1
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Bhardwaj KK, Dogra A, Kapoor S, Mehta A, Gupta R. Purification and Properties of an Esterase from Bacillus licheniformis and it’s Application in Synthesis of Octyl Acetate. Open Microbiol J 2020. [DOI: 10.2174/1874285802014010113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background:
Esterase plays a major role in the degradation of natural materials, industrial pollutants and also provides an immense contribution to the eco-friendly approaches in various industrial applications.
Objective:
In the present study, extracellular esterase from bacterial isolate Bacillus licheniformis was purified, characterized and used in the synthesis of octyl acetate.
Methods:
Purification of esterase from Bacillus licheniformis was achieved using Sephadex G-75 column chromatography. Gas chromatography was used to analyze the octyl acetate synthesis.
Results:
The enzyme was salted out using ammonium sulphate precipitation and 60-70% saturation gave maximum specific activity of the enzyme during precipitation. A purification fold of 6.46 and yield of 9.69% was achieved when esterase from Bacillus licheniformis was purified using Sephadex G-75 column chromatography. Native as well as SDS-PAGE analysis gave a single band of 42 kDa. This showed that the enzyme was purified to homogeneity and it was a monomer with molecular weight of 42 kDa. Biochemical characterization of the enzyme revealed that it had optimum temperature of 45°C in 0.1 M Tris-HCl buffer of pH 8.0. On optimizing different parameters, such as molar ratio of reactants, incubation time, temperature, and amount of protein, the % yield of octyl acetate was found to be 77.3%.
Conclusion:
In this work, simple method was used to purify esterase and the enzyme was further used in producing esters/products of commercial value within a reasonably short period of 12 h with a maximum yield of 77.3%.
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2
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Denesyuk A, Dimitriou PS, Johnson MS, Nakayama T, Denessiouk K. The acid-base-nucleophile catalytic triad in ABH-fold enzymes is coordinated by a set of structural elements. PLoS One 2020; 15:e0229376. [PMID: 32084230 PMCID: PMC7034887 DOI: 10.1371/journal.pone.0229376] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/05/2020] [Indexed: 01/09/2023] Open
Abstract
The alpha/beta-Hydrolases (ABH) are a structural class of proteins that are found widespread in nature and includes enzymes that can catalyze various reactions in different substrates. The catalytic versatility of the ABH fold enzymes, which has been a valuable property in protein engineering applications, is based on a similar acid-base-nucleophile catalytic mechanism. In our research, we are concerned with the structure that surrounds the key units of the catalytic machinery, and we have previously found conserved structural organizations that coordinate the catalytic acid, the catalytic nucleophile and the residues of the oxyanion hole. Here, we explore the architecture that surrounds the catalytic histidine at the active sites of enzymes from 40 ABH fold families, where we have identified six conserved interactions that coordinate the catalytic histidine next to the catalytic acid and the catalytic nucleophile. Specifically, the catalytic nucleophile is coordinated next to the catalytic histidine by two weak hydrogen bonds, while the catalytic acid is directly involved in the coordination of the catalytic histidine through by two weak hydrogen bonds. The imidazole ring of the catalytic histidine is coordinated by a CH-π contact and a hydrophobic interaction. Moreover, the catalytic triad residues are connected with a residue that is located at the core of the active site of ABH fold, which is suggested to be the fourth member of a “structural catalytic tetrad”. Besides their role in the stability of the catalytic mechanism, the conserved elements of the catalytic site are actively involved in ligand binding and affect other properties of the catalytic activity, such as substrate specificity, enantioselectivity, pH optimum and thermostability of ABH fold enzymes. These properties are regularly targeted in protein engineering applications, and thus, the identified conserved structural elements can serve as potential modification sites in order to develop ABH fold enzymes with altered activities.
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Affiliation(s)
- Alexander Denesyuk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, Russia
- * E-mail:
| | - Polytimi S. Dimitriou
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Toru Nakayama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
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3
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Bürger M, Chory J. Structural and chemical biology of deacetylases for carbohydrates, proteins, small molecules and histones. Commun Biol 2018; 1:217. [PMID: 30534609 PMCID: PMC6281622 DOI: 10.1038/s42003-018-0214-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/31/2018] [Indexed: 01/02/2023] Open
Abstract
Deacetylation is the removal of an acetyl group and occurs on a plethora of targets and for a wide range of biological reasons. Several pathogens deacetylate their surface carbohydrates to evade immune response or to support biofilm formation. Furthermore, dynamic acetylation/deacetylation cycles govern processes from chromatin remodeling to posttranslational modifications that compete with phosphorylation. Acetylation usually occurs on nitrogen and oxygen atoms and are referred to as N- and O-acetylation, respectively. This review discusses the structural prerequisites that enzymes must have to catalyze the deacetylation reaction, and how they adapted by formation of specific substrate and metal binding sites.
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Affiliation(s)
- Marco Bürger
- Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037 USA
| | - Joanne Chory
- Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037 USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037 USA
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4
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Dimitriou PS, Denesyuk AI, Nakayama T, Johnson MS, Denessiouk K. Distinctive structural motifs co-ordinate the catalytic nucleophile and the residues of the oxyanion hole in the alpha/beta-hydrolase fold enzymes. Protein Sci 2018; 28:344-364. [PMID: 30311984 DOI: 10.1002/pro.3527] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/04/2018] [Accepted: 10/08/2018] [Indexed: 12/17/2022]
Abstract
The alpha/beta-hydrolases (ABH) are among the largest structural families of proteins that are found in nature. Although they vary in their sequence and function, the ABH enzymes use a similar acid-base-nucleophile catalytic mechanism to catalyze reactions on different substrates. Because ABH enzymes are biocatalysts with a wide range of potential applications, protein engineering has taken advantage of their catalytic versatility to develop enzymes with industrial applications. This study is a comprehensive analysis of 40 ABH enzyme families focusing on two identified substructures: the nucleophile zone and the oxyanion zone, which co-ordinate the catalytic nucleophile and the residues of the oxyanion hole, and independently reported as critical for the enzymatic activity. We also frequently observed an aromatic cluster near the nucleophile and oxyanion zones, and opposite the ligand-binding site. The nucleophile zone, the oxyanion zone and the residue cluster enriched in aromatic side chains comprise a three-dimensional structural organization that shapes the active site of ABH enzymes and plays an important role in the enzymatic function by structurally stabilizing the catalytic nucleophile and the residues of the oxyanion hole. The structural data support the notion that the aromatic cluster can participate in co-ordination of the catalytic histidine loop, and properly place the catalytic histidine next to the catalytic nucleophile.
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Affiliation(s)
- Polytimi S Dimitriou
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland
| | - Alexander I Denesyuk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland.,Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Toru Nakayama
- Tohoku University, Biomolecular Engineering, Sendai, Miyagi, 980-8579, Japan
| | - Mark S Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland.,Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, Turku, 20520, Finland
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5
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Sista Kameshwar AK, Qin W. Understanding the structural and functional properties of carbohydrate esterases with a special focus on hemicellulose deacetylating acetyl xylan esterases. Mycology 2018; 9:273-295. [PMID: 30533253 PMCID: PMC6282417 DOI: 10.1080/21501203.2018.1492979] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/21/2018] [Indexed: 11/29/2022] Open
Abstract
Acetyl and methyl esterifications are two major naturally found substitutions in the plant cell-wall polysaccharides. The non-cellulosic plant cell-wall polysaccharides such as pectin and hemicellulose are differentially esterified by the O-acetyl and methyl groups to cease the action of various hydrolytic enzymes secreted by different fungi and bacterial species. Thus, microorganisms have emerged with a special class of enzymes known as carbohydrate esterases (CE). The CE catalyse O-de, N-deacetylation of acetylated saccharide residues (esters or amides, where sugars play the role of alcohol/amine/acid). Carbohydrate active enzyme (CAZy) database has classified CE into 16 classes, of which hemicellulose deacetylating CE were grouped into eight classes (CE-1 to CE-7 and CE-16). Various plant biomass degrading fungi and bacteria secretes acetyl xylan esterases (AcXE); however, these enzymes exhibit varied substrate specificities. AcXE and xylanases-coupled pretreatment methods exhibit significant applications, such as enhancing animal feedstock, baking industry, production of food additives, paper and pulp, xylitol production and biorefinery-based industries, respectively. Thus, understanding the structural and functional properties of acetyl xylan esterase will significantly aid in developing the efficient AcXE with wide range of industrial applications.
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Affiliation(s)
| | - Wensheng Qin
- Department of Biology, Lakehead University, Thunder Bay, Ontario, Canada
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6
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Singh MK, Shivakumaraswamy S, Gummadi SN, Manoj N. Role of an N-terminal extension in stability and catalytic activity of a hyperthermostable α/β hydrolase fold esterase. Protein Eng Des Sel 2017; 30:559-570. [PMID: 28967962 DOI: 10.1093/protein/gzx049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/25/2017] [Indexed: 12/15/2022] Open
Abstract
The carbohydrate esterase family 7 (CE7) enzymes catalyze the deacetylation of acetyl esters of a broad range of alcohols and is unique in its activity towards cephalosporin C. The CE7 fold contains a conserved N-terminal extension that distinguishes it from the canonical α/β hydrolase fold. The hexameric quaternary structure indicates that the N-terminus may affect activity and specificity by controlling access of substrates to the buried active sites via an entrance tunnel. In this context, we characterized the catalytic parameters, conformation and thermal stability of two truncation variants lacking four and ten residues of the N-terminal region of the hyperthermostable Thermotoga maritima CE7 acetyl esterase (TmAcE). The truncations did not affect the secondary structure or the fold but modulated the oligomerization dynamics. A modest increase was observed in substrate specificity for acetylated xylose compared with acetylated glucose. A drastic reduction of ~30-40°C in the optimum temperature for activity of the variants indicated lower thermal stability. The loss of hyperthermostability appears to be an indirect effect associated with an increase in the conformational flexibility of an otherwise rigid neighboring loop containing a catalytic triad residue. The results suggest that the N-terminal extension was evolutionarily selected to preserve the stability of the enzyme.
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Affiliation(s)
- Mrityunjay K Singh
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences Indian Institute of Technology Madras, Chennai 600036, India
| | - Santosh Shivakumaraswamy
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences Indian Institute of Technology Madras, Chennai 600036, India
| | - Sathyanarayana N Gummadi
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences Indian Institute of Technology Madras, Chennai 600036, India
| | - Narayanan Manoj
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences Indian Institute of Technology Madras, Chennai 600036, India
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7
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An extended loop in CE7 carbohydrate esterase family is dispensable for oligomerization but required for activity and thermostability. J Struct Biol 2016; 194:434-45. [DOI: 10.1016/j.jsb.2016.04.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/07/2016] [Accepted: 04/13/2016] [Indexed: 11/20/2022]
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8
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Collie GW, Pulka-Ziach K, Guichard G. In situ iodination and X-ray crystal structure of a foldamer helix bundle. Chem Commun (Camb) 2016; 52:1202-5. [DOI: 10.1039/c5cc07916k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We report here the efficient in situ iodination of tyrosine-type side-chains located within a foldamer helix bundle, permitting structure determination using single-wavelength anomalous diffraction (SAD) methods.
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Affiliation(s)
| | | | - Gilles Guichard
- Université de Bordeaux
- CNRS
- UMR 5248
- CBMN
- Institut Européen de Chimie et Biologie
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9
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Sayer C, Szabo Z, Isupov MN, Ingham C, Littlechild JA. The Structure of a Novel Thermophilic Esterase from the Planctomycetes Species, Thermogutta terrifontis Reveals an Open Active Site Due to a Minimal 'Cap' Domain. Front Microbiol 2015; 6:1294. [PMID: 26635762 PMCID: PMC4655241 DOI: 10.3389/fmicb.2015.01294] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/06/2015] [Indexed: 11/29/2022] Open
Abstract
A carboxyl esterase (TtEst2) has been identified in a novel thermophilic bacterium, Thermogutta terrifontis from the phylum Planctomycetes and has been cloned and over-expressed in Escherichia coli. The enzyme has been characterized biochemically and shown to have activity toward small p-nitrophenyl (pNP) carboxylic esters with optimal activity for pNP-acetate. The enzyme shows moderate thermostability retaining 75% activity after incubation for 30 min at 70°C. The crystal structures have been determined for the native TtEst2 and its complexes with the carboxylic acid products propionate, butyrate, and valerate. TtEst2 differs from most enzymes of the α/β-hydrolase family 3 as it lacks the majority of the ‘cap’ domain and its active site cavity is exposed to the solvent. The bound ligands have allowed the identification of the carboxyl pocket in the enzyme active site. Comparison of TtEst2 with structurally related enzymes has given insight into how differences in their substrate preference can be rationalized based upon the properties of their active site pockets.
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Affiliation(s)
- Christopher Sayer
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
| | | | - Michail N Isupov
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
| | | | - Jennifer A Littlechild
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
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10
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Coppens F, Iyyathurai J, Ruer S, Fioravanti A, Taganna J, Vereecke L, De Greve H, Remaut H. Structural and adhesive properties of the long polar fimbriae protein LpfD from adherent-invasive Escherichia coli. ACTA ACUST UNITED AC 2015; 71:1615-26. [PMID: 26249343 DOI: 10.1107/s1399004715009803] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 05/20/2015] [Indexed: 01/13/2023]
Abstract
Crohn's disease (CD) is an inflammatory bowel disease characterized by an exaggerated immune response to commensal microbiota in the intestines of patients. Metagenomic studies have identified specific bacterial species and strains with increased prevalence in CD patients, amongst which is the adherent-invasive Escherichia coli (AIEC) strain LF82. AIEC strains express long polar fimbriae (LPF), which are known to target Peyer's patches in a mouse CD model. Here, the recombinant production of a soluble, self-complemented construct of the LpfD protein of E. coli LF82 is reported and it is demonstrated that it forms the adhesive tip subunit of LPF. The LpfD crystal reveals an N-terminal adhesin domain and a C-terminal pilin domain that connects the adhesin to the minor pilus subunit LpfE. Surface topology and sequence conservation in the adhesin domain hint at a putative receptor-binding pocket as found in the Klebsiella pneumoniae MrkD and E. coli F17-G (GafD) adhesins. Immunohistostaining of murine intestinal tissue sections revealed that LpfD specifically binds to the intestinal mucosa and submucosa. LpfD binding was found to be resistant to treatment with O- or N-glycosidases, but was lost in collagenase-treated tissue sections, indicating the possible involvement of an intestinal matrix-associated protein as the LpfD receptor. LpfD strongly adhered to isolated fibronectin in an in vitro assay, and showed lower levels of binding to collagen V and laminin and no binding to collagens I, III and IV.
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Affiliation(s)
- Fanny Coppens
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jegan Iyyathurai
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Ségolène Ruer
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Antonella Fioravanti
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Joemar Taganna
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Lars Vereecke
- Inflammation Research Center, Unit of Molecular Signal Transduction in Inflammation, VIB, 9052 Ghent, Belgium
| | - Henri De Greve
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Han Remaut
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
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11
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Tong X, Lange L, Grell MN, Busk PK. Hydrolysis of wheat arabinoxylan by two acetyl xylan esterases from Chaetomium thermophilum. Appl Biochem Biotechnol 2014; 175:1139-52. [PMID: 25369895 DOI: 10.1007/s12010-014-1348-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 10/27/2014] [Indexed: 10/24/2022]
Abstract
The thermophilic filamentous ascomycete Chaetomium thermophilum produces functionally diverse hemicellulases when grown on hemicellulose as carbon source. Acetyl xylan esterase (EC 3.1.1.72) is an important accessory enzyme in hemicellulose biodegradation. Although the genome of C. thermophilum has been sequenced, its carbohydrate esterases are not annotated yet. We applied peptide pattern recognition (PPR) tool for sequence analysis of the C. thermophilum genome, and 11 carbohydrate esterase genes were discovered. Furthermore, we cloned and heterologously expressed two putative acetyl xylan esterase genes, CtAxeA and CtAxeB, in Pichia pastoris. The recombinant proteins, rCtAxeA and rCtAxeB, released acetic acids from p-nitrophenyl acetate and water-insoluble wheat arabinoxylan. These results indicate that CtAxeA and CtAxeB are true acetyl xylan esterases. For both recombinant esterases, over 93 % of the initial activity was retained after 24 h of incubation at temperatures up to 60 °C, and over 90 % of the initial activity was retained after 24 h of incubation in different buffers from pH 4.0 to 9.0 at 4 and 50 °C. The overall xylose yield from wheat arabinoxylan hydrolysis was 8 % with xylanase treatment and increased to 34 % when xylanase was combined with rCtAxeA and rCtAxeB. In sum, the present study first report the biochemical characterization of two acetyl xylan esterases from C. thermophilum, which are efficient in hydrolyzing hemicellulose with potential application in biomass bioconversion to high value chemicals or biofuels.
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Affiliation(s)
- Xiaoxue Tong
- Section for Sustainable Biotechnology, Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University Copenhagen, Copenhagen, Denmark
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12
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Fako VE, Zhang JT, Liu JY. Mechanism of Orlistat Hydrolysis by the Thioesterase of Human Fatty Acid Synthase. ACS Catal 2014; 4:3444-3453. [PMID: 25309810 PMCID: PMC4188697 DOI: 10.1021/cs500956m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 08/15/2014] [Indexed: 01/25/2023]
Abstract
Fatty acid synthase (FASN), the sole protein capable of de novo synthesis of free fatty acids, is overexpressed in a wide variety of human cancers and is associated with poor prognosis and aggressiveness of these cancers. Orlistat, an FDA-approved drug for obesity treatment that inhibits pancreatic lipases in the GI tract, also inhibits the thioesterase (TE) of human FASN. The cocrystal structure of TE with orlistat shows a pseudo TE dimer containing two different forms of orlistat in the active site, an intermediate that is covalently bound to a serine residue (Ser2308) and a hydrolyzed and inactivated product. In this study, we attempted to understand the mechanism of TE-catalyzed orlistat hydrolysis by examining the role of the hexyl tail of the covalently bound orlistat in water activation for hydrolysis using molecular dynamics simulations. We found that the hexyl tail of the covalently bound orlistat undergoes a conformational transition, which is accompanied by destabilization of a hydrogen bond between a hydroxyl moiety of orlistat and the catalytic His2481 of TE that in turn leads to an increased hydrogen bonding between water molecules and His2481 and increased chance for water activation to hydrolyze the covalent bond between orlistat and Ser2308. Thus, the conformation of the hexyl tail of orlistat plays an important role in orlistat hydrolysis. Strategies that stabilize the hexyl tail may lead to the design of more potent irreversible inhibitors that target FASN and block TE activity with greater endurance.
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Affiliation(s)
| | | | - Jing-Yuan Liu
- Department
of Computer and Information Science, Indiana University-Purdue University, 635 Barnhill Drive, Indianapolis, Indiana 46202, United States
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13
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Chen J, Cui W, Giblin D, Gross ML. New protein footprinting: fast photochemical iodination combined with top-down and bottom-up mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1306-18. [PMID: 22669760 PMCID: PMC3630512 DOI: 10.1007/s13361-012-0403-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 04/25/2012] [Accepted: 04/25/2012] [Indexed: 05/02/2023]
Abstract
We report a new approach for the fast photochemical oxidation of proteins (FPOP) whereby iodine species are used as the modifying reagent. We generate the radicals by photolysis of iodobenzoic acid at 248 nm; the putative iodine radical then rapidly modifies the target protein. This iodine-radical labeling is sensitive, tunable, and site-specific, modifying only histidine and tyrosine residues in contrast to OH radicals that modify 14 amino-acid side chains. We iodinated myoglobin (Mb) and apomyoglobin (aMb) in their native states and analyzed the outcome by both top-down and bottom-up proteomic strategies. Top-down sequencing selects a certain level (addition of one I, two I's) of modification and determines the major components produced in the modification reaction, whereas bottom-up reveals details for each modification site. Tyr146 is found to be modified for aMb but less so for Mb. His82, His93, and His97 are at least 10 times more modified for aMb than for Mb, in agreement with NMR studies. For carbonic anhydrase and its apo form, there are no significant differences of the modification extents, indicating their similarity in conformation and providing a control for this approach. For lispro insulin, insulin-EDTA, and insulin complexed with zinc, iodination yields are sensitive to differences in insulin oligomerization state. The iodine radical labeling is a promising addition to protein footprinting methods, offering higher specificity and lower reactivity than ∙OH and SO(4)(-∙), two other radicals already employed in FPOP.
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Affiliation(s)
- Jiawei Chen
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, MO 63130, USA
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14
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Langs DA, Hauptman HA. Relaxation of the resolution requirements for direct-methods phasing. Acta Crystallogr A 2011; 67:396-401. [PMID: 21694478 DOI: 10.1107/s0108767311013560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Accepted: 04/11/2011] [Indexed: 11/10/2022] Open
Abstract
Shake-and-bake phasing methods have permitted the ab initio solution of crystal structures containing more than 1000 independent non-H light atoms (C, N, O). The success of these procedures is critically dependent upon having diffraction data measured to at least 1.2 Å resolution. A new target function R(2)(φ(h)) is introduced into the shake-and-bake procedure along with a real difference map strategy whereby this resolution limit can be appreciably lowered toward 1.5 Å. These improvements, when applied to moderately high resolution data, may now allow one the possibility to solve structures that are twice as large as could have been solved previously.
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Affiliation(s)
- David A Langs
- Department of Structural Biology, Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA.
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15
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Crellin PK, Vivian JP, Scoble J, Chow FM, West NP, Brammananth R, Proellocks NI, Shahine A, Le Nours J, Wilce MCJ, Britton WJ, Coppel RL, Rossjohn J, Beddoe T. Tetrahydrolipstatin inhibition, functional analyses, and three-dimensional structure of a lipase essential for mycobacterial viability. J Biol Chem 2010; 285:30050-60. [PMID: 20656688 PMCID: PMC2943268 DOI: 10.1074/jbc.m110.150094] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Revised: 07/21/2010] [Indexed: 11/06/2022] Open
Abstract
The highly complex and unique mycobacterial cell wall is critical to the survival of Mycobacteria in host cells. However, the biosynthetic pathways responsible for its synthesis are, in general, incompletely characterized. Rv3802c from Mycobacterium tuberculosis is a partially characterized phospholipase/thioesterase encoded within a genetic cluster dedicated to the synthesis of core structures of the mycobacterial cell wall, including mycolic acids and arabinogalactan. Enzymatic assays performed with purified recombinant proteins Rv3802c and its close homologs from Mycobacterium smegmatis (MSMEG_6394) and Corynebacterium glutamicum (NCgl2775) show that they all have significant lipase activities that are inhibited by tetrahydrolipstatin, an anti-obesity drug that coincidently inhibits mycobacterial cell wall biosynthesis. The crystal structure of MSMEG_6394, solved to 2.9 Å resolution, revealed an α/β hydrolase fold and a catalytic triad typically present in esterases and lipases. Furthermore, we demonstrate direct evidence of gene essentiality in M. smegmatis and show the structural consequences of loss of MSMEG_6394 function on the cellular integrity of the organism. These findings, combined with the predicted essentiality of Rv3802c in M. tuberculosis, indicate that the Rv3802c family performs a fundamental and indispensable lipase-associated function in mycobacteria.
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Affiliation(s)
- Paul K Crellin
- Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria 3800, Australia.
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16
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Biochemical and domain analyses of FSUAxe6B, a modular acetyl xylan esterase, identify a unique carbohydrate binding module in Fibrobacter succinogenes S85. J Bacteriol 2009; 192:483-93. [PMID: 19897648 DOI: 10.1128/jb.00935-09] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acetyl xylan esterase (EC 3.1.1.72) is a member of a set of enzymes required to depolymerize hemicellulose, especially xylan that is composed of a main chain of beta-1,4-linked xylopyranoside residues decorated with acetyl side groups. Fibrobacter succinogenes S85 Axe6B (FSUAxe6B) is an acetyl xylan esterase encoded in the genome of this rumen bacterium. The enzyme is a modular protein comprised of an esterase domain, a carbohydrate-binding module, and a region of unknown function. Sequences that are homologous to the region of unknown function are paralogously distributed, thus far, only in F. succinogenes. Therefore, the sequences were designated Fibrobacter succinogenes-specific paralogous module 1 (FPm-1). The FPm-1s are associated with at least 24 polypeptides in the genome of F. succinogenes S85. A bioinformatics search showed that most of the FPm-1-appended polypeptides are putative carbohydrate-active enzymes, suggesting a potential role in carbohydrate metabolism. Truncational analysis of FSUAxe6B, together with catalytic and substrate binding studies, has allowed us to delineate the functional modules in the polypeptide. The N-terminal half of FSUAxe6B harbors the activity that cleaves side chain acetyl groups from xylan-like substrates, and the binding of insoluble xylan was determined to originate from FPm-1. Site-directed mutagenesis studies of highly conserved active-site residues in the esterase domain suggested that the esterase activity is derived from a tetrad composed of Ser(44), His(273), Glu(194), and Asp(270), with both Glu(194) and Asp(270) functioning as helper acids, instead of a single carboxylate residue proposed to initiate catalysis.
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17
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Liu Z, Julian RR. Deciphering the peptide iodination code: influence on subsequent gas-phase radical generation with photodissociation ESI-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:965-971. [PMID: 19185510 DOI: 10.1016/j.jasms.2008.12.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Revised: 12/17/2008] [Accepted: 12/17/2008] [Indexed: 05/27/2023]
Abstract
Iodination of tyrosine was recently discovered as a useful method for generating radical peptides via photodissociation of carbon-iodine bonds by an ultraviolet photon in the gas phase. The subsequent fragmentation behavior of the resulting odd-electron peptides is largely controlled by the radical. Although previous experiments have focused on mono-iodination of tyrosine, peptides and proteins can also be multiply iodinated. Tyrosine and, to a lesser extent, histidine can both be iodinated or doubly iodinated. The behavior of doubly iodinated residues is explored under conditions where the sites of iodination are carefully controlled. It is found that radical peptides generated by the loss of a single iodine from doubly iodinated tyrosine behave effectively identically to singly iodinated peptides. This suggests that the remaining iodine does not interfere with radical directed dissociation pathways. In contrast, the concerted loss of two iodines from doubly iodinated peptides yields substantially different results that suggest that radical recombination can occur. However, sequential activation can be used to generate multiple usable radicals in different steps of an MS(n) experiment. Furthermore, it is demonstrated that in actual peptides, the rate of iodination for tyrosine versus mono-iodotyrosine cannot be predicted easily a priori. In other words, previous assumptions that mono-iodination of tyrosine is the rate-limiting step to the formation of doubly iodinated tyrosine are incorrect.
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Affiliation(s)
- Zhenjiu Liu
- Department of Chemistry, University of California, Riverside, California 92508, USA
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18
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Aparna G, Chatterjee A, Sonti RV, Sankaranarayanan R. A cell wall-degrading esterase of Xanthomonas oryzae requires a unique substrate recognition module for pathogenesis on rice. THE PLANT CELL 2009; 21:1860-73. [PMID: 19525415 PMCID: PMC2714936 DOI: 10.1105/tpc.109.066886] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Revised: 05/13/2009] [Accepted: 05/23/2009] [Indexed: 05/20/2023]
Abstract
Xanthomonas oryzae pv oryzae (Xoo) causes bacterial blight, a serious disease of rice (Oryza sativa). LipA is a secretory virulence factor of Xoo, implicated in degradation of rice cell walls and the concomitant elicitation of innate immune responses, such as callose deposition and programmed cell death. Here, we present the high-resolution structural characterization of LipA that reveals an all-helical ligand binding module as a distinct functional attachment to the canonical hydrolase catalytic domain. We demonstrate that the enzyme binds to a glycoside ligand through a rigid pocket comprising distinct carbohydrate-specific and acyl chain recognition sites where the catalytic triad is situated 15 A from the anchored carbohydrate. Point mutations disrupting the carbohydrate anchor site or blocking the pocket, even at a considerable distance from the enzyme active site, can abrogate in planta LipA function, exemplified by loss of both virulence and the ability to elicit host defense responses. A high conservation of the module across genus Xanthomonas emphasizes the significance of this unique plant cell wall-degrading function for this important group of plant pathogenic bacteria. A comparison with the related structural families illustrates how a typical lipase is recruited to act on plant cell walls to promote virulence, thus providing a remarkable example of the emergence of novel functions around existing scaffolds for increased proficiency of pathogenesis during pathogen-plant coevolution.
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Affiliation(s)
- Gudlur Aparna
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, India
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19
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20
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Boersma YL, Pijning T, Bosma MS, van der Sloot AM, Godinho LF, Dröge MJ, Winter RT, van Pouderoyen G, Dijkstra BW, Quax WJ. Loop Grafting of Bacillus subtilis Lipase A: Inversion of Enantioselectivity. ACTA ACUST UNITED AC 2008; 15:782-9. [DOI: 10.1016/j.chembiol.2008.06.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Revised: 05/06/2008] [Accepted: 06/06/2008] [Indexed: 11/26/2022]
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21
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Iniesta J, Cooper HJ, Marshall AG, Heptinstall J, Walton DJ, Peterson IR. Specific electrochemical iodination of horse heart myoglobin at tyrosine 103 as determined by Fourier transform ion cyclotron resonance mass spectrometry. Arch Biochem Biophys 2008; 474:1-7. [PMID: 18348862 PMCID: PMC2568815 DOI: 10.1016/j.abb.2008.02.032] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Revised: 02/16/2008] [Accepted: 02/21/2008] [Indexed: 11/29/2022]
Abstract
The iodination of proteins remains a useful tool in biochemistry for radiolabelling. However, chemical or enzymatic iodination is difficult to control and can give deleterious polyiodination. Previously, we have shown that electrooxidation with nitrite is a rapid method for the selective nitration of tyrosine residues in proteins. In principle, it should be possible to substitute a number of electrooxidisable anions into the tyrosine phenol ring. Electrochemical iodination is more difficult to control than nitration because the rapid anodic oxidation of I− leads to persistent formation of the iodinating triiodide anion. However, application of pulsed electrooxidation and reduction cycles is shown to be an effective procedure for the selective mono and double-iodination of myoglobin, which may have general application to other proteins in controlling of the level of iodination. Mono- and double-iodination of myoglobin by this method was confirmed by electrospray FT-ICR mass spectrometry. Infrared multiphoton dissociation (IRMPD) enabled localization of the site of mono-iodination to be restricted to either His97 or Tyr103. More extensive sequence coverage was obtained with electron capture dissociation (ECD), allowing unambiguous assignment of the site of iodination to Tyr103.
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Affiliation(s)
- Jesus Iniesta
- Centre for Molecular and Biomedical Science, Faculty of Health and Life Sciences, Coventry University, Coventry CV1 5FB, UK
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22
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Colombres M, Garate JA, Lagos CF, Araya-Secchi R, Norambuena P, Quiroz S, Larrondo L, Pérez-Acle T, Eyzaguirre J. An eleven amino acid residue deletion expands the substrate specificity of acetyl xylan esterase II (AXE II) from Penicillium purpurogenum. J Comput Aided Mol Des 2007; 22:19-28. [PMID: 18060506 DOI: 10.1007/s10822-007-9149-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Accepted: 11/12/2007] [Indexed: 11/28/2022]
Abstract
The soft-rot fungus Penicillium purpurogenum secretes to the culture medium a variety of enzymes related to xylan biodegradation, among them three acetyl xylan esterases (AXE I, II and III). AXE II has 207 amino acids; it belongs to family 5 of the carbohydrate esterases and its structure has been determined by X-ray crystallography at 0.9 A resolution (PDB 1G66). The enzyme possesses the alpha/beta hydrolase fold and the catalytic triad typical of serine esterases (Ser90, His187 and Asp175). AXE II can hydrolyze esters of a large variety of alcohols, but it is restricted to short chain fatty acids. An analysis of its three-dimensional structure shows that a loop that covers the active site may be responsible for this strict specificity. Cutinase, an enzyme that hydrolyzes esters of long chain fatty acids and shows a structure similar to AXE II, lacks this loop. In order to generate an AXE II with this broader specificity, the preparation of a mutant lacking residues involving this loop (Gly104 to Ala114) was proposed. A set of molecular simulation experiments based on a comparative model of the mutant enzyme predicted a stable structure. Using site-directed mutagenesis, the loop's residues have been eliminated from the AXE II cDNA. The mutant protein has been expressed in Aspergillus nidulans A722 and Pichia pastoris, and it is active towards a range of fatty acid esters of up to at least 14 carbons. The availability of an esterase with broader specificity may have biotechnological applications for the synthesis of sugar esters.
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Affiliation(s)
- Marcela Colombres
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
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23
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Abstract
In this study, a simple method for selective iodination of peptides and proteins is established. Using angiotensin II as the model system, we demonstrate that nitrite catalyzed the selective iodination of the peptide at the N-terminus in an acidic solution. The N-terminal-iodinated peptides alkylated thiol-containing molecules such as N-acetylcysteine and glutathione to form peptide conjugates in a basic solution. Reactive species formed by increasing the pH of the reaction mixture of sodium nitrite and sodium iodide from 4 to 8 selectively iodinated peptides and proteins at tyrosine and histidine residues. These results show that nitrite is a useful catalyst for peptide and protein ligation.
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Affiliation(s)
- Haiteng Deng
- The Proteomics Resource Center, The Rockefeller University, NY 10021, New York, USA.
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Rockwell NC, Lagarias JC. Flexible mapping of homology onto structure with homolmapper. BMC Bioinformatics 2007; 8:123. [PMID: 17428344 PMCID: PMC1955750 DOI: 10.1186/1471-2105-8-123] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Accepted: 04/11/2007] [Indexed: 12/19/2022] Open
Abstract
Background Over the past decade, a number of tools have emerged for the examination of homology relationships among protein sequences in a structural context. Most recent software implementations for such analysis are tied to specific molecular viewing programs, which can be problematic for collaborations involving multiple viewing environments. Incorporation into larger packages also adds complications for users interested in adding their own scoring schemes or in analyzing proteins incorporating unusual amino acid residues such as selenocysteine. Results We describe homolmapper, a command-line application for mapping information from a multiple protein sequence alignment onto a protein structure for analysis in the viewing software of the user's choice. Homolmapper is small (under 250 K for the application itself) and is written in Python to ensure portability. It is released for non-commercial use under a modified University of California BSD license. Homolmapper permits facile import of additional scoring schemes and can incorporate arbitrary additional amino acids to allow handling of residues such as selenocysteine or pyrrolysine. Homolmapper also provides tools for defining and analyzing subfamilies relative to a larger alignment, for mutual information analysis, and for rapidly visualizing the locations of mutations and multi-residue motifs. Conclusion Homolmapper is a useful tool for analysis of homology relationships among proteins in a structural context. There is also extensive, example-driven documentation available. More information about homolmapper is available at .
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Affiliation(s)
- Nathan C Rockwell
- Section of Molecular and Cellular Biology, University of California, Davis, California 95616, USA
| | - J Clark Lagarias
- Section of Molecular and Cellular Biology, University of California, Davis, California 95616, USA
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Liu P, Ewis HE, Tai PC, Lu CD, Weber IT. Crystal structure of the Geobacillus stearothermophilus carboxylesterase Est55 and its activation of prodrug CPT-11. J Mol Biol 2007; 367:212-23. [PMID: 17239398 PMCID: PMC1950602 DOI: 10.1016/j.jmb.2006.12.067] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Revised: 12/21/2006] [Accepted: 12/27/2006] [Indexed: 01/07/2023]
Abstract
Several mammalian carboxylesterases were shown to activate the prodrug irinotecan (CPT-11) to produce 7-ethyl-10-hydroxycamptothecin (SN-38), a topoisomerase inhibitor used in cancer therapy. However, the potential use of bacterial carboxylesterases, which have the advantage of high stability, has not been explored. We present the crystal structure of the carboxyesterase Est55 from Geobacillus stearothermophilus and evaluation of its enzyme activity on CPT-11. Crystal structures were determined at pH 6.2 and pH 6.8 and resolution of 2.0 A and 1.58 A, respectively. Est55 folds into three domains, a catalytic domain, an alpha/beta domain and a regulatory domain. The structure is in an inactive form; the side-chain of His409, one of the catalytic triad residues, is directed away from the other catalytic residues Ser194 and Glu310. Moreover, the adjacent Cys408 is triply oxidized and lies in the oxyanion hole, which would block the binding of substrate, suggesting a regulatory role. However, Cys408 is not essential for enzyme activity. Mutation of Cys408 showed that hydrophobic side-chains were favorable, while polar serine was unfavorable for enzyme activity. Est55 was shown to hydrolyze CPT-11 into the active form SN-38. The mutant C408V provided a more stable enzyme for activation of CPT-11. Therefore, engineered thermostable Est55 is a candidate for use with irinotecan in enzyme-prodrug cancer therapy.
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Affiliation(s)
- Ping Liu
- Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA
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26
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Gordillo F, Caputo V, Peirano A, Chavez R, Van Beeumen J, Vandenberghe I, Claeyssens M, Bull P, Ravanal MC, Eyzaguirre J. Penicillium purpurogenum produces a family 1 acetyl xylan esterase containing a carbohydrate-binding module: characterization of the protein and its gene. ACTA ACUST UNITED AC 2006; 110:1129-39. [PMID: 17008082 DOI: 10.1016/j.mycres.2006.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Revised: 05/22/2006] [Accepted: 07/05/2006] [Indexed: 11/21/2022]
Abstract
At least three acetyl xylan esterases (AXE I, II and III) are secreted by Penicillium purpurogenum. This publication describes more detailed work on AXE I and its gene. AXE I binds cellulose but not xylan; it is glycosylated and inactivated by phenylmethylsulphonyl fluoride, showing that it is a serine esterase. The axe1 gene presents an open reading frame of 1278 bp, including two introns of 68 and 61 bp; it codes for a signal peptide of 31 residues and a mature protein of 351 amino acids (molecular weight 36,693). AXE I has a modular structure: a catalytic module at the amino terminus belonging to family 1 of the carbohydrate esterases, a linker rich in serines and threonines, and a family 1 carboxy terminal carbohydrate binding module (CBM). The CBM is similar to that of AXE from Trichoderma reesei, (with a family 5 catalytic module) indicating that the genes for catalytic modules and CBMs have evolved separately, and that they have been linked by gene fusion. The promoter sequence of axe1 contains several putative sequences for binding of gene expression regulators also found in other family 1 esterase gene promoters. It is proposed that AXE I and II act in succession in xylan degradation; first, xylan is attacked by AXE I and other xylanases possessing CBMs (which facilitate binding to lignocellulose), followed by other enzymes acting mainly on soluble substrates.
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Affiliation(s)
- Felipe Gordillo
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
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Mastihubová M, Biely P. Deoxy and deoxyfluoro analogues of acetylated methyl beta-D-xylopyranoside--substrates for acetylxylan esterases. Carbohydr Res 2005; 339:2101-10. [PMID: 15280055 DOI: 10.1016/j.carres.2004.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2003] [Revised: 06/04/2004] [Accepted: 06/05/2004] [Indexed: 10/26/2022]
Abstract
Four modified substrates for acetylxylan esterases, 2-deoxy, 3-deoxy, 2-deoxy-2-fluoro, and 3-deoxy-3-fluoro derivatives of di-O-acetylated methyl beta-D-xylopyranoside were synthesized via 2,3-anhydropentopyranoside precursors. Methyl 2,3-anhydro-4-O-benzyl-beta-D-ribopyranoside was transformed into methyl 2,3-anhydro-4-O-benzyl-beta-D-lyxopyranoside in three steps. The epoxide ring opening of 2,3-anhydropentopyranosides was accomplished either by hydride reduction or hydrofluorination. Methyl beta-D-xylopyranoside 2,3,4-tri-O-, 2,4-di-O-, and 3,4-di-O-acetates, and the prepared diacetate analogues were tested as substrates of acetylxylan esterases from Schizophyllum commune and Trichoderma reesei. Measurement of their rate of deacetylation pointed to unique structural requirements of the enzymes for the substrates. The enzymes differed particularly in the requirement for the trans vicinal hydroxy group in the deacetylation at C-2 and C-3 and in the tolerance to the presence of trans vicinal acetyl groups esterifying the OH group at C-2 and C-3.
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Affiliation(s)
- Mária Mastihubová
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 38 Bratislava, Slovakia.
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29
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Bourne Y, Hasper AA, Chahinian H, Juin M, De Graaff LH, Marchot P. Aspergillus niger Protein EstA Defines a New Class of Fungal Esterases within the α/β Hydrolase Fold Superfamily of Proteins. Structure 2004; 12:677-87. [PMID: 15062090 DOI: 10.1016/j.str.2004.03.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2003] [Revised: 01/22/2004] [Accepted: 01/23/2004] [Indexed: 10/26/2022]
Abstract
From the fungus Aspergillus niger, we identified a new gene encoding protein EstA, a member of the alpha/beta-hydrolase fold superfamily but of unknown substrate specificity. EstA was overexpressed and its crystal structure was solved by molecular replacement using a lipase-acetylcholinesterase chimera template. The 2.1 A resolution structure of EstA reveals a canonical Ser/Glu/His catalytic triad located in a small pocket at the bottom of a large solvent-accessible, bowl-shaped cavity. Potential substrates selected by manual docking procedures were assayed for EstA activity. Consistent with the pocket geometry, preference for hydrolysis of short acyl/propyl chain substrates was found. Identification of close homologs from the genome of other fungi, of which some are broad host-range pathogens, defines EstA as the first member of a novel class of fungal esterases within the superfamily. Hence the structure of EstA constitutes a lead template in the design of new antifungal agents directed toward its pathogenic homologs.
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Affiliation(s)
- Yves Bourne
- Architecture et Fonction des Macromolécules Biologiques, CNRS UMR-6098, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France.
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30
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Vincent F, Charnock SJ, Verschueren KHG, Turkenburg JP, Scott DJ, Offen WA, Roberts S, Pell G, Gilbert HJ, Davies GJ, Brannigan JA. Multifunctional xylooligosaccharide/cephalosporin C deacetylase revealed by the hexameric structure of the Bacillus subtilis enzyme at 1.9A resolution. J Mol Biol 2003; 330:593-606. [PMID: 12842474 DOI: 10.1016/s0022-2836(03)00632-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Esterases and deacetylases active on carbohydrate ligands have been classified into 14 families based upon amino acid sequence similarities. Enzymes from carbohydrate esterase family seven (CE-7) are unusual in that they display activity towards both acetylated xylooligosaccharides and the antibiotic, cephalosporin C. The 1.9A structure of the multifunctional CE-7 esterase (hereinafter CAH) from Bacillus subtilis 168 reveals a classical alpha/beta hydrolase fold encased within a 32 hexamer. This is the first example of a hexameric alpha/beta hydrolase and is further evidence of the versatility of this particular fold, which is used in a wide variety of biological contexts. A narrow entrance tunnel leads to the centre of the molecule, where the six active-centre catalytic triads point towards the tunnel interior and thus are sequestered away from cytoplasmic contents. By analogy to self-compartmentalising proteases, the tunnel entrance may function to hinder access of large substrates to the poly-specific active centre. This would explain the observation that the enzyme is active on a variety of small, acetylated molecules. The structure of an active site mutant in complex with the reaction product, acetate, reveals details of the putative oxyanion binding site, and suggests that substrates bind predominantly through non-specific contacts with protein hydrophobic residues. Protein residues involved in catalysis are tethered by interactions with protein excursions from the canonical alpha/beta hydrolase fold. These excursions also mediate quaternary structure maintenance, so it would appear that catalytic competence is only achieved on protein multimerisation. We suggest that the acetyl xylan esterase (EC 3.1.1.72) and cephalosporin C deacetylase (EC 3.1.1.41) enzymes of the CE-7 family represent a single class of proteins with a multifunctional deacetylase activity against a range of small substrates.
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Affiliation(s)
- Florence Vincent
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK
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31
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Acharya P, Rao NM. Stability studies on a lipase from Bacillus subtilis in guanidinium chloride. JOURNAL OF PROTEIN CHEMISTRY 2003; 22:51-60. [PMID: 12739898 DOI: 10.1023/a:1023067827678] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Lipase from Bacillus subtilis is a "lidless" lipase that does not show interfacial activation. Due to exposure of the active site to solvent, the lipase tends to aggregate. We have investigated the solution properties and unfolding of the lipase in guanidinium chloride (GdmCl) to understand its aggregation behavior and stability. Dynamic light scattering (DLS), near- and far-UV circular dichroism, activity and intrinsic fluorescence of lipase suggest that the protein undergoes unfolding between 1 M and 2 M GdmCl. The polarity sensitive dye, 1,1',-bis-(4anilino)naphthalene-5,5"-disulfonic acid (bis-ANS), a probe for hydrophobic pockets, binds cooperatively to the native lipase. An intermediate populated in 1.75 M GdmCl that strongly binds bis-ANS was identified. Tendency of the native protein to aggregate in solution and specific binding to bis-ANS confirms that the lipase has exposed hydrophobic pockets and this surface hydrophobicity strongly influences the unfolding pathway of the lipase in GdmCl.
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Affiliation(s)
- Priyamvada Acharya
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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32
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Steiner T. Hydrogen bonds from water molecules to aromatic acceptors in very high-resolution protein crystal structures. Biophys Chem 2002; 95:195-201. [PMID: 12062379 DOI: 10.1016/s0301-4622(01)00256-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Short contacts of water molecules with the pi-faces of aromatic residues were studied in a set of 75 very high resolution (<1.1 A) protein X-ray crystal structures. For 18 water molecules found at distances to aromatic midpoints <3.5 A, it was attempted to assign the hydrogen bond configuration (without experimental knowledge of the H-atom positions) by inspection of the surrounding. For approximately one-quarter of the cases, evidence for an O-H...pi hydrogen bond was found, another one-quarter does not form such a hydrogen bond, and for the remaining half, no conclusive assignment could be made. The results confirm the relatively frequent occurrence of aromatic hydrogen bonding in biomolecular hydration, but also underline difficulties in hydrogen bond assignment without reliable knowledge of the H-atom positions.
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Affiliation(s)
- Thomas Steiner
- Institut für Chemie-Kristallographie, Freie Universität Berlin, Takustr. 6, D-14195, Berlin, Germany.
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33
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van Pouderoyen G, Eggert T, Jaeger KE, Dijkstra BW. The crystal structure of Bacillus subtilis lipase: a minimal alpha/beta hydrolase fold enzyme. J Mol Biol 2001; 309:215-26. [PMID: 11491291 DOI: 10.1006/jmbi.2001.4659] [Citation(s) in RCA: 200] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The X-ray structure of the lipase LipA from Bacillus subtilis has been determined at 1.5 A resolution. It is the first structure of a member of homology family 1.4 of bacterial lipases. The lipase shows a compact minimal alpha/beta hydrolase fold with a six-stranded parallel beta-sheet flanked by five alpha-helices, two on one side of the sheet and three on the other side. The catalytic triad residues, Ser77, Asp133 and His156, and the residues forming the oxyanion hole (backbone amide groups of Ile12 and Met78) are in positions very similar to those of other lipases of known structure. However, no lid domain is present and the active-site nucleophile Ser77 is solvent-exposed. A model of substrate binding is proposed on the basis of a comparison with other lipases with a covalently bound tetrahedral intermediate mimic. It explains the preference of the enzyme for substrates with C8 fatty acid chains.
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Affiliation(s)
- G van Pouderoyen
- Laboratory of Biophysical Chemistry, University of Groningen, The Netherlands
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34
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Ghosh D, Sawicki M, Lala P, Erman M, Pangborn W, Eyzaguirre J, Gutierrez R, Jornvall H, Thiel DJ. Multiple conformations of catalytic serine and histidine in acetylxylan esterase at 0.90 A. J Biol Chem 2001; 276:11159-66. [PMID: 11134051 DOI: 10.1074/jbc.m008831200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Acetylxylan esterase (AXEII; 207 amino acids) from Penicillium purpurogenum has substrate specificities toward acetate esters of d-xylopyranose residues in xylan and belongs to a new class of alpha/beta hydrolases. The crystal structure of AXEII has been determined by single isomorphous replacement and anomalous scattering, and refined at 0.90- and 1.10-A resolutions with data collected at 85 K and 295 K, respectively. The tertiary structure consists of a doubly wound alpha/beta sandwich, having a central six-stranded parallel beta-sheet flanked by two parallel alpha-helices on each side. The catalytic residues Ser(90), His(187), and Asp(175) are located at the C-terminal end of the sheet, an exposed region of the molecule. The serine and histidine side chains in the 295 K structure show the frequently observed conformations in which Ser(90) is trans and the hydroxyl group is in the plane of the imidazole ring of His(187). However, the structure at 85 K displays an additional conformation in which Ser(90) side-chain hydroxyl is away from the plane of the imidazole ring of His(187). The His(187) side chain forms a hydrogen bond with a sulfate ion and adopts an altered conformation. The only other known hydrolase that has a similar tertiary structure is Fusarium solani cutinase. The exposed nature of the catalytic triad suggests that AXEII is a pure esterase, i.e. an alpha/beta hydrolase with specificity for nonlipidic polar substrates.
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Affiliation(s)
- D Ghosh
- Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203, USA.
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Hakulinen N, Tenkanen M, Rouvinen J. Three-dimensional structure of the catalytic core of acetylxylan esterase from Trichoderma reesei: insights into the deacetylation mechanism. J Struct Biol 2000; 132:180-90. [PMID: 11243887 DOI: 10.1006/jsbi.2000.4318] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Acetylxylan esterase from Trichoderma reesei removes acetyl side groups from xylan. The crystal structure of the catalytic core of the enzyme was solved at 1.9 A resolution. The core has an alpha/beta/alpha sandwich fold, similar to that of homologous acetylxylan esterase from Penicillium purpurogenum and cutinase from Fusarium solani. All three enzymes belong to family 5 of the carbohydrate esterases and the superfamily of the alpha/beta hydrolase fold. Evidently, the enzymes have diverged from a common ancestor and they share the same catalytic mechanism. The catalytic machinery of acetylxylan esterase from T. reesei was studied by comparison with cutinase, the catalytic site of which is well known. Acetylxylan esterase is a pure serine esterase having a catalytic triad (Ser90, His187, and Asp175) and an oxyanion hole (Thr13 N, and Thr13 O gamma). Although the catalytic triad of acetylxylan esterase has been reported previously, there has been no mention of the oxyanion hole. A model for the binding of substrates is presented on the basis of the docking of xylose. Acetylxylan esterase from T. reesei is able to deacetylate both mono- and double-acetylated residues, but it is not able to remove acetyl groups located close to large side groups such as 4-O-methylglucuronic acid. If the xylopyranoside residue is double-acetylated, both acetyl groups are removed by the catalytic triad: first one acetyl group is removed and then the residue is reorientated so that the nucleophilic oxygen of serine can attack the second acetyl group.
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Affiliation(s)
- N Hakulinen
- Department of Chemistry, University of Joensuu, FIN-80101 Joensuu, Finland.
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Pletnev VZ, Zamolodchikova TS, Pangborn WA, Duax WL. Crystal structure of bovine duodenase, a serine protease, with dual trypsin and chymotrypsin-like specificities. Proteins 2000. [DOI: 10.1002/1097-0134(20001001)41:1<8::aid-prot30>3.0.co;2-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Abstract
The alpha/beta hydrolase fold is a typical example of a tertiary fold adopted by proteins that have no obvious sequence similarity, but nevertheless, in the course of evolution, diverged from a common ancestor. Recently solved structures demonstrate a considerably increased variability in fold architecture and substrate specificity, necessitating the redefinition of the minimal features that distinguish the family.
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Affiliation(s)
- M Nardini
- Laboratory of Biophysical Chemistry, BIOSON Research Institute, University of Groningen, Groningen, 9747 AG, The Netherlands
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