51
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Sulzenbacher G, Roig-Zamboni V, Peumans WJ, Henrissat B, van Damme EJM, Bourne Y. Structural basis for carbohydrate binding properties of a plant chitinase-like agglutinin with conserved catalytic machinery. J Struct Biol 2015; 190:115-21. [PMID: 25727185 DOI: 10.1016/j.jsb.2015.01.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 01/24/2015] [Accepted: 01/27/2015] [Indexed: 01/13/2023]
Abstract
A new chitinase-like agglutinin, RobpsCRA, related to family GH18 chitinases, has previously been identified in black locust (Robinia pseudoacacia) bark. The crystal structure of RobpsCRA at 1.85Å resolution reveals unusual molecular determinants responsible for the lack of its ancestral chitinase activity. Unlike other chitinase-like proteins, which lack chitinase catalytic residues, RobpsCRA has conserved its catalytic machinery. However, concerted rearrangements of loop regions coupled to non-conservative substitutions of aromatic residues central to the chitin-binding groove explain the lack of hydrolytic activity against chitin and the switch toward recognition of high-mannose type N-glycans. Identification of close homologs in flowering plants with conservation of sequence motifs associated to the structural adaptations seen in RobpsCRA defines an emerging class of agglutinins, as emphasized by a phylogenetic analysis, that are likely to share a similar carbohydrate binding specificity for high-mannose type N-glycans. This study illustrates the recent evolution and molecular adaptation of a versatile TIM-barrel scaffold within the ancestral GH18 family.
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Affiliation(s)
- Gerlind Sulzenbacher
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - Véronique Roig-Zamboni
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - Willy J Peumans
- Department of Molecular Biotechnology, Laboratory of Biochemistry and Glycobiology, Ghent University, Coupure links 653, B-9000 Ghent, Belgium
| | - Bernard Henrissat
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - Els J M van Damme
- Department of Molecular Biotechnology, Laboratory of Biochemistry and Glycobiology, Ghent University, Coupure links 653, B-9000 Ghent, Belgium
| | - Yves Bourne
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France.
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Effects of C-Terminal Domain Truncation on Enzyme Properties of Serratia marcescens Chitinase C. Appl Biochem Biotechnol 2015; 175:3617-27. [DOI: 10.1007/s12010-015-1530-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 01/27/2015] [Indexed: 10/24/2022]
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53
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Catalytic efficiency of chitinase-D on insoluble chitinous substrates was improved by fusing auxiliary domains. PLoS One 2015; 10:e0116823. [PMID: 25615694 PMCID: PMC4304778 DOI: 10.1371/journal.pone.0116823] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/15/2014] [Indexed: 11/20/2022] Open
Abstract
Chitin is an abundant renewable polysaccharide, next only to cellulose. Chitinases are important for effective utilization of this biopolymer. Chitinase D from Serratia proteamaculans (SpChiD) is a single domain chitinase with both hydrolytic and transglycosylation (TG) activities. SpChiD had less of hydrolytic activity on insoluble polymeric chitin substrates due to the absence of auxiliary binding domains. We improved catalytic efficiency of SpChiD in degradation of insoluble chitin substrates by fusing with auxiliary domains like polycystic kidney disease (PKD) domain and chitin binding protein 21 (CBP21). Of the six different SpChiD fusion chimeras, two C-terminal fusions viz. ChiD+PKD and ChiD+CBP resulted in improved hydrolytic activity on α- and β-chitin, respectively. Time-course degradation of colloidal chitin also confirmed that these two C-terminal SpChiD fusion chimeras were more active than other chimeras. More TG products were produced for a longer duration by the fusion chimeras ChiD+PKD and PKD+ChiD+CBP.
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54
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Sugimoto H, Nakamura K, Nishino Y, Idezawa Y, Fujinuma A, Suzuki K, Watanabe T. Differences in the roles of the two surface-exposed tyrosine residues, Y240 and Y481, of Serratia marcescens chitinase B during processive degradation of crystalline chitin. J GEN APPL MICROBIOL 2015; 61:255-61. [DOI: 10.2323/jgam.61.255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Hayuki Sugimoto
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University
- Graduate School of Science and Technology, Niigata University
| | - Keita Nakamura
- Graduate School of Science and Technology, Niigata University
| | - Yuji Nishino
- Graduate School of Science and Technology, Niigata University
| | - Yuta Idezawa
- Graduate School of Science and Technology, Niigata University
| | - Akiko Fujinuma
- Graduate School of Science and Technology, Niigata University
| | - Kazushi Suzuki
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University
- Graduate School of Science and Technology, Niigata University
| | - Takeshi Watanabe
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University
- Graduate School of Science and Technology, Niigata University
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55
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Shu Z, Wang Y, An L, Yao L. The Slowdown of the Endoglucanase Trichoderma reesei Cel5A-Catalyzed Cellulose Hydrolysis Is Related to Its Initial Activity. Biochemistry 2014; 53:7650-8. [DOI: 10.1021/bi501059n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Zhiyu Shu
- Laboratory
of Biofuels, Qingdao
Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266061, China
| | - Yefei Wang
- Laboratory
of Biofuels, Qingdao
Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266061, China
| | - Liaoyuan An
- Laboratory
of Biofuels, Qingdao
Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266061, China
| | - Lishan Yao
- Laboratory
of Biofuels, Qingdao
Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266061, China
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Mutagenesis and molecular dynamics simulations revealed the chitooligosaccharide entry and exit points for chitinase D from Serratia proteamaculans. Biochim Biophys Acta Gen Subj 2014; 1840:2685-94. [DOI: 10.1016/j.bbagen.2014.06.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 05/27/2014] [Accepted: 06/18/2014] [Indexed: 12/17/2022]
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57
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Bai Y, Eijsink VGH, Kielak AM, van Veen JA, de Boer W. Genomic comparison of chitinolytic enzyme systems from terrestrial and aquatic bacteria. Environ Microbiol 2014; 18:38-49. [DOI: 10.1111/1462-2920.12545] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/12/2014] [Indexed: 12/01/2022]
Affiliation(s)
- Yani Bai
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); P.O. Box 50 Wageningen 6700 AB The Netherlands
| | - Vincent G. H. Eijsink
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Sciences; Aas Norway
| | - Anna M. Kielak
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); P.O. Box 50 Wageningen 6700 AB The Netherlands
| | - Johannes A. van Veen
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); P.O. Box 50 Wageningen 6700 AB The Netherlands
- Institute of Biology; Faculty of Science; Leiden University; Leiden The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); P.O. Box 50 Wageningen 6700 AB The Netherlands
- Soil Quality Group; Wageningen University; P.O. Box 9101 Wageningen 6700 HB The Netherlands
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58
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Igarashi K, Uchihashi T, Uchiyama T, Sugimoto H, Wada M, Suzuki K, Sakuda S, Ando T, Watanabe T, Samejima M. Two-way traffic of glycoside hydrolase family 18 processive chitinases on crystalline chitin. Nat Commun 2014; 5:3975. [DOI: 10.1038/ncomms4975] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 04/25/2014] [Indexed: 11/09/2022] Open
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Expression and Characterization of Endochitinase C fromSerratia marcescensBJL200 and Its Purification by a One-Step General Chitinase Purification Method. Biosci Biotechnol Biochem 2014; 72:715-23. [DOI: 10.1271/bbb.70594] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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60
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Takanao S, Honma S, Miura T, Ogawa C, Sugimoto H, Suzuki K, Watanabe T. Construction and basic characterization of deletion mutants of the genes involved in chitin utilization by Serratia marcescens 2170. Biosci Biotechnol Biochem 2014; 78:524-32. [DOI: 10.1080/09168451.2014.882755] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
In order to elucidate the roles of ChiP, ChiQ, and ChiX in chitin utilization by Serratia marcescens 2170, the construction of single-gene deletion mutants of the chiP, chiQ, and chiX genes was attempted by allelic exchange mutagenesis. ΔchiP formed smaller clearing zones and ΔchiX formed larger ones than wild-type 2170 on an agar plate containing colloidal chitin. ΔchiP grew slowly on the lower concentration of (GlcNAc)2, and there was essentially no growth on chitin oligosaccharides larger than (GlcNAc)3. The gene product of chiP was detected in the outer membrane fraction, consistently with the hypothesis that chiP encodes outer membrane chitoporin. Deletion of chiQ decreased and that of chiX increased the growth rates on chitin oligosaccharides. These observations strongly suggest that all three genes are involved in chitin utilization and that the deletion mutants obtained in this study might prove useful tools to clarify the details of the chitin utilization system of this bacterium.
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Affiliation(s)
- Shinya Takanao
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Syouta Honma
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Takuma Miura
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Chisana Ogawa
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Hayuki Sugimoto
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
- Faculty of Agriculture, Department of Applied Biological Chemistry, Niigata University, Niigata, Japan
| | - Kazushi Suzuki
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
- Faculty of Agriculture, Department of Applied Biological Chemistry, Niigata University, Niigata, Japan
| | - Takeshi Watanabe
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
- Faculty of Agriculture, Department of Applied Biological Chemistry, Niigata University, Niigata, Japan
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61
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Kostylev M, Alahuhta M, Chen M, Brunecky R, Himmel ME, Lunin VV, Brady J, Wilson DB. Cel48A fromThermobifida fusca: Structure and site directed mutagenesis of key residues. Biotechnol Bioeng 2013; 111:664-73. [DOI: 10.1002/bit.25139] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 10/05/2013] [Accepted: 10/21/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Maxim Kostylev
- Department of Molecular Biology and Genetics; Cornell University; 458 Biotechnology Building Ithaca New York 14853
| | - Markus Alahuhta
- Biosciences Center; National Renewable Energy Laboratory; Golden Colorado
| | - Mo Chen
- Department of Food Science; Cornell University; Ithaca New York
| | - Roman Brunecky
- Biosciences Center; National Renewable Energy Laboratory; Golden Colorado
| | - Michael E. Himmel
- Biosciences Center; National Renewable Energy Laboratory; Golden Colorado
| | - Vladimir V. Lunin
- Biosciences Center; National Renewable Energy Laboratory; Golden Colorado
| | - John Brady
- Department of Food Science; Cornell University; Ithaca New York
| | - David B. Wilson
- Department of Molecular Biology and Genetics; Cornell University; 458 Biotechnology Building Ithaca New York 14853
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62
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Sehar U, Mehmood MA, Hussain K, Nawaz S, Nadeem S, Siddique MH, Nadeem H, Gull M, Ahmad N, Sohail I, Gill SS, Majeed S. Domain wise docking analyses of the modular chitin binding protein CBP50 from Bacillus thuringiensis serovar konkukian S4. Bioinformation 2013; 9:901-7. [PMID: 24307767 PMCID: PMC3842575 DOI: 10.6026/97320630009901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 10/19/2013] [Indexed: 11/23/2022] Open
Abstract
This paper presents an in silico characterization of the chitin binding protein CBP50 from B. thuringiensis serovar konkukian S4 through homology modeling and molecular docking. The CBP50 has shown a modular structure containing an N-terminal CBM33 domain, two consecutive fibronectin-III (Fn-III) like domains and a C-terminal CBM5 domain. The protein presented a unique modular structure which could not be modeled using ordinary procedures. So, domain wise modeling using MODELLER and docking analyses using Autodock Vina were performed. The best conformation for each domain was selected using standard procedure. It was revealed that four amino acid residues Glu-71, Ser-74, Glu-76 and Gln-90 from N-terminal domain are involved in protein-substrate interaction. Similarly, amino acid residues Trp-20, Asn-21, Ser-23 and Val-30 of Fn-III like domains and Glu-15, Ala-17, Ser-18 and Leu-35 of C-terminal domain were involved in substrate binding. Site-directed mutagenesis of these proposed amino acid residues in future will elucidate the key amino acids involved in chitin binding activity of CBP50 protein.
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Affiliation(s)
- Ujala Sehar
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University Faisalabad, Faisalabad, Pakistan
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63
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Wang Q, Qu L, Zhang Z, Wang Y, Zhang Y. Characterization of a novel chitinase, DkChi, from Dendrolimus kikuchii nucleopolyhedrovirus. Arch Virol 2013; 158:2523-30. [DOI: 10.1007/s00705-013-1775-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Accepted: 05/21/2013] [Indexed: 11/24/2022]
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64
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Potentiation of the synergistic activities of chitinases ChiA, ChiB and ChiC from Serratia marcescens CFFSUR-B2 by chitobiase (Chb) and chitin binding protein (CBP). World J Microbiol Biotechnol 2013; 30:33-42. [PMID: 23824666 DOI: 10.1007/s11274-013-1421-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 06/24/2013] [Indexed: 10/26/2022]
Abstract
With the goal of understanding the chitinolytic mechanism of the potential biological control strain Serratia marcescens CFFSUR-B2, genes encoding chitinases ChiA, ChiB and ChiC, chitobiase (Chb) and chitin binding protein (CBP) were cloned, the protein products overexpressed in Escherichia coli as 6His-Sumo fusion proteins and purified by affinity chromatography. Following affinity tag removal, the chitinolytic activity of the recombinant proteins was evaluated individually and in combination using colloidal chitin as substrate. ChiB and ChiC were highly active while ChiA was inactive. Reactions containing both ChiB and ChiC showed significantly increased N-acetylglucosamine trimer and dimer formation, but decreased monomer formation, compared to reactions with either enzyme alone. This suggests that while both ChiB and ChiC have a general affinity for the same substrate, they attack different sites and together degrade chitin more efficiently than either enzyme separately. Chb and CBP in combination with ChiB and ChiC (individually or together) increased their chitinase activity. We report for the first time the potentiating effect of Chb on the activity of the chitinases and the synergistic activity of a mixture of all five proteins (the three chitinases, Chb and CBP). These results contribute to our understanding of the mechanism of action of the chitinases produced by strain CFFSUR-B2 and provide a molecular basis for its high potential as a biocontrol agent against fungal pathogens.
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65
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Fukuda S, Uchihashi T, Iino R, Okazaki Y, Yoshida M, Igarashi K, Ando T. High-speed atomic force microscope combined with single-molecule fluorescence microscope. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2013; 84:073706. [PMID: 23902075 DOI: 10.1063/1.4813280] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
High-speed atomic force microscopy (HS-AFM) and total internal reflection fluorescence microscopy (TIRFM) have mutually complementary capabilities. Here, we report techniques to combine these microscopy systems so that both microscopy capabilities can be simultaneously used in the full extent. To combine the two systems, we have developed a tip-scan type HS-AFM instrument equipped with a device by which the laser beam from the optical lever detector can track the cantilever motion in the X- and Y-directions. This stand-alone HS-AFM system is mounted on an inverted optical microscope stage with a wide-area scanner. The capability of this combined system is demonstrated by simultaneous HS-AFM∕TIRFM imaging of chitinase A moving on a chitin crystalline fiber and myosin V walking on an actin filament.
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Affiliation(s)
- Shingo Fukuda
- Department of Physics, College of Science and Engineering, Kanazawa University, Ishikawa 920-1192, Japan
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66
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Vaaje-Kolstad G, Horn SJ, Sørlie M, Eijsink VGH. The chitinolytic machinery ofSerratia marcescens- a model system for enzymatic degradation of recalcitrant polysaccharides. FEBS J 2013; 280:3028-49. [DOI: 10.1111/febs.12181] [Citation(s) in RCA: 210] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 01/30/2013] [Accepted: 02/05/2013] [Indexed: 01/13/2023]
Affiliation(s)
- Gustav Vaaje-Kolstad
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås; Norway
| | - Svein J. Horn
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås; Norway
| | - Morten Sørlie
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås; Norway
| | - Vincent G. H. Eijsink
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås; Norway
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67
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Bodelón G, Palomino C, Fernández LÁ. Immunoglobulin domains inEscherichia coliand other enterobacteria: from pathogenesis to applications in antibody technologies. FEMS Microbiol Rev 2013; 37:204-50. [DOI: 10.1111/j.1574-6976.2012.00347.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 06/07/2012] [Accepted: 06/14/2012] [Indexed: 11/28/2022] Open
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68
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Synthesis of long-chain chitooligosaccharides by a hypertransglycosylating processive endochitinase of Serratia proteamaculans 568. J Bacteriol 2012; 194:4260-71. [PMID: 22685288 DOI: 10.1128/jb.06473-11] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe the heterologous expression and characterization of a 407-residue single-domain glycosyl hydrolase family 18 chitinase (SpChiD) from Gram-negative Serratia proteamaculans 568 that has unprecedented catalytic properties. SpChiD was optimally active at pH 6.0 and 40 °C, where it showed a K(m) of 83 mg ml(-1), a k(cat) of 3.9 × 10(2) h(-1), and a k(cat)/K(m) of 4.7 h mg(-1) ml(-1) on colloidal chitin. On chitobiose, the K(m), k(cat), and k(cat)/K(m) were 203 μM, 1.3 × 10(2) h(-1), and 0.62 h(-1) μM(-1), respectively. Hydrolytic activity on chitooligosaccharides (CHOS) and colloidal chitin indicated that SpChiD was an endo-acting processive enzyme, with the unique ability to convert released chitobiose to N-acetylglucosamine, the major end product. SpChiD showed hyper transglycosylation (TG) with trimer-hexamer CHOS substrates, generating considerable amounts of long-chain CHOS. The TG activity of SpChiD was dependent on both the length and concentration of the oligomeric substrate and also on the enzyme concentration. The length and amount of accumulated TG products increased with increases in the length of the substrate and its concentration and decreased with increases in the enzyme concentration. The SpChiD bound to insoluble and soluble chitin substrates despite the absence of accessory domains. Sequence alignments and structural modeling indicated that SpChiD would have a deep substrate-binding groove lined with aromatic residues, which is characteristic of processive enzymes. SpChiD shows a combination of properties that seems rare among family 18 chitinases and that may resemble the properties of human chitotriosidase.
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69
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Sørlie M, Zakariassen H, Norberg AL, Eijsink VGH. Processivity and substrate-binding in family 18 chitinases. BIOCATAL BIOTRANSFOR 2012. [DOI: 10.3109/10242422.2012.676282] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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70
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Purushotham P, Sarma PVSRN, Podile AR. Multiple chitinases of an endophytic Serratia proteamaculans 568 generate chitin oligomers. BIORESOURCE TECHNOLOGY 2012; 112:261-269. [PMID: 22406064 DOI: 10.1016/j.biortech.2012.02.062] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 02/10/2012] [Accepted: 02/13/2012] [Indexed: 05/31/2023]
Abstract
Serratia proteamaculans 568 genome revealed the presence of four family 18 chitinases (Sp ChiA, Sp ChiB, Sp ChiC, and Sp ChiD). Heterologous expression and characterization of Sp ChiA, Sp ChiB, and Sp ChiC showed that these enzymes were optimally active at pH 6.0-7.0, and 40°C. The three Sp chitinases displayed highest activity/binding to β-chitin and showed broad range of substrate specificities, and released dimer as major end product from oligomeric and polymeric substrates. Longer incubation was required for hydrolysis of trimer for the three Sp chitinases. The three Sp chitinases released up to tetramers from colloidal chitin substrate. Sp ChiA and Sp ChiB were processive chitinases, while Sp ChiC was a non-processive chitinase. Based on the known structures of ChiA and ChiB from S. marcescens, 3D models of Sp ChiA and Sp ChiB were generated.
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Affiliation(s)
- Pallinti Purushotham
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad-500 046, India
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71
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Abstract
Natural cellulolytic enzyme systems as well as leading commercial cellulase cocktails are dominated by enzymes that degrade cellulose chains in a processive manner. Despite the abundance of processivity among natural cellulases, the molecular basis as well as the biotechnological implications of this mechanism are only partly understood. One of the major limitations lies in the fact that it is not straightforward to measure and quantify processivity in what essentially are biphasic experimental systems. Here, we describe and discuss both well-established methods and newer methods for measuring cellulase processivity. In addition, we discuss recent insights from studies on chitinases that may help direct further studies on processivity in cellulases.
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Affiliation(s)
- Svein J Horn
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
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72
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Eide KB, Norberg AL, Heggset EB, Lindbom AR, Vårum KM, Eijsink VGH, Sørlie M. Human chitotriosidase-catalyzed hydrolysis of chitosan. Biochemistry 2011; 51:487-95. [PMID: 22192075 DOI: 10.1021/bi2015585] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Chitotriosidase (HCHT) is one of two family 18 chitinases produced by humans, the other being acidic mammalian chitinase (AMCase). The enzyme is thought to be part of the human defense mechanism against fungal parasites, but its precise role and the details of its enzymatic properties have not yet been fully unraveled. We have studied the properties of HCHT by analyzing how the enzyme acts on high-molecular weight chitosans, soluble copolymers of β-1,4-linked N-acetylglucosamine (GlcNAc, A), and glucosamine (GlcN, D). Using methods for in-depth studies of the chitinolytic machinery of bacterial family 18 enzymes, we show that HCHT degrades chitosan primarily via an endoprocessive mechanism, as would be expected on the basis of the structural features of its substrate-binding cleft. The preferences of HCHT subsites for acetylated versus nonacetylated sugars were assessed by sequence analysis of obtained oligomeric products showing a very strong, absolute, and a relative weak preference for an acetylated unit in the -2, -1, and +1 subsites, respectively. The latter information is important for the design of inhibitors that are specific for the human chitinases and also provides insight into what kind of products may be formed in vivo upon administration of chitosan-containing medicines or food products.
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Affiliation(s)
- Kristine Bistrup Eide
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
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Payne CM, Bomble YJ, Taylor CB, McCabe C, Himmel ME, Crowley MF, Beckham GT. Multiple functions of aromatic-carbohydrate interactions in a processive cellulase examined with molecular simulation. J Biol Chem 2011; 286:41028-35. [PMID: 21965672 DOI: 10.1074/jbc.m111.297713] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Proteins employ aromatic residues for carbohydrate binding in a wide range of biological functions. Glycoside hydrolases, which are ubiquitous in nature, typically exhibit tunnels, clefts, or pockets lined with aromatic residues for processing carbohydrates. Mutation of these aromatic residues often results in significant activity differences on insoluble and soluble substrates. However, the thermodynamic basis and molecular level role of these aromatic residues remain unknown. Here, we calculate the relative ligand binding free energy by mutating tryptophans in the Trichoderma reesei family 6 cellulase (Cel6A) to alanine. Removal of aromatic residues near the catalytic site has little impact on the ligand binding free energy, suggesting that aromatic residues immediately upstream of the active site are not directly involved in binding, but play a role in the glucopyranose ring distortion necessary for catalysis. Removal of aromatic residues at the entrance and exit of the Cel6A tunnel, however, dramatically impacts the binding affinity, suggesting that these residues play a role in chain acquisition and product stabilization, respectively. The roles suggested from differences in binding affinity are confirmed by molecular dynamics and normal mode analysis. Surprisingly, our results illustrate that aromatic-carbohydrate interactions vary dramatically depending on the position in the enzyme tunnel. As aromatic-carbohydrate interactions are present in all carbohydrate-active enzymes, these results have implications for understanding protein structure-function relationships in carbohydrate metabolism and recognition, carbon turnover in nature, and protein engineering strategies for biomass utilization. Generally, these results suggest that nature employs aromatic-carbohydrate interactions with a wide range of binding affinities for diverse functions.
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Affiliation(s)
- Christina M Payne
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
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74
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Kudan S, Kuttiyawong K, Pichyangkura R. Carboxy-terminus truncations of Bacillus licheniformis SK-1 CHI72 with distinct substrate specificity. BMB Rep 2011; 44:375-80. [PMID: 21699749 DOI: 10.5483/bmbrep.2011.44.6.375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus licheniformis SK-1 naturally produces chitinase 72 (CHI72) with two truncation derivatives at the C-terminus, one with deletion of the chitin binding domain (ChBD), and the other with deletions of both fibronectin type III domain (FnIIID) and ChBD. We constructed deletions mutants of CHI72 with deletion of ChBD (CHI72ΔChBD) and deletions of both FnIIID and ChBD (CHI72ΔFnIIIDΔChBD), and studied their activity on soluble, amorphous and crystalline substrates. Interestingly, when equivalent amount of specific activity of each enzyme on soluble substrate was used, the product yield from CHI72- ΔChBD and CHI72ΔFnIIIDΔChBD on colloidal chitin was 2.5 and 1.6 fold higher than CHI72, respectively. In contrast, the product yield from CHI72ΔChBD and CHI72ΔFnIIID- ΔChBD on Β-chitin reduced to 0.7 and 0.5 fold of CHI72, respectively. These results suggest that CHI72 can modulate its substrate specificities through truncations of the functional domains at the C-terminus, producing a mixture of enzymes with elevated efficiency of hydrolysis.
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Affiliation(s)
- Sanya Kudan
- Biotechnology Program, Biochemistry Department, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
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75
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Norberg AL, Dybvik AI, Zakariassen H, Mormann M, Peter-Katalinić J, Eijsink VGH, Sørlie M. Substrate positioning in chitinase A, a processive chito-biohydrolase from Serratia marcescens. FEBS Lett 2011; 585:2339-44. [PMID: 21683074 DOI: 10.1016/j.febslet.2011.06.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 06/02/2011] [Accepted: 06/03/2011] [Indexed: 10/18/2022]
Abstract
The contributions of the -3 subsite and a putative +3 subsite to substrate positioning in ChiA from Serratia marcescens have been investigated by comparing how ChiA and its -3 subsite mutant W167A interact with soluble substrates. The data show that Trp - GlcNAc stacking in the -3 subsite rigidifies the protein backbone supporting the formation of the intermolecular interaction network that is necessary for the recognition and positioning of the N-acetyl groups before the -1 subsite. The +3 subsite exhibits considerable substrate affinity that may promote endo-activity in ChiA and/or assist in expelling dimeric products from the +1 and +2 subsites during processive hydrolysis.
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Affiliation(s)
- Anne Line Norberg
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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76
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Mehmood MA, Xiao X, Hafeez FY, Gai Y, Wang F. Molecular characterization of the modular chitin binding protein Cbp50 from Bacillus thuringiensis serovar konkukian. Antonie van Leeuwenhoek 2011; 100:445-53. [PMID: 21647612 DOI: 10.1007/s10482-011-9601-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 05/27/2011] [Indexed: 11/29/2022]
Abstract
Bacillus thuringiensis is an insecticidal bacterium whose chitinolytic system may be exploited to improve the insecticidal system of Bt-crops. A nucleotide fragment of 1368 bp from B. thuringiensis serovar konkukian S4, containing the complete coding sequence of the chitin binding protein Cbp50, was cloned and sequenced. Analyses have shown the protein to contain a modular structure consisting of an N-terminal CBM33 domain, two copies of a fibronectin-like domain and a C-terminal chitin binding domain classified as CBM5. The Cbp50 protein was heterologously expressed in Escherichia coli, purified and assessed for chitin binding activity. A deletion mutant (CBD-N; containing only the N-terminal CBM33 domain) of Cbp50 was produced to determine the role of C-terminal domains in the binding activity of the protein. The full-length Cbp50 was shown to bind β-chitin most efficiently followed by α-chitin, colloidal chitin and cellulose. The polysaccharide binding activity of CBD-N was drastically decreased. The data demonstrate that both the N-terminal and C-terminal domains of Cbp50 are essential for the efficient binding of chitin. The purified Cbp50 showed antifungal activity against the phytopathogenic fungus Fusarium oxysporum and the opportunistic human pathogen Aspergillus niger. This is the first report of a modular chitin binding protein in bacteria.
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77
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Alcazar-Fuoli L, Clavaud C, Lamarre C, Aimanianda V, Seidl-Seiboth V, Mellado E, Latgé JP. Functional analysis of the fungal/plant class chitinase family in Aspergillus fumigatus. Fungal Genet Biol 2010; 48:418-29. [PMID: 21184840 DOI: 10.1016/j.fgb.2010.12.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 12/14/2010] [Accepted: 12/17/2010] [Indexed: 11/28/2022]
Abstract
A quintuple mutant was constructed to delete the entire family of the fungal/plant (class III) chitinases of Aspergillus fumigatus. Only a limited reduction in the total chitinolytic activity was seen for the different chitinase mutants including the quintuple mutant. In spite of this reduction in chitinolytic activity, no growth or germination defects were observed in these chitinase mutants. This result demonstrated that the fungal/plant chitinases do not have an essential role in the morphogenesis of A. fumigatus. A slight diminution of the growth during autolysis was seen for the quintuple mutant suggesting that class III chitinases may play only a nutritional role during this phase of the cycle, retarding fungal death.
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Affiliation(s)
- Laura Alcazar-Fuoli
- Servicio de Micologia, Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo Km2 (28220), Majadahonda, Madrid, Spain
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78
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Neeraja C, Anil K, Purushotham P, Suma K, Sarma P, Moerschbacher BM, Podile AR. Biotechnological approaches to develop bacterial chitinases as a bioshield against fungal diseases of plants. Crit Rev Biotechnol 2010; 30:231-41. [PMID: 20572789 DOI: 10.3109/07388551.2010.487258] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Fungal diseases of plants continue to contribute to heavy crop losses in spite of the best control efforts of plant pathologists. Breeding for disease-resistant varieties and the application of synthetic chemical fungicides are the most widely accepted approaches in plant disease management. An alternative approach to avoid the undesired effects of chemical control could be biological control using antifungal bacteria that exhibit a direct action against fungal pathogens. Several biocontrol agents, with specific fungal targets, have been registered and released in the commercial market with different fungal pathogens as targets. However, these have not yet achieved their full commercial potential due to the inherent limitations in the use of living organisms, such as relatively short shelf life of the products and inconsistent performance in the field. Different mechanisms of action have been identified in microbial biocontrol of fungal plant diseases including competition for space or nutrients, production of antifungal metabolites, and secretion of hydrolytic enzymes such as chitinases and glucanases. This review focuses on the bacterial chitinases that hydrolyze the chitinous fungal cell wall, which is the most important targeted structural component of fungal pathogens. The application of the hydrolytic enzyme preparations, devoid of live bacteria, could be more efficacious in fungal control strategies. This approach, however, is still in its infancy, due to prohibitive production costs. Here, we critically examine available sources of bacterial chitinases and the approaches to improve enzymatic properties using biotechnological tools. We project that the combination of microbial and recombinant DNA technologies will yield more effective environment-friendly products of bacterial chitinases to control fungal diseases of crops.
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Affiliation(s)
- Chilukoti Neeraja
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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79
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Kurasin M, Väljamäe P. Processivity of cellobiohydrolases is limited by the substrate. J Biol Chem 2010; 286:169-77. [PMID: 21051539 DOI: 10.1074/jbc.m110.161059] [Citation(s) in RCA: 184] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Processive cellobiohydrolases (CBHs) are the key components of fungal cellulase systems. Despite the wealth of structural data confirming the processive mode of action, little quantitative information on the processivity of CBHs is available. Here, we developed a method for measuring cellulase processivity. Sensitive fluorescence detection of enzyme-generated insoluble reducing groups on cellulose after labeling with diaminopyridine enabled quantification of the number of reducing-end exo-mode and endo-mode initiations. Both CBHs TrCel7A from Trichoderma reesei and PcCel7D from Phanerochaete chrysosporium employed reducing-end exo- and endo-mode initiation in parallel. Processivity values measured for TrCel7A and PcCel7D on cellulose hydrolysis were more than an order of magnitude lower than the values of intrinsic processivity that were found from the ratio of catalytic constant (k(cat)) and dissociation rate constant (k(off)). We propose that the length of the obstacle-free path available for a processive run on cellulose chain limits the processivity of CBHs on cellulose. TrCel7A and PcCel7D differed in their k(off) values, whereas the k(cat) values were similar. Furthermore, the k(off) values for endoglucanases (EGs) were much higher than the k(off) values for CBHs, whereas the k(cat) values for EGs and CBHs were within the same order of magnitude. These results suggest that the value of k(off) may be the primary target for the selection of cellulases.
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Affiliation(s)
- Mihhail Kurasin
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51014, Estonia
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80
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81
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Hsieh YC, Wu YJ, Chiang TY, Kuo CY, Shrestha KL, Chao CF, Huang YC, Chuankhayan P, Wu WG, Li YK, Chen CJ. Crystal structures of Bacillus cereus NCTU2 chitinase complexes with chitooligomers reveal novel substrate binding for catalysis: a chitinase without chitin binding and insertion domains. J Biol Chem 2010; 285:31603-15. [PMID: 20685646 DOI: 10.1074/jbc.m110.149310] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chitinases hydrolyze chitin, an insoluble linear polymer of N-acetyl-d-glucosamine (NAG)(n), into nutrient sources. Bacillus cereus NCTU2 chitinase (ChiNCTU2) predominantly produces chitobioses and belongs to glycoside hydrolase family 18. The crystal structure of wild-type ChiNCTU2 comprises only a catalytic domain, unlike other chitinases that are equipped with additional chitin binding and insertion domains to bind substrates into the active site. Lacking chitin binding and chitin insertion domains, ChiNCTU2 utilizes two dynamic loops (Gly-67-Thr-69 and Ile-106-Val-112) to interact with (NAG)(n), generating novel substrate binding and distortion for catalysis. Gln-109 is crucial for direct binding with substrates, leading to conformational changes of two loops with a maximum shift of ∼4.6 Å along the binding cleft. The structures of E145Q, E145Q/Y227F, and E145G/Y227F mutants complexed with (NAG)(n) reveal (NAG)(2), (NAG)(2), and (NAG)(4) in the active site, respectively, implying various stages of reaction: before hydrolysis, E145G/Y227F with (NAG)(4); in an intermediate state, E145Q/Y227F with a boat-form NAG at the -1 subsite, -1-(NAG); after hydrolysis, E145Q with a chair form -1-(NAG). Several residues were confirmed to play catalytic roles: Glu-145 in cleavage of the glycosidic bond between -1-(NAG) and +1-(NAG); Tyr-227 in the conformational change of -1-(NAG); Asp-143 and Gln-225 in stabilizing the conformation of -1-(NAG). Additionally, Glu-190 acts in the process of product release, and Tyr-193 coordinates with water for catalysis. Residues Asp-143, E145Q, Glu-190, and Tyr-193 exhibit multiple conformations for functions. The inhibitors zinc ions and cyclo-(l-His-l-Pro) are located at various positions and confirm the catalytic-site topology. Together with kinetics analyses of related mutants, the structures of ChiNCTU2 and its mutant complexes with (NAG)(n) provide new insights into its substrate binding and the mechanistic action.
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Affiliation(s)
- Yin-Cheng Hsieh
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
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82
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Doxey AC, Cheng Z, Moffatt BA, McConkey BJ. Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d. BMC STRUCTURAL BIOLOGY 2010; 10:23. [PMID: 20678238 PMCID: PMC2924342 DOI: 10.1186/1472-6807-10-23] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2010] [Accepted: 08/03/2010] [Indexed: 01/10/2023]
Abstract
BACKGROUND Aromatic amino acids play a critical role in protein-glycan interactions. Clusters of surface aromatic residues and their features may therefore be useful in distinguishing glycan-binding sites as well as predicting novel glycan-binding proteins. In this work, a structural bioinformatics approach was used to screen the Protein Data Bank (PDB) for coplanar aromatic motifs similar to those found in known glycan-binding proteins. RESULTS The proteins identified in the screen were significantly associated with carbohydrate-related functions according to gene ontology (GO) enrichment analysis, and predicted motifs were found frequently within novel folds and glycan-binding sites not included in the training set. In addition to numerous binding sites predicted in structural genomics proteins of unknown function, one novel prediction was a surface motif (W34/W36/W192) in the tobacco pathogenesis-related protein, PR-5d. Phylogenetic analysis revealed that the surface motif is exclusive to a subfamily of PR-5 proteins from the Solanaceae family of plants, and is absent completely in more distant homologs. To confirm PR-5d's insoluble-polysaccharide binding activity, a cellulose-pulldown assay of tobacco proteins was performed and PR-5d was identified in the cellulose-binding fraction by mass spectrometry. CONCLUSIONS Based on the combined results, we propose that the putative binding site in PR-5d may be an evolutionary adaptation of Solanaceae plants including potato, tomato, and tobacco, towards defense against cellulose-containing pathogens such as species of the deadly oomycete genus, Phytophthora. More generally, the results demonstrate that coplanar aromatic clusters on protein surfaces are a structural signature of glycan-binding proteins, and can be used to computationally predict novel glycan-binding proteins from 3 D structure.
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Affiliation(s)
- Andrew C Doxey
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
- Department of Developmental Biology, Stanford University, Stanford, CA, 94305, USA
| | - Zhenyu Cheng
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Barbara A Moffatt
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Brendan J McConkey
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
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83
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Signatures of activation parameters reveal substrate-dependent rate determining steps in polysaccharide turnover by a family 18 chitinase. Carbohydr Polym 2010. [DOI: 10.1016/j.carbpol.2010.01.048] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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84
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Li H, Greene LH. Sequence and structural analysis of the chitinase insertion domain reveals two conserved motifs involved in chitin-binding. PLoS One 2010; 5:e8654. [PMID: 20084296 PMCID: PMC2805709 DOI: 10.1371/journal.pone.0008654] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 12/05/2009] [Indexed: 01/01/2023] Open
Abstract
Background Chitinases are prevalent in life and are found in species including archaea, bacteria, fungi, plants, and animals. They break down chitin, which is the second most abundant carbohydrate in nature after cellulose. Hence, they are important for maintaining a balance between carbon and nitrogen trapped as insoluble chitin in biomass. Chitinases are classified into two families, 18 and 19 glycoside hydrolases. In addition to a catalytic domain, which is a triosephosphate isomerase barrel, many family 18 chitinases contain another module, i.e., chitinase insertion domain. While numerous studies focus on the biological role of the catalytic domain in chitinase activity, the function of the chitinase insertion domain is not completely understood. Bioinformatics offers an important avenue in which to facilitate understanding the role of residues within the chitinase insertion domain in chitinase function. Results Twenty-seven chitinase insertion domain sequences, which include four experimentally determined structures and span five kingdoms, were aligned and analyzed using a modified sequence entropy parameter. Thirty-two positions with conserved residues were identified. The role of these conserved residues was explored by conducting a structural analysis of a number of holo-enzymes. Hydrogen bonding and van der Waals calculations revealed a distinct subset of four conserved residues constituting two sequence motifs that interact with oligosaccharides. The other conserved residues may be key to the structure, folding, and stability of this domain. Conclusions Sequence and structural studies of the chitinase insertion domains conducted within the framework of evolution identified four conserved residues which clearly interact with the substrates. Furthermore, evolutionary studies propose a link between the appearance of the chitinase insertion domain and the function of family 18 chitinases in the subfamily A.
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Affiliation(s)
- Hai Li
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, United States of America
| | - Lesley H. Greene
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, United States of America
- * E-mail:
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85
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Chitinolytic activity of cold tolerant antagonistic species of streptomyces isolated from glacial sites of Indian himalaya. Curr Microbiol 2009; 59:502-8. [PMID: 19688382 DOI: 10.1007/s00284-009-9466-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Revised: 07/15/2009] [Accepted: 07/16/2009] [Indexed: 10/20/2022]
Abstract
Seventy-eight isolates of actinomycetes were isolated from the soil samples collected from alpine zones of Pindari glacier region in Indian Himalaya. Following a plate based rapid screening using two test fungi, five efficient isolates (nos. HA1, HA2, HA6, HA40, and HA142) were selected for further characterization with special reference to their antagonistic properties. Based on phenotypic and genotypic characters, the isolates were identified up to species level. All the isolates belonged to the genus Streptomyces. The isolate nos. HA1 and HA2 were S. sampsonii and HA6, HA40 and HA142 were S. griseobrunneus, S. aurantiacus, and S. griseoluteus, respectively. The isolates showed strong antifungal properties against phytopathogenic test fungi in plate assays. All the isolates hydrolyzed glycol-chitin as a substrate in denaturing conditions showing variable amount of different isoforms.
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86
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A flexible loop controlling the enzymatic activity and specificity in a glycosyl hydrolase family 19 endochitinase from barley seeds (Hordeum vulgare L.). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1159-67. [DOI: 10.1016/j.bbapap.2009.03.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Revised: 03/12/2009] [Accepted: 03/13/2009] [Indexed: 10/21/2022]
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87
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Lienemann M, Boer H, Paananen A, Cottaz S, Koivula A. Toward understanding of carbohydrate binding and substrate specificity of a glycosyl hydrolase 18 family (GH-18) chitinase from Trichoderma harzianum. Glycobiology 2009; 19:1116-26. [PMID: 19596709 DOI: 10.1093/glycob/cwp102] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Surface plasmon resonance (SPR) has been used to assay the roles of amino acid residues in the substrate binding cleft of Trichoderma harzianum chitinase Chit42, which belongs to the glycoside hydrolase family 18 (GH-18). Nine different Chit42 variants having amino acid mutations along the binding site cleft at subsites -4 to +2 were created and characterized with regard to their affinity toward chitinous and non-chitinous oligosaccharides. The catalytically inactive Chit42 mutant E172Q was used as the template for making the additional mutations. The E172Q mutant bound chitinoligosaccharides (tetra-, penta- and hexamer) with an increasing affinity from 12 to 0.2 microM whereas no binding of chitinbiose, -triose or 3'-sialyl-N-acetyllactosamine (Neu5Acalpha-3Galbeta-4GlcNAc) could be measured, indicative of significantly lower affinity for these shorter oligosaccharides. The strongest binding affinity was displayed toward allosamidin, a transition state analog (K(d) = 3 nM), and this was shown to be dependent on the E172 residue, the acid/base catalyst of Chit42. Hydrogen bonding by the glutamic acid E317 between subsites -2 and -3 and particularly the stacking interactions by tryptophanes at subsites -3 and +2 provided to be important, as mutations to these amino acids had a substantial negative effect to the overall binding affinity. Moreover, the substrate binding specificity of Chit42 could be altered toward binding of GlcNbeta-4(GlcNAc)(4) by providing a counter charge through substitution of residue T133 at subsite -3 against aspartic acid. In addition, the introduction of glutamine and particularly an asparagine residue at position 133 seemed to broaden the substrate preference of Chit42 toward Galbeta-4(GlcNAc)(4).
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88
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Horn SJ, Sørlie M, Vaaje-Kolstad G, Norberg AL, Synstad B, Vårum KM, Eijsink VGH. Comparative studies of chitinases A, B and C fromSerratia marcescens. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420500518482] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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89
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Mehmood MA, Xiao X, Hafeez FY, Gai Y, Wang F. Purification and characterization of a chitinase from Serratia proteamaculans. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-0094-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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90
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Suginta W, Pantoom S, Prinz H. Substrate binding modes and anomer selectivity of chitinase A from Vibrio harveyi. J Chem Biol 2009; 2:191-202. [PMID: 19568782 PMCID: PMC2763143 DOI: 10.1007/s12154-009-0021-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Accepted: 05/07/2009] [Indexed: 11/30/2022] Open
Abstract
High-performance liquid chromatography mass spectrometry (HPLC MS) was employed to assess the binding behaviors of various substrates to Vibrio harveyi chitinase A. Quantitative analysis revealed that hexaNAG preferred subsites −2 to +2 over subsites −3 to +2 and pentaNAG only required subsites −2 to +2, while subsites −4 to +2 were not used at all by both substrates. The results suggested that binding of the chitooligosaccharides to the enzyme essentially occurred in compulsory fashion. The symmetrical binding mode (−2 to +2) was favored presumably to allow the natural form of sugars to be utilized effectively. Crystalline α chitin was initially hydrolyzed into a diverse ensemble of chitin oligomers, providing a clear sign of random attacks that took place within chitin chains. However, the progressive degradation was shown to occur in greater extent at later time to complete hydrolysis. The effect of the reducing-end residues were also investigated by means of HPLC MS. Substitutions of Trp275 to Gly and Trp397 to Phe significantly shifted the anomer selectivity of the enzyme toward β substrates. The Trp275 mutation modulated the kinetic property of the enzyme by decreasing the catalytic constant (kcat) and the substrate specificity (kcat/Km) toward all substrates by five- to tenfold. In contrast, the Trp397 mutation weakened the binding strength at subsite (+2), thereby speeding up the rate of the enzymatic cleavage toward soluble substrates but slowing down the rate of the progressive degradation toward insoluble chitin.
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Affiliation(s)
- Wipa Suginta
- Biochemistry-Electrochemistry Research Unit, School of Chemistry and Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon, Ratchasima, 30000, Thailand,
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91
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Ling Z, Suits MD, Bingham RJ, Bruce NC, Davies GJ, Fairbanks AJ, Moir JW, Taylor EJ. The X-ray Crystal Structure of an Arthrobacter protophormiae Endo-β-N-Acetylglucosaminidase Reveals a (β/α)8 Catalytic Domain, Two Ancillary Domains and Active Site Residues Key for Transglycosylation Activity. J Mol Biol 2009; 389:1-9. [PMID: 19327363 DOI: 10.1016/j.jmb.2009.03.050] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 03/16/2009] [Accepted: 03/19/2009] [Indexed: 10/21/2022]
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92
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Physical state of κ-carrageenan modulates the mode of action of κ-carrageenase from Pseudoalteromonas carrageenovora. Biochem J 2009; 419:545-53. [DOI: 10.1042/bj20080619] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Pseudoalteromonas carrageenovora κ-carrageenase is a glycoside hydrolase involved in the bioconversion of carrageenans. Carrageenans are sulfated galactans that are densely packed in red algal cell walls. Previous crystallographic investigations revealed that the active site of κ-carrageenase has a tunnel-shaped topology, suggesting a processive mode of action for this enzyme. To biochemically characterize the enzymatic depolymerization of κ-carrageenan, soluble and solid substrates (in both gel and powder forms) were incubated with P. carrageenovora κ-carrageenase. The average molecular mass of soluble carrageenan decreased rapidly, and all possible degradation products were observed, suggesting random degradation of κ-carrageenan. In contrast, as expected for a processive-type carrageenase, the average molecular mass of solid carrageenan decreased very slowly, and tetrasaccharide production was high. Interestingly, experimentally determined processivity was similar for gel and powder, suggesting that, in addition to an adapted catalytic site, the substrate must be in the solid state for κ-carrageenase processivity to operate, whatever the level of carrageenan ordering.
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93
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Zakariassen H, Aam BB, Horn SJ, Vårum KM, Sørlie M, Eijsink VGH. Aromatic residues in the catalytic center of chitinase A from Serratia marcescens affect processivity, enzyme activity, and biomass converting efficiency. J Biol Chem 2009; 284:10610-7. [PMID: 19244232 DOI: 10.1074/jbc.m900092200] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The processive Serratia marcescens chitinases A (ChiA) and B (ChiB) are thought to degrade chitin in the opposite directions. A recent study of ChiB suggested that processivity is governed by aromatic residues in the +1 and +2 (aglycon) subsites close to the catalytic center. To further investigate the roles of aromatic residues in processivity and to gain insight into the structural basis of directionality, we have mutated Trp(167), Trp(275), and Phe(396) in the -3, +1, and +2 subsites of ChiA, respectively, and characterized the hydrolytic activities of the mutants toward beta-chitin and the soluble chitin-derivative chitosan. Although the W275A and F396A mutants showed only modest reductions in processivity, it was almost abolished by the W167A mutation. Thus, although aglycon subsites seem to steer processivity in ChiB, a glycon (-3) subsite seems to be adapted to do so in ChiA, in line with the notion that the two enzymes have different directionalities. Remarkably, whereas all three single mutants and the W167A/W275A double mutant showed reduced efficiency toward chitin, they showed up to 20-fold higher activities toward chitosan. These results show that the processive mechanism is essential for an efficient conversion of crystalline substrates but comes at a large cost in terms of intrinsic enzyme speed. This needs to be taken into account when devising enzymatic strategies for biomass turnover.
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Affiliation(s)
- Henrik Zakariassen
- Department of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences, 1432 As, Norway
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94
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Effects of C-terminal amino acids truncation on enzyme properties of Aeromonas caviae D1 chitinase. Arch Microbiol 2008; 191:265-73. [DOI: 10.1007/s00203-008-0451-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Revised: 11/24/2008] [Accepted: 11/28/2008] [Indexed: 10/21/2022]
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95
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Petter C, Scholz C, Wessner H, Hansen G, Henklein P, Watanabe T, Höhne W. Phage display screening for peptidic chitinase inhibitors. J Mol Recognit 2008; 21:401-9. [DOI: 10.1002/jmr.911] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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96
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Kuttiyawong K, Nakapong S, Pichyangkura R. The dual exo/endo-type mode and the effect of ionic strength on the mode of catalysis of chitinase 60 (CHI60) from Serratia sp. TU09 and its mutants. Carbohydr Res 2008; 343:2754-62. [DOI: 10.1016/j.carres.2008.05.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Revised: 05/19/2008] [Accepted: 05/24/2008] [Indexed: 10/22/2022]
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97
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Insights into the role of the (alpha+beta) insertion in the TIM-barrel catalytic domain, regarding the stability and the enzymatic activity of chitinase A from Serratia marcescens. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1794:23-31. [PMID: 18973833 DOI: 10.1016/j.bbapap.2008.09.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2008] [Revised: 09/16/2008] [Accepted: 09/17/2008] [Indexed: 11/20/2022]
Abstract
Chitinase A (ChiA) from Serratia marcescens is a mesophilic enzyme with high catalytic activity and high stability. The crystal structure of ChiA has revealed a TIM-barrel fold of the catalytic domain, an (alpha+beta) insertion between the B7 beta-strand and A7 alpha-helix of the TIM-barrel, an FnIII domain at the N-terminus of the molecule and a hinge region that connects the latter to the catalytic domain. In this study, the role of the (alpha+beta) domain on the stability, catalytic activity and specificity of the enzyme was investigated by deleting this domain and studying the enzymatic and structural properties of the resulting truncated enzyme. The obtained data clearly show that by removing the (alpha+beta) domain, the thermal stability of the enzyme is substantially reduced, with an apparent T(m) of 42.0+/-1.0 degrees C, compared to the apparent T(m) of 58.1+/-1.0 degrees C of ChiA at pH 9.0. The specific activity of ChiADelta(alpha+beta) was substantially decreased, the pH optimum was shifted from 6.5 to 5.0 and the substrate and product specificities were altered.
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98
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Han Y, Li Z, Miao X, Zhang F. Statistical optimization of medium components to improve the chitinase activity of Streptomyces sp. Da11 associated with the South China Sea sponge Craniella australiensis. Process Biochem 2008. [DOI: 10.1016/j.procbio.2008.05.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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99
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Chuang HH, Lin HY, Lin FP. Biochemical characteristics of C-terminal region of recombinant chitinase from Bacillus licheniformis: implication of necessity for enzyme properties. FEBS J 2008; 275:2240-54. [PMID: 18397326 DOI: 10.1111/j.1742-4658.2008.06376.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The functional and structural significance of the C-terminal region of Bacillus licheniformis chitinase was explored using C-terminal truncation mutagenesis. Comparative studies between full-length and truncated mutant molecules included initial rate kinetics, fluorescence and CD spectrometric properties, substrate binding and hydrolysis abilities, thermostability, and thermodenaturation kinetics. Kinetic analyses revealed that the overall catalytic efficiency, k(cat)/K(m), was slightly increased for the truncated enzymes toward the soluble 4-methylumbelliferyl-N-N'-diacetyl chitobiose or 4-methylumbelliferyl-N-N''-N'''-triacetyl chitotriose or insoluble alpha-chitin substrate. By contrast, changes to substrate affinity, K(m), and turnover rate, k(cat), varied considerably for both types of chitin substrates between the full-length and truncated enzymes. Both truncated enzymes exhibited significantly higher thermostabilities than the full-length enzyme. The truncated mutants retained similar substrate-binding specificities and abilities against the insoluble substrate but only had approximately 75% of the hydrolyzing efficiency of the full-length chitinase molecule. Fluorescence spectroscopy indicated that both C-terminal deletion mutants retained an active folding conformation similar to the full-length enzyme. However, a CD melting unfolding study was able to distinguish between the full-length and truncated mutant molecules by the two phases of apparent transition temperatures in the mutants. These results indicate that up to 145 amino acid residues, including the putative C-terminal chitin-binding region and the fibronectin (III) motif of B. licheniformis chitinase, could be removed without causing a seriously aberrant change in structure and a dramatic decrease in insoluble chitin hydrolysis. The results of the present study provide evidence demonstrating that the binding and hydrolyzing of insoluble chitin substrate for B. licheniformis chitinase was not dependent solely on the putative C-terminal chitin-binding region and the fibronectin (III) motif.
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Affiliation(s)
- Hsu-Han Chuang
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
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100
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Seidl V. Chitinases of filamentous fungi: a large group of diverse proteins with multiple physiological functions. FUNGAL BIOL REV 2008. [DOI: 10.1016/j.fbr.2008.03.002] [Citation(s) in RCA: 184] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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