| | - Ivo Crnolatac
- Division of Organic Chemistry and Biochemistry, Institute Ruđer Bošković, 10000 Zagreb, Croatia; (I.C.); (M.A.)
| | - Sanja Tomić
- Division of Organic Chemistry and Biochemistry, Institute Ruđer Bošković, 10000 Zagreb, Croatia; (I.C.); (M.A.)
| | - Dušica Vujaklija
- Division of Physical Chemistry, Institute Ruđer Bošković, 10000 Zagreb, Croatia; (Ž.F.); (E.Š.); (M.Ć.)
| | - Marija Abramić
- Division of Organic Chemistry and Biochemistry, Institute Ruđer Bošković, 10000 Zagreb, Croatia; (I.C.); (M.A.)
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Coyle JF, Pagliai FA, Zhang D, Lorca GL, Gonzalez CF. Purification and partial characterization of LdtP, a cell envelope modifying enzyme in Liberibacter asiaticus. BMC Microbiol 2018; 18:201. [PMID: 30497377 PMCID: PMC6267092 DOI: 10.1186/s12866-018-1348-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 11/19/2018] [Indexed: 01/09/2023] Open
Abstract
Background The aggressive spread of Liberibacter asiaticus, a bacterium closely associated with citrus greening, has given rise to an acute crisis in the citrus industry, making it imperative to expand the scientific knowledge base regarding L. asiaticus. Despite several endeavors to culture L. asiaticus, this bacterium has yet to be maintained in axenic culture, rendering identification and analysis of potential treatment targets challenging. Accordingly, a thorough understanding of biological mechanisms involved in the citrus host-microbe relationship is critical as a means of directing the search for future treatment targets. In this study, we evaluate the biochemical characteristics of CLIBASIA_01175, renamed LdtP (L,D-transpeptidase). Surrogate strains were used to evaluate its potential biological significance in gram-negative bacteria. A strain of E. coli carrying quintuple knock-outs of all genes encoding L,D-transpeptidases was utilized to demonstrate the activity of L. asiaticus LdtP. Results This complementation study demonstrated the periplasmic localization of mature LdtP and provided evidence for the biological role of LdtP in peptidoglycan modification. Further investigation highlighted the role of LdtP as a periplasmic esterase involved in modification of the lipid A moiety of the lipopolysaccharide. This work described, for the first time, an enzyme of the L,D-transpeptidase family with moonlighting enzyme activity directed to the modification of the bacterial cell wall and LPS. Conclusions Taken together, the data indicates that LdtP is a novel protein involved in an alternative pathway for modification of the bacterial cell, potentially affording L. asiaticus a means to survive within the host. Electronic supplementary material The online version of this article (10.1186/s12866-018-1348-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Janelle F Coyle
- Department of Microbiology and Cell Science, Genetics Institute and Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Fernando A Pagliai
- Department of Microbiology and Cell Science, Genetics Institute and Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Dan Zhang
- Department of Microbiology and Cell Science, Genetics Institute and Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Graciela L Lorca
- Department of Microbiology and Cell Science, Genetics Institute and Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Claudio F Gonzalez
- Department of Microbiology and Cell Science, Genetics Institute and Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA.
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Razeq FM, Jurak E, Stogios PJ, Yan R, Tenkanen M, Kabel MA, Wang W, Master ER. A novel acetyl xylan esterase enabling complete deacetylation of substituted xylans. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:74. [PMID: 29588659 PMCID: PMC5863359 DOI: 10.1186/s13068-018-1074-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 03/09/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Acetylated 4-O-(methyl)glucuronoxylan (GX) is the main hemicellulose in deciduous hardwood, and comprises a β-(1→4)-linked xylopyranosyl (Xylp) backbone substituted by both acetyl groups and α-(1→2)-linked 4-O-methylglucopyranosyluronic acid (MeGlcpA). Whereas enzymes that target singly acetylated Xylp or doubly 2,3-O-acetyl-Xylp have been well characterized, those targeting (2-O-MeGlcpA)3-O-acetyl-Xylp structures in glucuronoxylan have remained elusive. RESULTS An unclassified carbohydrate esterase (FjoAcXE) was identified as a protein of unknown function from a polysaccharide utilization locus (PUL) otherwise comprising carbohydrate-active enzyme families known to target xylan. FjoAcXE was shown to efficiently release acetyl groups from internal (2-O-MeGlcpA)3-O-acetyl-Xylp structures, an activity that has been sought after but lacking in known carbohydrate esterases. FjoAcXE action boosted the activity of α-glucuronidases from families GH67 and GH115 by five and nine times, respectively. Moreover, FjoAcXE activity was not only restricted to GX, but also deacetylated (3-O-Araf)2-O-acetyl-Xylp of feruloylated xylooligomers, confirming the broad substrate range of this new carbohydrate esterase. CONCLUSION This study reports the discovery and characterization of the novel carbohydrate esterase, FjoAcXE. In addition to cleaving singly acetylated Xylp, and doubly 2,3-O-acetyl-Xylp, FjoAcXE efficiently cleaves internal 3-O-acetyl-Xylp linkages in (2-O-MeGlcpA)3-O-acetyl-Xylp residues along with densely substituted and branched xylooligomers; activities that until now were missing from the arsenal of enzymes required for xylan conversion.
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Affiliation(s)
- Fakhria M. Razeq
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Edita Jurak
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 00076 Aalto Espoo, Finland
| | - Peter J. Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Ruoyu Yan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Maija Tenkanen
- Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 66, 00014 Helsinki, Finland
| | - Mirjam A. Kabel
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Weijun Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Emma R. Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 00076 Aalto Espoo, Finland
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Bae SY, Ryu BH, Jang E, Kim S, Kim TD. Characterization and immobilization of a novel SGNH hydrolase (Est24) from Sinorhizobium meliloti. Appl Microbiol Biotechnol 2012; 97:1637-47. [PMID: 22526795 DOI: 10.1007/s00253-012-4038-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 03/11/2012] [Accepted: 03/16/2012] [Indexed: 12/13/2022]
Abstract
A novel oligomeric SGNH hydrolase (Est24) from Sinorhizobium meliloti was identified, actively expressed in Escherichia coli, characterized, and immobilized for industrial application. Sequence analysis of Est24 revealed a putative catalytic triad (Ser¹³-Asp¹⁶³-His¹⁶⁹), with moderate homology to other SGNH hydrolases. Est24 was more active toward short-chain esters, such as p-nitrophenyl acetate, butyrate, and valerate, while the S13A mutant completely lost its activity. Moreover, the activity of Est24 toward α- and β-naphthyl acetate, and enantioselectivity on (R)- and (S)-methyl-3-hydroxy-2-methylpropionate were tested. Est24 exhibited optimum activity at mesophilic temperature ranges (45-55 °C), and slightly alkaline pH (8.0). Structural and mutagenesis studies revealed critical residues involved in the formation of a catalytic triad and substrate-binding pocket. Cross-linked enzyme aggregates (CLEAs) of Est24 with and without amyloid fibrils were prepared, and amyloid fibril-linked Est24 with amyloid fibrils retained 83 % of its initial activity after 1 h of incubation at 60 °C. The high thermal stability of immobilized Est24 highlights its potential in the pharmaceutical and chemical industries.
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Affiliation(s)
- Song Yi Bae
- Department of Molecular Science and Technology, Graduate School of Interdisciplinary Programs, Ajou University, Suwon 443-749, South Korea
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Kim S, Bae SY, Kim SJ, Ngo TD, Kim KK, Kim TD. Characterization, amyloid formation, and immobilization of a novel SGNH hydrolase from Listeria innocua 11262. Int J Biol Macromol 2011; 50:103-11. [PMID: 22020155 DOI: 10.1016/j.ijbiomac.2011.10.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 10/04/2011] [Accepted: 10/07/2011] [Indexed: 10/16/2022]
Abstract
A novel oligomeric hydrolase (LI22) from Listeria innocua CLIP 11262 was identified, characterized, and immobilized for industrial application. Sequence analysis of LI22 revealed a putative catalytic triad (Ser(10)-Asp(176)-His(179)), and a conserved sequence motif Ser(S)(10)-Gly(G)(77)-Asn(N)(79)-His(H)(179) with moderate identities (<30%) with other members of the SGNH-hydrolase superfamily. LI22 was able to hydrolyze p-nitrophenyl acetate, α- and β-naphthyl acetate, while the S10A mutant completely lost its activity. Structural properties of LI22 were investigated using gel filtration, circular dichroism (CD), fluorescence, molecular modeling, and gel filtration. We have shown that upon incubation in 30% TFE or 50% ethanol solution, LI22 was transformed into curly amyloid fibrils. Cross-linked enzyme aggregates of LI22 were prepared by precipitating the enzyme with ammonium sulfate and subsequent cross-linking with glutaraldehyde. Higher thermal and chemical stability, as well as good durability after repeated use of the LI22-CLEA, highlight its potential applicability as a biocatalyst in the pharmaceutical and chemical industries.
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Affiliation(s)
- Seulgi Kim
- Department of Molecular Science and Technology, Graduate School of Interdisciplinary Programs, Ajou University, Suwon, South Korea
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Alalouf O, Balazs Y, Volkinshtein M, Grimpel Y, Shoham G, Shoham Y. A new family of carbohydrate esterases is represented by a GDSL hydrolase/acetylxylan esterase from Geobacillus stearothermophilus. J Biol Chem 2011; 286:41993-42001. [PMID: 21994937 DOI: 10.1074/jbc.m111.301051] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Acetylxylan esterases hydrolyze the ester linkages of acetyl groups at positions 2 and/or 3 of the xylose moieties in xylan and play an important role in enhancing the accessibility of xylanases to the xylan backbone. The hemicellulolytic system of the thermophilic bacterium Geobacillus stearothermophilus T-6 comprises a putative acetylxylan esterase gene, axe2. The gene product belongs to the GDSL hydrolase family and does not share sequence homology with any of the carbohydrate esterases in the CAZy Database. The axe2 gene is induced by xylose, and the purified gene product completely deacetylates xylobiose peracetate (fully acetylated) and hydrolyzes the synthetic substrates 2-naphthyl acetate, 4-nitrophenyl acetate, 4-methylumbelliferyl acetate, and phenyl acetate. The pH profiles for k(cat) and k(cat)/K(m) suggest the existence of two ionizable groups affecting the binding of the substrate to the enzyme. Using NMR spectroscopy, the regioselectivity of Axe2 was directly determined with the aid of one-dimensional selective total correlation spectroscopy. Methyl 2,3,4-tri-O-acetyl-β-d-xylopyranoside was rapidly deacetylated at position 2 or at positions 3 and 4 to give either diacetyl or monoacetyl intermediates, respectively; methyl 2,3,4,6-tetra-O-acetyl-β-d-glucopyranoside was initially deacetylated at position 6. In both cases, the complete hydrolysis of the intermediates occurred at a much slower rate, suggesting that the preferred substrate is the peracetate sugar form. Site-directed mutagenesis of Ser-15, His-194, and Asp-191 resulted in complete inactivation of the enzyme, consistent with their role as the catalytic triad. Overall, our results show that Axe2 is a serine acetylxylan esterase representing a new carbohydrate esterase family.
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Affiliation(s)
- Onit Alalouf
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000
| | - Yael Balazs
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000
| | - Margarita Volkinshtein
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000
| | - Yael Grimpel
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000
| | - Gil Shoham
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000.
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Molecular cloning and characterization of a novel SGNH arylesterase from the goat rumen contents. Appl Microbiol Biotechnol 2011; 91:1561-70. [PMID: 21533577 DOI: 10.1007/s00253-011-3289-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 03/26/2011] [Accepted: 03/27/2011] [Indexed: 10/18/2022]
Abstract
An esterase-encoding gene, estR5, was directly obtained from the genomic DNA of goat rumen contents. The 555-bp full-length gene encodes a 184-residue polypeptide (EstR5) without putative signal peptide. Deduced EstR5 shared the highest identity (50%) to a putative arylesterase from Ruminococcaceae bacterium D16. Phylogenetic analysis indicated that EstR5 was closely related with microbial esterases of gastrointestinal source. A comparison of the conserved motifs shared with GDSL proteins revealed that EstR5 could be grouped into the GDSL family and was further classified into the subfamily of SGNH hydrolases. The gene estR5 was expressed in Escherichia coli BL21 (DE3) and purified to electrophoretic homogeneity. Recombinant EstR5 exhibited highest catalytic efficiency towards α-naphthyl acetate followed by phenyl acetate and p-nitrophenyl acetate and had no activity towards PNP esters with acyl chains longer than C8. The enzyme exhibited optimal activity at around 60°C and pH 8.0, was stable at pH ranging from 6.0 to 11.0 and was slightly activated by detergent Tween, Nonidet P-40, and Triton X-100. These properties suggest that EstR5 has great potential for basic research and industrial applications. To our knowledge, this is the first arylesterase obtained from rumen microenvironment.
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Leščić Ašler I, Ivić N, Kovačić F, Schell S, Knorr J, Krauss U, Wilhelm S, Kojić-Prodić B, Jaeger KE. Probing Enzyme Promiscuity of SGNH Hydrolases. Chembiochem 2010; 11:2158-67. [DOI: 10.1002/cbic.201000398] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Hwang H, Kim S, Yoon S, Ryu Y, Lee SY, Kim TD. Characterization of a novel oligomeric SGNH-arylesterase from Sinorhizobium meliloti 1021. Int J Biol Macromol 2010; 46:145-52. [PMID: 20060410 DOI: 10.1016/j.ijbiomac.2009.12.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 12/29/2009] [Accepted: 12/29/2009] [Indexed: 11/17/2022]
Abstract
A novel oligomeric SGNH-arylesterase (Sm23) from Sinorhizobium meliloti 1021 was characterized using biochemical and biophysical methods. A sequence comparison of Sm23 with other SGNH members confirmed the presence of catalytic triad (Ser(10), Asp(187), and His(190)) and oxyanion holes (Ser(10)-Gly(50)-Asn(90)). The wild type enzyme was able to hydrolyze p-nitrophenyl acetate, alpha- and beta-naphthyl acetate, while S10A mutant completely lost its activity. Structural properties of Sm23 were investigated using circular dichroism (CD), fluorescence, dynamic light scattering (DLS), chemical cross-linking, electron microscopy (EM), and time of flight (TOF) mass spectrometry. Furthermore, spherical or globular aggregates were observed with 1-butyl-3-methylimidazolium tetrafluoroborate, while amorphous aggregates were formed with 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide.
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Affiliation(s)
- Heejin Hwang
- Department of Molecular Science and Technology, Graduate School of Interdisciplinary Programs, Ajou University, Suwon 443-749, South Korea
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