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Dementiev A, Lillington SP, Jin S, Kim Y, Jedrzejczak R, Michalska K, Joachimiak A, O'Malley MA. Structure and enzymatic characterization of CelD endoglucanase from the anaerobic fungus Piromyces finnis. Appl Microbiol Biotechnol 2023; 107:5999-6011. [PMID: 37548665 PMCID: PMC10485095 DOI: 10.1007/s00253-023-12684-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/24/2023] [Accepted: 06/29/2023] [Indexed: 08/08/2023]
Abstract
Anaerobic fungi found in the guts of large herbivores are prolific biomass degraders whose genomes harbor a wealth of carbohydrate-active enzymes (CAZymes), of which only a handful are structurally or biochemically characterized. Here, we report the structure and kinetic rate parameters for a glycoside hydrolase (GH) family 5 subfamily 4 enzyme (CelD) from Piromyces finnis, a modular, cellulosome-incorporated endoglucanase that possesses three GH5 domains followed by two C-terminal fungal dockerin domains (double dockerin). We present the crystal structures of an apo wild-type CelD GH5 catalytic domain and its inactive E154A mutant in complex with cellotriose at 2.5 and 1.8 Å resolution, respectively, finding the CelD GH5 catalytic domain adopts the (β/α)8-barrel fold common to many GH5 enzymes. Structural superimposition of the apo wild-type structure with the E154A mutant-cellotriose complex supports a catalytic mechanism in which the E154 carboxylate side chain acts as an acid/base and E278 acts as a complementary nucleophile. Further analysis of the cellotriose binding pocket highlights a binding groove lined with conserved aromatic amino acids that when docked with larger cellulose oligomers is capable of binding seven glucose units and accommodating branched glucan substrates. Activity analyses confirm P. finnis CelD can hydrolyze mixed linkage glucan and xyloglucan, as well as carboxymethylcellulose (CMC). Measured kinetic parameters show the P. finnis CelD GH5 catalytic domain has CMC endoglucanase activity comparable to other fungal endoglucanases with kcat = 6.0 ± 0.6 s-1 and Km = 7.6 ± 2.1 g/L CMC. Enzyme kinetics were unperturbed by the addition or removal of the native C-terminal dockerin domains as well as the addition of a non-native N-terminal dockerin, suggesting strict modularity among the domains of CelD. KEY POINTS: • Anaerobic fungi host a wealth of industrially useful enzymes but are understudied. • P. finnis CelD has endoglucanase activity and structure common to GH5_4 enzymes. • CelD's kinetics do not change with domain fusion, exhibiting high modularity.
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Affiliation(s)
- Alexey Dementiev
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Stephen P Lillington
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA
| | - Shiyan Jin
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA
| | - Youngchang Kim
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Robert Jedrzejczak
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Karolina Michalska
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Andrzej Joachimiak
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA.
- Biological Engineering Program, University of California, Santa Barbara, CA, USA.
- Joint BioEnergy Institute (JBEI), Emeryville, CA, 94608, USA.
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Mendonça M, Barroca M, Collins T. Endo-1,4-β-xylanase-containing glycoside hydrolase families: Characteristics, singularities and similarities. Biotechnol Adv 2023; 65:108148. [PMID: 37030552 DOI: 10.1016/j.biotechadv.2023.108148] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 04/02/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
Endo-1,4-β-xylanases (EC 3.2.1.8) are O-glycoside hydrolases that cleave the internal β-1,4-D-xylosidic linkages of the complex plant polysaccharide xylan. They are produced by a vast array of organisms where they play critical roles in xylan saccharification and plant cell wall hydrolysis. They are also important industrial biocatalysts with widespread application. A large and ever growing number of xylanases with wildly different properties and functionalites are known and a better understanding of these would enable a more effective use in various applications. The Carbohydrate-Active enZYmes database (CAZy), which classifies evolutionarily related proteins into a glycoside hydrolase family-subfamily organisational scheme has proven powerful in understanding these enzymes. Nevertheless, ambiguity currently exists as to the number of glycoside hydrolase families and subfamilies harbouring catalytic domains with true endoxylanase activity and as to the specific characteristics of each of these families/subfamilies. This review seeks to clarify this, identifying 9 glycoside hydrolase families containing enzymes with endo-1,4-β-xylanase activity and discussing their properties, similarities, differences and biotechnological perspectives. In particular, substrate specificities and hydrolysis patterns and the structural determinants of these are detailed, with taxonomic aspects of source organisms being also presented. Shortcomings in current knowledge and research areas that require further clarification are highlighted and suggestions for future directions provided. This review seeks to motivate further research on these enzymes and especially of the lesser known endo-1,4-β-xylanase containing families. A better understanding of these enzymes will serve as a foundation for the knowledge-based development of process-fitted endo-1,4-β-xylanases and will accelerate their development for use with even the most recalcitrant of substrates in the biobased industries of the future.
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Characterization of a novel bifunctional enzyme from buffalo rumen metagenome and its effect on in vitro ruminal fermentation and microbial community composition. ANIMAL NUTRITION 2023; 13:137-149. [PMID: 37123618 PMCID: PMC10130076 DOI: 10.1016/j.aninu.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 12/26/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
To efficiently use lignocellulosic materials in ruminants, it is crucial to explore effective enzymes, especially bifunctional enzymes. In this study, a novel stable bifunctional cellulase-xylanase protein from buffalo rumen metagenome was expressed and characterized, CelXyn2. The enzyme displayed optimal activity at pH 6.0 and 45 °C. The residual endoglucanase and xylanase activities were 90.6% and 86.4% after a 60-min pre-incubation at 55 °C. Hydrolysis of rice straw, wheat straw, sheepgrass and sugar beet pulp by CelXyn2 showed its ability to degrade both cellulose and hemicellulose polymers. Treatment with CelXyn2 improved the hydrolysis of agricultural residues with an evident increase in production of total gas, lactate and volatile fatty acids. The results of 16S rRNA and real-time PCR showed that the effect on in vitro ruminal microbial community depended on fermentation substrates. This study demonstrated that CelXyn2 could strengthen lignocellulose hydrolysis and in vitro ruminal fermentation. These characteristics of CelXyn2 distinguish it as a promising candidate for agricultural application.
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Mafa MS, Dirr HW, Malgas S, Krause RWM, Rashamuse K, Pletschke BI. A Novel Dimeric Exoglucanase (GH5_38): Biochemical and Structural Characterisation towards its Application in Alkyl Cellobioside Synthesis. Molecules 2020; 25:E746. [PMID: 32050450 PMCID: PMC7036808 DOI: 10.3390/molecules25030746] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/14/2020] [Accepted: 01/21/2020] [Indexed: 01/02/2023] Open
Abstract
An exoglucanase (Exg-D) from the glycoside hydrolase family 5 subfamily 38 (GH5_38) was heterologously expressed and structurally and biochemically characterised at a molecular level for its application in alkyl glycoside synthesis. The purified Exg-D existed in both dimeric and monomeric forms in solution, which showed highest activity on mixed-linked β-glucan (88.0 and 86.7 U/mg protein, respectively) and lichenin (24.5 and 23.7 U/mg protein, respectively). They displayed a broad optimum pH range from 5.5 to 7 and a temperature optimum from 40 to 60 °C. Kinetic studies demonstrated that Exg-D had a higher affinity towards β-glucan, with a Km of 7.9 mg/mL and a kcat of 117.2 s-1, compared to lichenin which had a Km of 21.5 mg/mL and a kcat of 70.0 s-1. The circular dichroism profile of Exg-D showed that its secondary structure consisted of 11% α-helices, 36% β-strands and 53% coils. Exg-D performed transglycosylation using p-nitrophenyl cellobioside as a glycosyl donor and several primary alcohols as acceptors to produce methyl-, ethyl- and propyl-cellobiosides. These products were identified and quantified via thin-layer chromatography (TLC) and liquid chromatography-mass spectrometry (LC-MS). We concluded that Exg-D is a novel and promising oligomeric glycoside hydrolase for the one-step synthesis of alkyl glycosides with more than one monosaccharide unit.
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Affiliation(s)
- Mpho S. Mafa
- Protein Structure-Function Research Unit East Campus, Gate House, School of Molecular and Cell Biology University of the Witwatersrand, Johannesburg 2050, South Africa; (M.S.M.); (H.W.D.)
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa;
| | - Heinrich W. Dirr
- Protein Structure-Function Research Unit East Campus, Gate House, School of Molecular and Cell Biology University of the Witwatersrand, Johannesburg 2050, South Africa; (M.S.M.); (H.W.D.)
| | - Samkelo Malgas
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa;
| | - Rui W. M. Krause
- Department of Chemistry, Rhodes University, Grahamstown 6140, South Africa;
| | | | - Brett I. Pletschke
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa;
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Cui J, Mai G, Wang Z, Liu Q, Zhou Y, Ma Y, Liu C. Metagenomic Insights Into a Cellulose-Rich Niche Reveal Microbial Cooperation in Cellulose Degradation. Front Microbiol 2019; 10:618. [PMID: 30984144 PMCID: PMC6447707 DOI: 10.3389/fmicb.2019.00618] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 03/11/2019] [Indexed: 11/22/2022] Open
Abstract
Background Cellulose is the most abundant organic polymer mainly produced by plants in nature. It is insoluble and highly resistant to enzymatic hydrolysis. Cellulolytic microorganisms that are capable of producing a battery of related enzymes play an important role in recycling cellulose-rich plant biomass. Effective cellulose degradation by multiple synergic microorganisms has been observed within a defined microbial consortium in the lab culture. Metagenomic analysis may enable us to understand how microbes cooperate in cellulose degradation in a more complex microbial free-living ecosystem in nature. Results Here we investigated a typical cellulose-rich and alkaline niche where constituent microbes survive through inter-genera cooperation in cellulose utilization. The niche has been generated in an ancient paper-making plant, which has served as an isolated habitat for over 7 centuries. Combined amplicon-based sequencing of 16S rRNA genes and metagenomic sequencing, our analyses showed a microbial composition with 6 dominant genera including Cloacibacterium, Paludibacter, Exiguobacterium, Acetivibrio, Tolumonas, and Clostridium in this cellulose-rich niche; the composition is distinct from other cellulose-rich niches including a modern paper mill, bamboo soil, wild giant panda guts, and termite hindguts. In total, 11,676 genes of 96 glucoside hydrolase (GH) families, as well as 1,744 genes of carbohydrate transporters were identified, and modeling analysis of two representative genes suggested that these glucoside hydrolases likely evolved to adapt to alkaline environments. Further reconstruction of the microbial draft genomes by binning the assembled contigs predicted a mutualistic interaction between the dominant microbes regarding the cellulolytic process in the niche, with Paludibacter and Clostridium acting as helpers that produce endoglucanases, and Cloacibacterium, Exiguobacterium, Acetivibrio, and Tolumonas being beneficiaries that cross-feed on the cellodextrins by oligosaccharide uptake. Conclusion The analysis of the key genes involved in cellulose degradation and reconstruction of the microbial draft genomes by binning the assembled contigs predicted a mutualistic interaction based on public goods regarding the cellulolytic process in the niche, suggesting that in the studied microbial consortium, free-living bacteria likely survive on each other by acquisition and exchange of metabolites. Knowledge gained from this study will facilitate the design of complex microbial communities with a better performance in industrial bioprocesses.
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Affiliation(s)
- Jinming Cui
- Institute of Synthetic Biology - Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Guoqin Mai
- Institute of Synthetic Biology - Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zuowei Wang
- Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Quan Liu
- Institute of Synthetic Biology - Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yan Zhou
- Institute of Synthetic Biology - Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yingfei Ma
- Institute of Synthetic Biology - Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Chenli Liu
- Institute of Synthetic Biology - Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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6
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Tan H, Miao R, Liu T, Yang L, Yang Y, Chen C, Lei J, Li Y, He J, Sun Q, Peng W, Gan B, Huang Z. A bifunctional cellulase-xylanase of a new Chryseobacterium strain isolated from the dung of a straw-fed cattle. Microb Biotechnol 2018; 11:381-398. [PMID: 29205864 PMCID: PMC5812240 DOI: 10.1111/1751-7915.13034] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 11/10/2017] [Indexed: 12/17/2022] Open
Abstract
A new cellulolytic strain of Chryseobacterium genus was screened from the dung of a cattle fed with cereal straw. A putative cellulase gene (cbGH5) belonging to glycoside hydrolase family 5 subfamily 46 (GH5_46) was identified and cloned by degenerate PCR plus genome walking. The CbGH5 protein was overexpressed in Pichia pastoris, purified and characterized. It is the first bifunctional cellulase-xylanase reported in GH5_46 as well as in Chryseobacterium genus. The enzyme showed an endoglucanase activity on carboxymethylcellulose of 3237 μmol min-1 mg-1 at pH 9, 90 °C and a xylanase activity on birchwood xylan of 1793 μmol min-1 mg-1 at pH 8, 90 °C. The activity level and thermophilicity are in the front rank of all the known cellulases and xylanases. Core hydrophobicity had a positive effect on the thermophilicity of this enzyme. When similar quantity of enzymatic activity units was applied on the straws of wheat, rice, corn and oilseed rape, CbGH5 could obtain 3.5-5.0× glucose and 1.2-1.8× xylose than a mixed commercial cellulase plus xylanase of Novozymes. When applied on spent mushroom substrates made from the four straws, CbGH5 could obtain 9.2-15.7× glucose and 3.5-4.3× xylose than the mixed Novozymes cellulase+xylanase. The results suggest that CbGH5 could be a promising candidate for industrial lignocellulosic biomass conversion.
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Affiliation(s)
- Hao Tan
- National‐local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Soil and Fertilizer InstituteSichuan Academy of Agricultural SciencesChengduChina
- Scientific Observing and Experimental Station of Agro‐microbial Resource and Utilization in Southwest ChinaMinistry of AgricultureChengduChina
| | - Renyun Miao
- National‐local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Soil and Fertilizer InstituteSichuan Academy of Agricultural SciencesChengduChina
- Scientific Observing and Experimental Station of Agro‐microbial Resource and Utilization in Southwest ChinaMinistry of AgricultureChengduChina
| | - Tianhai Liu
- National‐local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Soil and Fertilizer InstituteSichuan Academy of Agricultural SciencesChengduChina
- Scientific Observing and Experimental Station of Agro‐microbial Resource and Utilization in Southwest ChinaMinistry of AgricultureChengduChina
| | - Lufang Yang
- Scientific Observing and Experimental Station of Agro‐microbial Resource and Utilization in Southwest ChinaMinistry of AgricultureChengduChina
| | - Yumin Yang
- Scientific Observing and Experimental Station of Agro‐microbial Resource and Utilization in Southwest ChinaMinistry of AgricultureChengduChina
| | - Chunxiu Chen
- Scientific Observing and Experimental Station of Agro‐microbial Resource and Utilization in Southwest ChinaMinistry of AgricultureChengduChina
| | - Jianrong Lei
- Scientific Observing and Experimental Station of Agro‐microbial Resource and Utilization in Southwest ChinaMinistry of AgricultureChengduChina
| | - Yuhui Li
- National‐local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Soil and Fertilizer InstituteSichuan Academy of Agricultural SciencesChengduChina
- College of Life SciencesSichuan UniversityChengduChina
| | - Jiabei He
- National‐local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Soil and Fertilizer InstituteSichuan Academy of Agricultural SciencesChengduChina
- College of Life SciencesSichuan UniversityChengduChina
| | - Qun Sun
- College of Life SciencesSichuan UniversityChengduChina
| | - Weihong Peng
- National‐local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Soil and Fertilizer InstituteSichuan Academy of Agricultural SciencesChengduChina
- Scientific Observing and Experimental Station of Agro‐microbial Resource and Utilization in Southwest ChinaMinistry of AgricultureChengduChina
| | - Bingcheng Gan
- National‐local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Soil and Fertilizer InstituteSichuan Academy of Agricultural SciencesChengduChina
- Scientific Observing and Experimental Station of Agro‐microbial Resource and Utilization in Southwest ChinaMinistry of AgricultureChengduChina
| | - Zhongqian Huang
- National‐local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Soil and Fertilizer InstituteSichuan Academy of Agricultural SciencesChengduChina
- Scientific Observing and Experimental Station of Agro‐microbial Resource and Utilization in Southwest ChinaMinistry of AgricultureChengduChina
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Nakajima D, Nagano A, Shibata T, Tanaka R, Kuroda K, Ueda M, Miyake H. Xylanase B from Clostridium cellulovorans 743B: overexpression, purification, crystallization and X-ray diffraction analysis. Acta Crystallogr F Struct Biol Commun 2018; 74:113-116. [PMID: 29400321 PMCID: PMC5947682 DOI: 10.1107/s2053230x18000341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 01/06/2018] [Indexed: 11/11/2022] Open
Abstract
Clostridium cellulovorans produces multi-enzyme complexes called cellulosomes capable of efficiently degrading cellulosic biomass. There are three xylanase genes containing a sequence corresponding to a dockerin domain that are necessary for constructing cellulosomes in the genome. Among the xylanases encoded by these genes, xylanase B (XynB) contains a catalytic domain belonging to glycoside hydrolase family 10 and a carbohydrate-binding module (CBM) at the N-terminus, making it a member of CBM family 22. In this study, XynB was cloned, overexpressed, purified and crystallized. XynB was crystallized using the hanging-drop vapour-diffusion method in the presence of 0.2 M sodium acetate trihydrate, 0.1 M Tris-HCl pH 8.5, 32%(w/v) PEG 4000 at 293 K. X-ray diffraction analysis revealed that the crystal diffracted to 1.95 Å resolution and belonged to space group P212121, with unit-cell parameters a = 74.28, b = 77.55, c = 88.20 Å, α = β = γ = 90°. The data-evaluation statistics revealed high quality of the collected data, thereby establishing a solid basis for determination of the structure of cellulosomal xylanase from C. cellulovorans.
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Affiliation(s)
- Daichi Nakajima
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
| | - Akihiko Nagano
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
| | - Toshiyuki Shibata
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
- Seaweed Biorefinery Research Center, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
| | - Reiji Tanaka
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
- Seaweed Biorefinery Research Center, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
| | - Kouichi Kuroda
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Mitsuyoshi Ueda
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hideo Miyake
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
- Seaweed Biorefinery Research Center, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
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Microbial xylanases and their industrial application in pulp and paper biobleaching: a review. 3 Biotech 2017; 7:11. [PMID: 28391477 PMCID: PMC5385172 DOI: 10.1007/s13205-016-0584-6] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/02/2016] [Indexed: 10/25/2022] Open
Abstract
Xylanases are hydrolytic enzymes which cleave the β-1, 4 backbone of the complex plant cell wall polysaccharide xylan. Xylan is the major hemicellulosic constituent found in soft and hard food. It is the next most abundant renewable polysaccharide after cellulose. Xylanases and associated debranching enzymes produced by a variety of microorganisms including bacteria, actinomycetes, yeast and fungi bring hydrolysis of hemicelluloses. Despite thorough knowledge of microbial xylanolytic systems, further studies are required to achieve a complete understanding of the mechanism of xylan degradation by xylanases produced by microorganisms and their promising use in pulp biobleaching. Cellulase-free xylanases are important in pulp biobleaching as alternatives to the use of toxic chlorinated compounds because of the environmental hazards and diseases caused by the release of the adsorbable organic halogens. In this review, we have focused on the studies of structural composition of xylan in plants, their classification, sources of xylanases, extremophilic xylanases, modes of fermentation for the production of xylanases, factors affecting xylanase production, statistical approaches such as Plackett Burman, Response Surface Methodology to enhance xylanase production, purification, characterization, molecular cloning and expression. Besides this, review has focused on the microbial enzyme complex involved in the complete breakdown of xylan and the studies on xylanase regulation and their potential industrial applications with special reference to pulp biobleaching, which is directly related to increasing pulp brightness and reduction in environmental pollution.
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9
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Attigani A, Sun L, Wang Q, Liu Y, Bai D, Li S, Huang X. The crystal structure of the endoglucanase Cel10, a family 8 glycosyl hydrolase from Klebsiella pneumoniae. Acta Crystallogr F Struct Biol Commun 2016; 72:870-876. [PMID: 27917834 PMCID: PMC5137463 DOI: 10.1107/s2053230x16017891] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/08/2016] [Indexed: 02/04/2023] Open
Abstract
Cellulases are produced by microorganisms that grow on cellulose biomass. Here, a cellulase, Cel10, was identified in a strain of Klebsiella pneumoniae isolated from Chinese bamboo rat gut. Analysis of substrate specificity showed that Cel10 is able to hydrolyze amorphous carboxymethyl cellulose (CMC) and crystalline forms of cellulose (Avicel and xylan) but is unable to hydrolyze p-nitrophenol β-D-glucopyranoside (p-NPG), proving that Cel10 is an endoglucanase. A phylogenetic tree analysis indicates that Cel10 belongs to the glycoside hydrolase 8 (GH8) subfamily. In order to further understanding of its substrate specificity, the structure of Cel10 was solved by molecular replacement and refined to 1.76 Å resolution. The overall fold is distinct from those of most other enzymes belonging to the GH8 subfamily. Although it forms the typical (α/α)6-barrel motif fold, like Acetobacterxylinum CMCax, one helix is missing. Structural comparisons with Clostridium thermocellum CelA (CtCelA), the best characterized GH8 endoglucanase, revealed that sugar-recognition subsite -3 is completely missing in Cel10. The absence of this subsite correlates to a more open substrate-binding cleft on the cellooligosaccharide reducing-end side.
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Affiliation(s)
- Ayman Attigani
- Key Laboratory for Integrated Chinese Traditional and Western Veterinary Medicine and Animal Healthcare, College of Animal Science, Fujian Agriculture and Forestry University, 15 Shang Xia Dian Road, Fuzhou 350002, People’s Republic of China
| | - Lifang Sun
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 West Yangqiao Road, Fuzhou 350002, People’s Republic of China
| | - Qing Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 West Yangqiao Road, Fuzhou 350002, People’s Republic of China
| | - Yadan Liu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 West Yangqiao Road, Fuzhou 350002, People’s Republic of China
| | - Dingping Bai
- Key Laboratory for Integrated Chinese Traditional and Western Veterinary Medicine and Animal Healthcare, College of Animal Science, Fujian Agriculture and Forestry University, 15 Shang Xia Dian Road, Fuzhou 350002, People’s Republic of China
| | - Shengping Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 West Yangqiao Road, Fuzhou 350002, People’s Republic of China
| | - Xiaohong Huang
- Key Laboratory for Integrated Chinese Traditional and Western Veterinary Medicine and Animal Healthcare, College of Animal Science, Fujian Agriculture and Forestry University, 15 Shang Xia Dian Road, Fuzhou 350002, People’s Republic of China
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10
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Lafond M, Sulzenbacher G, Freyd T, Henrissat B, Berrin JG, Garron ML. The Quaternary Structure of a Glycoside Hydrolase Dictates Specificity toward β-Glucans. J Biol Chem 2016; 291:7183-94. [PMID: 26755730 DOI: 10.1074/jbc.m115.695999] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Indexed: 02/05/2023] Open
Abstract
In the Carbohydrate-Active Enzyme (CAZy) database, glycoside hydrolase family 5 (GH5) is a large family with more than 6,000 sequences. Among the 51 described GH5 subfamilies, subfamily GH5_26 contains members that display either endo-β(1,4)-glucanase or β(1,3;1,4)-glucanase activities. In this study, we focused on the GH5_26 enzyme fromSaccharophagus degradans(SdGluc5_26A), a marine bacterium known for its capacity to degrade a wide diversity of complex polysaccharides.SdGluc5_26A displays lichenase activity toward β(1,3;1,4)-glucans with a side cellobiohydrolase activity toward β(1,4)-glucans. The three-dimensional structure ofSdGluc5_26A adopts a stable trimeric quaternary structure also observable in solution. The N-terminal region ofSdGluc5_26A protrudes into the active site of an adjacent monomer. To understand whether this occupation of the active site could influence its activity, we conducted a comprehensive enzymatic characterization ofSdGluc5_26A and of a mutant truncated at the N terminus. Ligand complex structures and kinetic analyses reveal that the N terminus governs the substrate specificity ofSdGluc5_26A. Its deletion opens the enzyme cleft at the -3 subsite and turns the enzyme into an endo-β(1,4)-glucanase. This study demonstrates that experimental approaches can reveal structure-function relationships out of reach of current bioinformatic predictions.
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Affiliation(s)
- Mickael Lafond
- From the Institut des Sciences Moléculaires de Marseille-BiosCiences, UMR7313 CNRS, Aix-Marseille University, Pôle de l'Etoile, 13284 Marseille, France, the INRA, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille University, Polytech'Marseille, F-13288 Marseille, France
| | - Gerlind Sulzenbacher
- the Architecture et Fonction des Macromolécules Biologiques, UMR7257 CNRS, Aix-Marseille University, F-13288 Marseille, France, the INRA, USC1408 Architecture et Fonction des Macromolécules Biologiques, F-13288 Marseille, France, and
| | - Thibaud Freyd
- the Architecture et Fonction des Macromolécules Biologiques, UMR7257 CNRS, Aix-Marseille University, F-13288 Marseille, France
| | - Bernard Henrissat
- the Architecture et Fonction des Macromolécules Biologiques, UMR7257 CNRS, Aix-Marseille University, F-13288 Marseille, France, the INRA, USC1408 Architecture et Fonction des Macromolécules Biologiques, F-13288 Marseille, France, and the Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jean-Guy Berrin
- the INRA, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille University, Polytech'Marseille, F-13288 Marseille, France,
| | - Marie-Line Garron
- the Architecture et Fonction des Macromolécules Biologiques, UMR7257 CNRS, Aix-Marseille University, F-13288 Marseille, France, the INRA, USC1408 Architecture et Fonction des Macromolécules Biologiques, F-13288 Marseille, France, and
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11
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Gomes E, de Souza AR, Orjuela GL, Da Silva R, de Oliveira TB, Rodrigues A. Applications and Benefits of Thermophilic Microorganisms and Their Enzymes for Industrial Biotechnology. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_21] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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12
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Elgharbi F, Hlima HB, Farhat-Khemakhem A, Ayadi-Zouari D, Bejar S, Hmida-Sayari A. Expression of A. niger US368 xylanase in E. coli: Purification, characterization and copper activation. Int J Biol Macromol 2015; 74:263-70. [DOI: 10.1016/j.ijbiomac.2014.12.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 12/10/2014] [Accepted: 12/11/2014] [Indexed: 10/24/2022]
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13
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Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Ståhlberg J, Beckham GT. Fungal Cellulases. Chem Rev 2015; 115:1308-448. [DOI: 10.1021/cr500351c] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, Kentucky 40506, United States
| | - Brandon C. Knott
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrik Hansson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Mats Sandgren
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
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14
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Structure and Function of Carbohydrate-Binding Module Families 13 and 42 of Glycoside Hydrolases, Comprising a β-Trefoil Fold. Biosci Biotechnol Biochem 2014; 77:1363-71. [DOI: 10.1271/bbb.130183] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Al Balaa B, Wouters J, Dogne S, Rossini C, Schaus JM, Depiereux E, Vandenhaute J, Housen I. Identification, Cloning, and Expression of theScytalidium acidophilumXYL1 Gene Encoding for an Acidophilic Xylanase. Biosci Biotechnol Biochem 2014; 70:269-72. [PMID: 16428847 DOI: 10.1271/bbb.70.269] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We cloned XYL1, a Scytalidium acidophilum gene encoding for an acidophilic family 11 xylanase. The XYL1p protein was expressed in Pichia pastoris using the pPICZalphaA expression plasmid. The secreted protein was purified by TAXI affinity column chromatography. The purified XYL1p showed an optimum activity at pH 3.2 and 56 degrees C. The Michaelis-Menten constants were determined.
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Affiliation(s)
- Bassam Al Balaa
- Research Unit in Molecular Biology, University of Namur, Namur, Belgium
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16
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Sugimura M, Nishimoto M, Kitaoka M. Characterization of Glycosynthase Mutants Derived from Glycoside Hydrolase Family 10 Xylanases. Biosci Biotechnol Biochem 2014; 70:1210-7. [PMID: 16717424 DOI: 10.1271/bbb.70.1210] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Four xylanases belonging to glycoside hydrolase family 10-Thermotoga maritima XylB (TM), Clostridium stercorarium XynB (CS), Bacillus halodurans XynA (BH), and Cellulomonas fimi Cex (CF)-were converted to glycosynthases by substituting the nucleophilic glutamic acid residues with glycine, alanine, and serine. The glycine mutants exhibited the highest levels of glycosynthase activity with all four enzymes. All the glycine mutants formed polymeric beta-1,4-linked xylopyranose as a precipitate during reaction with alpha-xylobiosyl fluoride. Two glycine mutants (TM and CF) recognized X(2) as an effective acceptor molecule to prohibit the formation of the polymer, while the other two (CS and BH) did not. The difference in acceptor specificity is considered to reflect the difference in substrate affinity at their +2 subsites. The results agreed with the structural predictions of the subsite, where TM and CF exhibit high affinity at subsite 2, suggesting that the glycosynthase technique is useful for investigating the affinity of +subsites.
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17
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Nagao C, Nagano N, Mizuguchi K. Prediction of detailed enzyme functions and identification of specificity determining residues by random forests. PLoS One 2014; 9:e84623. [PMID: 24416252 PMCID: PMC3885575 DOI: 10.1371/journal.pone.0084623] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 11/15/2013] [Indexed: 12/03/2022] Open
Abstract
Determining enzyme functions is essential for a thorough understanding of cellular processes. Although many prediction methods have been developed, it remains a significant challenge to predict enzyme functions at the fourth-digit level of the Enzyme Commission numbers. Functional specificity of enzymes often changes drastically by mutations of a small number of residues and therefore, information about these critical residues can potentially help discriminate detailed functions. However, because these residues must be identified by mutagenesis experiments, the available information is limited, and the lack of experimentally verified specificity determining residues (SDRs) has hindered the development of detailed function prediction methods and computational identification of SDRs. Here we present a novel method for predicting enzyme functions by random forests, EFPrf, along with a set of putative SDRs, the random forests derived SDRs (rf-SDRs). EFPrf consists of a set of binary predictors for enzymes in each CATH superfamily and the rf-SDRs are the residue positions corresponding to the most highly contributing attributes obtained from each predictor. EFPrf showed a precision of 0.98 and a recall of 0.89 in a cross-validated benchmark assessment. The rf-SDRs included many residues, whose importance for specificity had been validated experimentally. The analysis of the rf-SDRs revealed both a general tendency that functionally diverged superfamilies tend to include more active site residues in their rf-SDRs than in less diverged superfamilies, and superfamily-specific conservation patterns of each functional residue. EFPrf and the rf-SDRs will be an effective tool for annotating enzyme functions and for understanding how enzyme functions have diverged within each superfamily.
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Affiliation(s)
- Chioko Nagao
- National Institute of Biomedical Innovation, Ibaraki, Osaka, Japan
- * E-mail: (CN); (KM)
| | - Nozomi Nagano
- Computational Biology Research Center, AIST, Koto-ku, Tokyo, Japan
| | - Kenji Mizuguchi
- National Institute of Biomedical Innovation, Ibaraki, Osaka, Japan
- * E-mail: (CN); (KM)
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18
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Alvarez TM, Paiva JH, Ruiz DM, Cairo JPLF, Pereira IO, Paixão DAA, de Almeida RF, Tonoli CCC, Ruller R, Santos CR, Squina FM, Murakami MT. Structure and function of a novel cellulase 5 from sugarcane soil metagenome. PLoS One 2013; 8:e83635. [PMID: 24358302 PMCID: PMC3866126 DOI: 10.1371/journal.pone.0083635] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 11/04/2013] [Indexed: 11/26/2022] Open
Abstract
Cellulases play a key role in enzymatic routes for degradation of plant cell-wall polysaccharides into simple and economically-relevant sugars. However, their low performance on complex substrates and reduced stability under industrial conditions remain the main obstacle for the large-scale production of cellulose-derived products and biofuels. Thus, in this study a novel cellulase with unusual catalytic properties from sugarcane soil metagenome (CelE1) was isolated and characterized. The polypeptide deduced from the celE1 gene encodes a unique glycoside hydrolase domain belonging to GH5 family. The recombinant enzyme was active on both carboxymethyl cellulose and β-glucan with an endo-acting mode according to capillary electrophoretic analysis of cleavage products. CelE1 showed optimum hydrolytic activity at pH 7.0 and 50 °C with remarkable activity at alkaline conditions that is attractive for industrial applications in which conventional acidic cellulases are not suitable. Moreover, its three-dimensional structure was determined at 1.8 Å resolution that allowed the identification of an insertion of eight residues in the β8-α8 loop of the catalytic domain of CelE1, which is not conserved in its psychrophilic orthologs. This 8-residue-long segment is a prominent and distinguishing feature of thermotolerant cellulases 5 suggesting that it might be involved with thermal stability. Based on its unconventional characteristics, CelE1 could be potentially employed in biotechnological processes that require thermotolerant and alkaline cellulases.
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Affiliation(s)
- Thabata M Alvarez
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Joice H Paiva
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Diego M Ruiz
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - João Paulo L F Cairo
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Isabela O Pereira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Douglas A A Paixão
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Rodrigo F de Almeida
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Celisa C C Tonoli
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Roberto Ruller
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Camila R Santos
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Fabio M Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Mario T Murakami
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
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19
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Oyama T, Schmitz GE, Dodd D, Han Y, Burnett A, Nagasawa N, Mackie RI, Nakamura H, Morikawa K, Cann I. Mutational and structural analyses of Caldanaerobius polysaccharolyticus Man5B reveal novel active site residues for family 5 glycoside hydrolases. PLoS One 2013; 8:e80448. [PMID: 24278284 PMCID: PMC3835425 DOI: 10.1371/journal.pone.0080448] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 10/03/2013] [Indexed: 11/30/2022] Open
Abstract
CpMan5B is a glycoside hydrolase (GH) family 5 enzyme exhibiting both β-1,4-mannosidic and β-1,4-glucosidic cleavage activities. To provide insight into the amino acid residues that contribute to catalysis and substrate specificity, we solved the structure of CpMan5B at 1.6 Å resolution. The structure revealed several active site residues (Y12, N92 and R196) in CpMan5B that are not present in the active sites of other structurally resolved GH5 enzymes. Residue R196 in GH5 enzymes is thought to be strictly conserved as a histidine that participates in an electron relay network with the catalytic glutamates, but we show that an arginine fulfills a functionally equivalent role and is found at this position in every enzyme in subfamily GH5_36, which includes CpMan5B. Residue N92 is required for full enzymatic activity and forms a novel bridge over the active site that is absent in other family 5 structures. Our data also reveal a role of Y12 in establishing the substrate preference for CpMan5B. Using these molecular determinants as a probe allowed us to identify Man5D from Caldicellulosiruptor bescii as a mannanase with minor endo-glucanase activity.
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Affiliation(s)
- Takuji Oyama
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - George E. Schmitz
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Dylan Dodd
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - Yejun Han
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Alanna Burnett
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - Naoko Nagasawa
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Roderick I. Mackie
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Kosuke Morikawa
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Isaac Cann
- Institute for Protein Research, Osaka University, Osaka, Japan
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
- * E-mail:
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20
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Khan MIM, Sajjad M, Sadaf S, Zafar R, Niazi UHK, Akhtar MW. The nature of the carbohydrate binding module determines the catalytic efficiency of xylanase Z of Clostridium thermocellum. J Biotechnol 2013; 168:403-8. [PMID: 24095983 DOI: 10.1016/j.jbiotec.2013.09.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/22/2013] [Accepted: 09/12/2013] [Indexed: 11/30/2022]
Abstract
Xylanase Z of Clostridium thermocellum exists as a complex in the cellulosome with N-terminus feruloyl esterase, a carbohydrate binding module (CBM6) and a dockerin domain. To study the role of the binding modules on the activity of XynZ, different variants with the CBM6 attached to the catalytic domain at its C-terminal (XynZ-CB) and N-terminal (XynZ-BC), and the CBM22 attached at N-terminus (XynZ-B'C) were expressed in Escherichia coli at levels around 30% of the total cell proteins. The activities of XynZ-BC, XynZ-CB and XynZ-B'C were 4200, 4180 and 20,700U μM(-1) against birchwood xylan, respectively. Substrate binding studies showed that in case of XynZ-BC and XynZ-CB the substrate birchwood xylan remaining unbound were 51 and 52%, respectively, whereas in the case of XynZ-B'C the substrate remaining unbound was 39% under the assay conditions used. The molecular docking studies showed that the binding site of CBM22 in XynZ-B'C is more exposed and thus available for substrate binding as compared to the tunnel shape binding pocket produced in XynZ-BC and thus hindering the substrate binding. The substrate binding data for the two constructs are in agreement with this explanation.
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21
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Shifting the optimum pH of Bacillus circulans xylanase towards acidic side by introducing arginine. BIOTECHNOL BIOPROC E 2013. [DOI: 10.1007/s12257-012-0455-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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22
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Xu H, Zhang F, Shang H, Li X, Wang J, Qiao D, Cao Y. Alkalophilic adaptation of XynB endoxylanase from Aspergillus niger via rational design of pKa of catalytic residues. J Biosci Bioeng 2013; 115:618-22. [PMID: 23290994 DOI: 10.1016/j.jbiosc.2012.12.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 11/22/2012] [Accepted: 12/05/2012] [Indexed: 11/18/2022]
Abstract
Based on the strategy of changing pH-stability profiles by altering pKa values of catalytic residues, rational protein engineering was applied to improve alkalophilic adaptation of Aspergillus niger endoxylanase XynB. Computational predictions and molecular modeling were carried out using PROPKA server and SWISS-MODEL server, respectively. Three endoxylanase mutant of S108V, N151E, and Q178R, in which the pKa values of either catalytic glutamate residues shifted, were generated. In agreement with expectation, the variant of Q178R improved alkalophilic performances. The mutant Q178R raised the optimum pH of XynB from 5.5 to 6.0 and retained 37% of the maximum activity at pH 8.0. Interestingly, the pKa values of Glu84 and Glu175 in Q178R are 7.91 and 6.32, respectively. The pKa of Glu175 is lower than that of Glu84, as opposed to the fact that the pKa of Glu84 is lower than that of Glu175 in other GH11 xylanases. It indicated that Glu175 may convert into a nucleophile residue and Glu84 into an acid/base residue.
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Affiliation(s)
- Hui Xu
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, PR China
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23
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24
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25
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Zheng B, Yang W, Zhao X, Wang Y, Lou Z, Rao Z, Feng Y. Crystal structure of hyperthermophilic endo-β-1,4-glucanase: implications for catalytic mechanism and thermostability. J Biol Chem 2011; 287:8336-46. [PMID: 22128157 DOI: 10.1074/jbc.m111.266346] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Endo-β-1,4-glucanase from thermophilic Fervidobacterium nodosum Rt17-B1 (FnCel5A), a new member of glycosyl hydrolase family 5, is highly thermostable and exhibits the highest activity on carboxymethylcellulose among the reported homologues. To understand the structural basis for the thermostability and catalytic mechanism, we report here the crystal structures of FnCel5A and the complex with glucose at atomic resolution. FnCel5A exhibited a (β/α)(8)-barrel structure typical of clan GH-A of the glycoside hydrolase families with a large and deep catalytic pocket located in the C-terminal end of the β-strands that may permit substrate access. A comparison of the structure of FnCel5A with related structures from thermopile Clostridium thermocellum, mesophile Clostridium cellulolyticum, and psychrophile Pseudoalteromonas haloplanktis showed significant differences in intramolecular interactions (salt bridges and hydrogen bonds) that may account for the difference in their thermostabilities. The substrate complex structure in combination with a mutagenesis analysis of the catalytic residues implicates a distinctive catalytic module Glu(167)-His(226)-Glu(283), which suggests that the histidine may function as an intermediate for the electron transfer network between the typical Glu-Glu catalytic module. Further investigation suggested that the aromatic residues Trp(61), Trp(204), Phe(231), and Trp(240) as well as polar residues Asn(51), His(127), Tyr(228), and His(235) in the active site not only participated in substrate binding but also provided a unique microenvironment suitable for catalysis. These results provide substantial insight into the unique characteristics of FnCel5A for catalysis and adaptation to extreme temperature.
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Affiliation(s)
- Baisong Zheng
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun 130023, China
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26
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Badieyan S, Bevan DR, Zhang C. Study and design of stability in GH5 cellulases. Biotechnol Bioeng 2011; 109:31-44. [PMID: 21809329 DOI: 10.1002/bit.23280] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 06/30/2011] [Accepted: 07/11/2011] [Indexed: 11/07/2022]
Abstract
Thermostable enzymes that hydrolyze lignocellulosic materials provide potential advantages in process configuration and enhancement of production efficiency over their mesophilic counterparts in the bioethanol industry. In this study, the dynamics of β-1,4-endoglucanases (EC: 3.2.1.4) from family 5 of glycoside hydrolases (GH5) were investigated computationally. The conformational flexibility of 12 GH5 cellulases, ranging from psychrophilic to hyperthermophilic, was investigated by molecular dynamics (MD) simulations at elevated temperatures. The results indicated that the protein flexibility and optimum activity temperatures are appreciably correlated. Intra-protein interactions, packing density and solvent accessible area were further examined in crystal structures to investigate factors that are possibly involved in higher rigidity of thermostable cellulases. The MD simulations and the rules learned from analyses of stabilizing factors were used in design of mutations toward the thermostabilization of cellulase C, one of the GH5 endoglucanases. This enzyme was successfully stabilized both chemically and thermally by introduction of a new disulfide cross-link to its highly mobile 56-amino acid subdomain.
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Affiliation(s)
- Somayesadat Badieyan
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
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27
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Bomble YJ, Beckham GT, Matthews JF, Nimlos MR, Himmel ME, Crowley MF. Modeling the self-assembly of the cellulosome enzyme complex. J Biol Chem 2011; 286:5614-23. [PMID: 21098021 PMCID: PMC3037675 DOI: 10.1074/jbc.m110.186031] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 11/16/2010] [Indexed: 11/06/2022] Open
Abstract
Most bacteria use free enzymes to degrade plant cell walls in nature. However, some bacteria have adopted a different strategy wherein enzymes can either be free or tethered on a protein scaffold forming a complex called a cellulosome. The study of the structure and mechanism of these large macromolecular complexes is an active and ongoing research topic, with the goal of finding ways to improve biomass conversion using cellulosomes. Several mechanisms involved in cellulosome formation remain unknown, including how cellulosomal enzymes assemble on the scaffoldin and what governs the population of cellulosomes created during self-assembly. Here, we present a coarse-grained model to study the self-assembly of cellulosomes. The model captures most of the physical characteristics of three cellulosomal enzymes (Cel5B, CelS, and CbhA) and the scaffoldin (CipA) from Clostridium thermocellum. The protein structures are represented by beads connected by restraints to mimic the flexibility and shapes of these proteins. From a large simulation set, the assembly of cellulosomal enzyme complexes is shown to be dominated by their shape and modularity. The multimodular enzyme, CbhA, binds statistically more frequently to the scaffoldin than CelS or Cel5B. The enhanced binding is attributed to the flexible nature and multimodularity of this enzyme, providing a longer residence time around the scaffoldin. The characterization of the factors influencing the cellulosome assembly process may enable new strategies to create designers cellulosomes.
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Affiliation(s)
- Yannick J Bomble
- Biosciences Center, Colorado School of Mines, Golden, Colorado 80401, USA.
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Pereira JH, Chen Z, McAndrew RP, Sapra R, Chhabra SR, Sale KL, Simmons BA, Adams PD. Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima. J Struct Biol 2010; 172:372-9. [DOI: 10.1016/j.jsb.2010.06.018] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 06/16/2010] [Accepted: 06/23/2010] [Indexed: 11/29/2022]
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Barbier P, Dorléans A, Devred F, Sanz L, Allegro D, Alfonso C, Knossow M, Peyrot V, Andreu JM. Stathmin and interfacial microtubule inhibitors recognize a naturally curved conformation of tubulin dimers. J Biol Chem 2010; 285:31672-81. [PMID: 20675373 PMCID: PMC2951239 DOI: 10.1074/jbc.m110.141929] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Tubulin is able to switch between a straight microtubule-like structure and a curved structure in complex with the stathmin-like domain of the RB3 protein (T(2)RB3). GTP hydrolysis following microtubule assembly induces protofilament curvature and disassembly. The conformation of the labile tubulin heterodimers is unknown. One important question is whether free GDP-tubulin dimers are straightened by GTP binding or if GTP-tubulin is also curved and switches into a straight conformation upon assembly. We have obtained insight into the bending flexibility of tubulin by analyzing the interplay of tubulin-stathmin association with the binding of several small molecule inhibitors to the colchicine domain at the tubulin intradimer interface, combining structural and biochemical approaches. The crystal structures of T(2)RB3 complexes with the chiral R and S isomers of ethyl-5-amino-2-methyl-1,2-dihydro-3-phenylpyrido[3,4-b]pyrazin-7-yl-carbamate, show that their binding site overlaps with colchicine ring A and that both complexes have the same curvature as unliganded T(2)RB3. The binding of these ligands is incompatible with a straight tubulin structure in microtubules. Analytical ultracentrifugation and binding measurements show that tubulin-stathmin associations (T(2)RB3, T(2)Stath) and binding of ligands (R, S, TN-16, or the colchicine analogue MTC) are thermodynamically independent from one another, irrespective of tubulin being bound to GTP or GDP. The fact that the interfacial ligands bind equally well to tubulin dimers or stathmin complexes supports a bent conformation of the free tubulin dimers. It is tempting to speculate that stathmin evolved to recognize curved structures in unassembled and disassembling tubulin, thus regulating microtubule assembly.
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Affiliation(s)
- Pascale Barbier
- From INSERM UMR 911, Centre de Recherche en Oncologie Biologique et Oncopharmacologie, Aix-Marseille Université, Faculté de Pharmacie, 27 bd Jean Moulin, 13385 Marseille Cedex 05, France, , To whom correspondence may be addressed. E-mail:
| | - Audrey Dorléans
- the Laboratoire d'Enzymologie et Biochimie Structurales, CNRS UPR3082, 91198 Gif sur Yvette, France, and
| | - Francois Devred
- From INSERM UMR 911, Centre de Recherche en Oncologie Biologique et Oncopharmacologie, Aix-Marseille Université, Faculté de Pharmacie, 27 bd Jean Moulin, 13385 Marseille Cedex 05, France
| | - Laura Sanz
- the Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Diane Allegro
- From INSERM UMR 911, Centre de Recherche en Oncologie Biologique et Oncopharmacologie, Aix-Marseille Université, Faculté de Pharmacie, 27 bd Jean Moulin, 13385 Marseille Cedex 05, France
| | - Carlos Alfonso
- the Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Marcel Knossow
- the Laboratoire d'Enzymologie et Biochimie Structurales, CNRS UPR3082, 91198 Gif sur Yvette, France, and
| | - Vincent Peyrot
- From INSERM UMR 911, Centre de Recherche en Oncologie Biologique et Oncopharmacologie, Aix-Marseille Université, Faculté de Pharmacie, 27 bd Jean Moulin, 13385 Marseille Cedex 05, France
| | - Jose M. Andreu
- the Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain, To whom correspondence may be addressed. E-mail:
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Turnbaugh PJ, Henrissat B, Gordon JI. Viewing the human microbiome through three-dimensional glasses: integrating structural and functional studies to better define the properties of myriad carbohydrate-active enzymes. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1261-4. [PMID: 20944220 PMCID: PMC2954214 DOI: 10.1107/s1744309110029088] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Accepted: 07/21/2010] [Indexed: 12/13/2022]
Abstract
Recent studies have provided an unprecedented view of the trillions of microbes associated with the human body. The human microbiome harbors tremendous diversity at multiple levels: the species that colonize each individual and each body habitat; the genes that are found in each organism's genome; the expression of these genes and the interactions and activities of their protein products. The sources of this diversity are wide-ranging and reflect both environmental and host factors. A major challenge moving forward is defining the precise functions of members of various families of proteins represented in our microbiomes, including the highly diverse carbohydrate-active enzymes (CAZymes) involved in numerous biologically important chemical transformations, such as the degradation of complex dietary polysaccharides. Coupling metagenomic analyses to structural genomics initiatives and to biochemical and other functional assays of CAZymes will be essential for determining how these as well as other microbiome-encoded proteins operate to shape the properties of microbial communities and their human hosts.
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Affiliation(s)
- Peter J. Turnbaugh
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Marseille, France
| | - Jeffrey I. Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63108, USA
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Yi X, Shi Y, Xu H, Li W, Xie J, Yu R, Zhu J, Cao Y, Qiao D. Hyperexpression of two Aspergillus Niger Xylanase Genes in Escherichia Coli and Characterization of the Gene Products. Braz J Microbiol 2010; 41:778-86. [PMID: 24031555 PMCID: PMC3768633 DOI: 10.1590/s1517-83822010000300030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Revised: 10/07/2009] [Accepted: 02/18/2010] [Indexed: 11/22/2022] Open
Abstract
The analysis of individual gene product should enable to clarify the role of a particular enzyme in a complex xylanase system of A. niger. The two genes encoding precursors of co-produced endo-1,4-β-D-xylanases, xynA1 and xynB, were isolated from Aspergillus niger SCTCC 400264 (SCTCC, China) by using RT-PCR technique and then successfully expressed in Escherichia coli BL21. The nucleotide sequences of the xynA1 and xynB genes revealed that they were only 52.5% homology to each other. Characterization of the recombinant enzymes revealed the different properties: the specific activity of recombinant XYNA1 was 16.58 U/mg compared to 1201.7 U/mg for recombinant XYNB; The optimum temperature and pH of the recombinant XYNA1 were 35 °C and 3.0, respectively, whereas the corresponding values for the recombinant XYNB were 55 °C and 5.0, respectively; The recombinant XYNB showed much more thermostability than recombinant XYNA1; The recombinant XYNB showed 94% of maximal activity after incubating in water for 60 min at 60 °C compared to no activity for recombinant XYNA1. Various metal ions had different effects on activity between the two recombinant xylanases.
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Affiliation(s)
- Xiuli Yi
- College of Life Science , Sichuan University, Chengdu 610064 , China ; Microbiology and Metabolic Engineering key Laboratory of Sichuan Province , Chengdu 610064 , China
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Najmudin S, Pinheiro BA, Prates JAM, Gilbert HJ, Romão MJ, Fontes CMGA. Putting an N-terminal end to the Clostridium thermocellum xylanase Xyn10B story: crystal structure of the CBM22-1-GH10 modules complexed with xylohexaose. J Struct Biol 2010; 172:353-62. [PMID: 20682344 DOI: 10.1016/j.jsb.2010.07.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 07/26/2010] [Accepted: 07/29/2010] [Indexed: 10/19/2022]
Abstract
In general, plant cell wall degrading enzymes are modular proteins containing catalytic domains linked to one or more non-catalytic carbohydrate-binding modules (CBMs). Xyn10B from Clostridium thermocellum is a typical modular enzyme containing an N-terminal family 22 CBM (CBM22-1), a family 10 glycoside hydrolase catalytic domain (GH10), a second CBM22 (CBM22-2), a dockerin sequence and a C-terminal family 1 carbohydrate esterase (CE1) catalytic domain. The structure of the N-terminal bi-modular CBM22-1-GH10 component of Xyn10B has been determined using a SeMet derivative by SAD to 2.5Å. The data was extended to 2.0Å for the non-SeMet mutant complexed with xylohexaose. CBM22-1-GH10 is a 60kDa protein with an E337A mutation to render the GH10 subunit inactive. Three of the six xylose residues of xylohexaose are shown to be bound in the inactivated GH10 substrate binding cleft, with the other three sugars presumably disordered in the solvent channel. The protein is a dimer in the asymmetric unit with extensive surface contacts between the two GH10 modules and between the CBM22-1 and GH10 modules. Residues from helix H4 of the GH10 module provide the major contacts by fitting into the minor groove of the CBM22-1 module. The orientation of CBM22-1 is such that it would allow the substrate to be loosely bound and subsequently delivered to the active site in a processive manner.
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Affiliation(s)
- Shabir Najmudin
- CIISA - Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal.
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Comparative analyses of two thermophilic enzymes exhibiting both beta-1,4 mannosidic and beta-1,4 glucosidic cleavage activities from Caldanaerobius polysaccharolyticus. J Bacteriol 2010; 192:4111-21. [PMID: 20562312 DOI: 10.1128/jb.00257-10] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The hydrolysis of polysaccharides containing mannan requires endo-1,4-beta-mannanase and 1,4-beta-mannosidase activities. In the current report, the biochemical properties of two endo-beta-1,4-mannanases (Man5A and Man5B) from Caldanaerobius polysaccharolyticus were studied. Man5A is composed of an N-terminal signal peptide (SP), a catalytic domain, two carbohydrate-binding modules (CBMs), and three surface layer homology (SLH) repeats, whereas Man5B lacks the SP, CBMs, and SLH repeats. To gain insights into how the two glycoside hydrolase family 5 (GH5) enzymes may aid the bacterium in energy acquisition and also the potential application of the two enzymes in the biofuel industry, two derivatives of Man5A (Man5A-TM1 [TM1 stands for truncational mutant 1], which lacks the SP and SLH repeats, and Man5A-TM2, which lacks the SP, CBMs, and SLH repeats) and the wild-type Man5B were biochemically analyzed. The Man5A derivatives displayed endo-1,4-beta-mannanase and endo-1,4-beta-glucanase activities and hydrolyzed oligosaccharides with a degree of polymerization (DP) of 4 or higher. Man5B exhibited endo-1,4-beta-mannanase activity and little endo-1,4-beta-glucanase activity; however, this enzyme also exhibited 1,4-beta-mannosidase and cellodextrinase activities. Man5A-TM1, compared to either Man5A-TM2 or Man5B, had higher catalytic activity with soluble and insoluble polysaccharides, indicating that the CBMs enhance catalysis of Man5A. Furthermore, Man5A-TM1 acted synergistically with Man5B in the hydrolysis of beta-mannan and carboxymethyl cellulose. The versatility of the two enzymes, therefore, makes them a resource for depolymerization of mannan-containing polysaccharides in the biofuel industry. Furthermore, on the basis of the biochemical and genomic data, a molecular mechanism for utilization of mannan-containing nutrients by C. polysaccharolyticus is proposed.
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An alkaline active xylanase: Insights into mechanisms of high pH catalytic adaptation. Biochimie 2009; 91:1187-96. [DOI: 10.1016/j.biochi.2009.06.017] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Accepted: 06/18/2009] [Indexed: 11/21/2022]
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35
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Variations in the colchicine-binding domain provide insight into the structural switch of tubulin. Proc Natl Acad Sci U S A 2009; 106:13775-9. [PMID: 19666559 DOI: 10.1073/pnas.0904223106] [Citation(s) in RCA: 214] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Structural changes occur in the alphabeta-tubulin heterodimer during the microtubule assembly/disassembly cycle. Their most prominent feature is a transition from a straight, microtubular structure to a curved structure. There is a broad range of small molecule compounds that disturbs the microtubule cycle, a class of which targets the colchicine-binding site and prevents microtubule assembly. This class includes compounds with very different chemical structures, and it is presently unknown whether they prevent tubulin polymerization by the same mechanism. To address this issue, we have determined the structures of tubulin complexed with a set of such ligands and show that they interfere with several of the movements of tubulin subunits structural elements upon its transition from curved to straight. We also determined the structure of tubulin unliganded at the colchicine site; this reveals that a beta-tubulin loop (termed T7) flips into this site. As with colchicine site ligands, this prevents a helix which is at the interface with alpha-tubulin from stacking onto a beta-tubulin beta sheet as in straight protofilaments. Whereas in the presence of these ligands the interference with microtubule assembly gets frozen, by flipping in and out the beta-subunit T7 loop participates in a reversible way in the resistance to straightening that opposes microtubule assembly. Our results suggest that it thereby contributes to microtubule dynamic instability.
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Zheng B, Yang W, Wang Y, Feng Y, Lou Z. Crystallization and preliminary crystallographic analysis of thermophilic cellulase from Fervidobacterium nodosum Rt17-B1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:219-22. [PMID: 19255469 DOI: 10.1107/s1744309109001316] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Accepted: 01/12/2009] [Indexed: 11/10/2022]
Abstract
FnCel5A, a thermostable endoglucanase, is a member of glycohydrolase family 5 which catalyzes the hydrolysis of cellulose to glucose in the thermophilic bacterium Fervidobacterium nodosum Rt17-B1. FnCel5A is particularly interesting because of its high thermostability (T(opt) = 353 K, half-life 48 h) and its high specific activity towards carboxymethylcellulose. These properties make FnCel5A an attractive target for protein engineering to improve cellulase activity. In order to resolve the crystal structure of FnCel5A and to gain a better understanding of its biological function, recombinant FnCel5A was expressed, purified and crystallized at 291 K using NaH(2)PO(4)/KH(2)PO(4) as a precipitant. A 2.4 A resolution native data set was collected from a single flash-cooled crystal (100 K) using 20%(v/v) glycerol as a cryoprotectant. These crystals belonged to space group P2(1)2(1)2, with unit-cell parameters a = 53.5, b = 81.7, c = 85.2 A, alpha = beta = gamma = 90 degrees . One molecule is assumed to be present per asymmetric unit, which gives a Matthews coefficient of 2.5 A(3) Da(-1). A data set was also collected to 1.7 A resolution from a selenomethionyl derivative; it belonged to space group P2(1)2(1)2(1) with the same unit-cell parameters as the native crystals.
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Affiliation(s)
- Baisong Zheng
- Tsinghua University, Beijing, People's Republic of China
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Polysaccharide hydrolase folds diversity of structure and convergence of function. Appl Biochem Biotechnol 2008; 63-65:315-25. [PMID: 18576090 DOI: 10.1007/bf02920433] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Polysaccharide glycosyl hydrolases are a group of enzymes that hydrolyze the glycosidic bond between carbohydrates or between a carbohydrate and a noncarbohydrate moiety. Here we illustrate that traditional schemes for grouping enzymes, such as by substrate specificity or by organism of origin, are not appropriate when thinking of structure-function relationships and protein engineering. Instead, sequence comparisons and structural studies reveal that enzymes with diverse specificities and from diverse organisms can be placed into groups among which mechanisms are largely conserved and insights are likely to be transferrable. In particular, we illustrate how enzymes have been grouped using protein sequence alignment algorithms and hydrophobic cluster analysis. Unfortunately for those who seek to improve cellulase function by design, cellulases are distributed throughout glycosyl hydrolase Families 1,5,6,7,9, and 45. These cellulase families include members from widely different fold types, i.e., the TIM-barrel, betaalphabeta-barrel variant (a TIM-barrel-like structure that is imperfectly superimposable on the TIM-barrel template), beta-sandwich, and alpha-helix circular array. This diversity in cellulase fold structure must be taken into account when considering the transfer and application of design strategies between various cellulases.
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Najmudin S, Pinheiro BA, Romão MJ, Prates JAM, Fontes CMGA. Purification, crystallization and crystallographic analysis of Clostridium thermocellum endo-1,4-beta-D-xylanase 10B in complex with xylohexaose. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:715-8. [PMID: 18678939 PMCID: PMC2494957 DOI: 10.1107/s1744309108019696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Accepted: 06/27/2008] [Indexed: 11/10/2022]
Abstract
The cellulosome of Clostridium thermocellum is a highly organized multi-enzyme complex of cellulases and hemicellulases involved in the hydrolysis of plant cell-wall polysaccharides. The bifunctional multi-modular xylanase Xyn10B is one of the hemicellulase components of the C. thermocellum cellulosome. The enzyme contains an internal glycoside hydrolase family 10 catalytic domain (GH10) and a C-terminal family 1 carbohydrate esterase domain (CE1). The N-terminal moiety of Xyn10B (residues 32-551), comprising a carbohydrate-binding module (CBM22-1) and the GH10 E337A mutant, was crystallized in complex with xylohexaose. The crystals belong to the trigonal space group P3(2)21 and contain a dimer in the asymmetric unit. The crystals diffracted to beyond 2.0 A resolution.
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Affiliation(s)
- Shabir Najmudin
- REQUIMTE, Departamento de Química, FCT-UNL, 2829-516 Caparica, Portugal
| | - Benedita A. Pinheiro
- CIISA – Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Maria J. Romão
- REQUIMTE, Departamento de Química, FCT-UNL, 2829-516 Caparica, Portugal
| | - José A. M. Prates
- CIISA – Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Carlos M. G. A. Fontes
- CIISA – Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
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Opassiri R, Pomthong B, Akiyama T, Nakphaichit M, Onkoksoong T, Ketudat Cairns M, Ketudat Cairns J. A stress-induced rice (Oryza sativa L.) beta-glucosidase represents a new subfamily of glycosyl hydrolase family 5 containing a fascin-like domain. Biochem J 2007; 408:241-9. [PMID: 17705786 PMCID: PMC2267349 DOI: 10.1042/bj20070734] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
GH5BG, the cDNA for a stress-induced GH5 (glycosyl hydrolase family 5) beta-glucosidase, was cloned from rice (Oryza sativa L.) seedlings. The GH5BG cDNA encodes a 510-amino-acid precursor protein that comprises 19 amino acids of prepeptide and 491 amino acids of mature protein. The protein was predicted to be extracellular. The mature protein is a member of a plant-specific subgroup of the GH5 exoglucanase subfamily that contains two major domains, a beta-1,3-exoglucanase-like domain and a fascin-like domain that is not commonly found in plant enzymes. The GH5BG mRNA is highly expressed in the shoot during germination and in leaf sheaths of mature plants. The GH5BG was up-regulated in response to salt stress, submergence stress, methyl jasmonate and abscisic acid in rice seedlings. A GUS (glucuronidase) reporter tagged at the C-terminus of GH5BG was found to be secreted to the apoplast when expressed in onion (Allium cepa) cells. A thioredoxin fusion protein produced from the GH5BG cDNA in Escherichia coli hydrolysed various pNP (p-nitrophenyl) glycosides, including beta-D-glucoside, alpha-L-arabinoside, beta-D-fucoside, beta-D-galactoside, beta-D-xyloside and beta-D-cellobioside, as well as beta-(1,4)-linked glucose oligosaccharides and beta-(1,3)-linked disaccharide (laminaribiose). The catalytic efficiency (kcat/K(m)) for hydrolysis of beta-(1,4)-linked oligosaccharides by the enzyme remained constant as the DP (degree of polymerization) increased from 3 to 5. This substrate specificity is significantly different from fungal GH5 exoglucanases, such as the exo-beta-(1,3)-glucanase of the yeast Candida albicans, which may correlate with a marked reduction in a loop that makes up the active-site wall in the Candida enzyme.
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Affiliation(s)
- Rodjana Opassiri
- *School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Busarakum Pomthong
- *School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Takashi Akiyama
- †Department of Low-Temperature Science, National Agricultural Research Center for Hokkaido Region, Sapporo 062-8555, Japan
| | - Massalin Nakphaichit
- ‡School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Tassanee Onkoksoong
- *School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Mariena Ketudat Cairns
- ‡School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - James R. Ketudat Cairns
- *School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
- To whom correspondence should be addressed (email )
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OmPraba G, Velmurugan D, Arumugam P, Govindasamy V, Kalaichelvan PT. Homology Model of a Novel Thermostable Xylanase fromBacillus subtilis-AK1. J Biomol Struct Dyn 2007; 25:311-20. [DOI: 10.1080/07391102.2007.10507179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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41
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Enhancement of the thermostability and hydrolytic activity of GH10 xylanase by module shuffling between Cellulomonas fimi Cex and Thermomonospora alba XylA. World J Microbiol Biotechnol 2007. [DOI: 10.1007/s11274-006-9263-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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42
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Sriprang R, Asano K, Gobsuk J, Tanapongpipat S, Champreda V, Eurwilaichitr L. Improvement of thermostability of fungal xylanase by using site-directed mutagenesis. J Biotechnol 2006; 126:454-62. [PMID: 16757052 DOI: 10.1016/j.jbiotec.2006.04.031] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Revised: 12/13/2005] [Accepted: 04/22/2006] [Indexed: 10/24/2022]
Abstract
Replacing several serine and threonine residues on the Ser/Thr surface of the xylanase from Aspergillus niger BCC14405 with four and five arginines effectively increases the thermostability of the enzyme. The modified enzymes showed 80% of maximal activity after incubating in xylan substrate for 2h at 50 degrees C compared to only 15% activity for wild-type enzyme. The half-life of the mutated enzymes increased to 257+/-16 and 285+/-10 min for the four- and five-arginine mutants, respectively, compared to 14+/-1 min for the wild-type enzyme. Thus, the arginine substitutions effectively increase stability by 18-20-fold. Kinetic parameters of the four-arginine-substitution enzyme were maintained at the level of the wild-type enzyme with the K(m) and V(max) values of 8.3+/-0.1 mgml(-1) and 9556+/-66 (n=3) U mg(-1) protein, respectively. The five-arginine-substitution enzyme showed only slight alteration in K(m) and V(max) with K(m) of 11.7+/-1.7 mgml(-1) and V(max) of 8502+/-65 Umg(-1) protein, indicating lower substrate affinity and catalytic rate. Our study demonstrated that properly introduced arginine residues on the Ser/Thr surface of xylanase family 11 might be very effective in improvement of enzyme thermostability.
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Affiliation(s)
- Rutchadaporn Sriprang
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Patumthani 12120, Thailand.
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43
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Wakelyn P, Bertoniere N, French A, Thibodeaux D, Triplett B, Rousselle MA, Goynes W, Edwards J, Hunter L, McAlister D, Gamble G. Cotton Fibers. HANDBOOK OF FIBER CHEMISTRY, THIRD EDITION 2006. [DOI: 10.1201/9781420015270.ch9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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44
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Manikandan K, Bhardwaj A, Gupta N, Lokanath NK, Ghosh A, Reddy VS, Ramakumar S. Crystal structures of native and xylosaccharide-bound alkali thermostable xylanase from an alkalophilic Bacillus sp. NG-27: structural insights into alkalophilicity and implications for adaptation to polyextreme conditions. Protein Sci 2006; 15:1951-60. [PMID: 16823036 PMCID: PMC2242578 DOI: 10.1110/ps.062220206] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Crystal structures are known for several glycosyl hydrolase family 10 (GH10) xylanases. However, none of them is from an alkalophilic organism that can grow in alkaline conditions. We have determined the crystal structures at 2.2 Angstroms of a GH10 extracellular endoxylanase (BSX) from an alkalophilic Bacillus sp. NG-27, for the native and the complex enzyme with xylosaccharides. The industrially important enzyme is optimally active and stable at 343 K and at a pH of 8.4. Comparison of the structure of BSX with those of other thermostable GH10 xylanases optimally active at acidic or close to neutral pH showed that the solvent-exposed acidic amino acids, Asp and Glu, are markedly enhanced in BSX, while solvent-exposed Asn was noticeably depleted. The BSX crystal structure when compared with putative three-dimensional homology models of other extracellular alkalophilic GH10 xylanases from alkalophilic organisms suggests that a protein surface rich in acidic residues may be an important feature common to these alkali thermostable enzymes. A comparison of the surface features of BSX and of halophilic proteins allowed us to predict the activity of BSX at high salt concentrations, which we verified through experiments. This offered us important lessons in the polyextremophilicity of proteins, where understanding the structural features of a protein stable in one set of extreme conditions provided clues about the activity of the protein in other extreme conditions. The work brings to the fore the role of the nature and composition of solvent-exposed residues in the adaptation of enzymes to polyextreme conditions, as in BSX.
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45
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Kumasaka T, Kaneko T, Morokuma C, Yatsunami R, Sato T, Nakamura S, Tanaka N. Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8. Proteins 2005; 61:999-1009. [PMID: 16247799 DOI: 10.1002/prot.20700] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The crystal structure of xylanase 10B from Thermotoga maritima MSB8 (TmxB), a hyperthermostable xylanase, has been solved in its native form and in complex with xylobiose or xylotriose at 1.8 A resolution. In order to gain insight into the substrate subsite and the molecular features for thermal stability, we compared TmxB with family 10 xylanase structures from nine microorganisms. As expected, TmxB folds into a (beta/alpha)8-barrel structure, which is common among the glycoside hydrolase family 10. The enzyme active site and the environment surrounding the xylooligosaccharide of TmxB are highly similar to those of family 10 xylanases. However, only two xylose moieties were found in its binding pocket from the TmxB-xylotriose complex structure. This finding suggests that TmxB could be a potential biocatalyst for the large-scale production of xylobiose. The result of structural analyses also indicated that TmxB possesses some additional features that account for its thermostability. In particular, clusters of aromatic residues together with a lack of exposed hydrophobic residues are characteristic of the TmxB structure. TmxB has also a significant number of ion pairs on the protein surface that are not found in other thermophilic family 10 xylanases.
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46
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Manikandan K, Bhardwaj A, Ghosh A, Reddy VS, Ramakumar S. Crystallization and preliminary X-ray study of a family 10 alkali-thermostable xylanase from alkalophilic Bacillus sp. strain NG-27. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:747-9. [PMID: 16511146 PMCID: PMC1952343 DOI: 10.1107/s1744309105020518] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2005] [Accepted: 06/28/2005] [Indexed: 11/10/2022]
Abstract
Xylanases (EC 3.2.1.8) catalyze the hydrolysis of beta-1,4-glycosidic linkages within xylan, a major hemicellulose component in the biosphere. The extracellular endoxylanase (XylnA) from the alkalophilic Bacillus sp. strain NG-27 belongs to family 10 of the glycoside hydrolases. It is active at 343 K and pH 8.4. Moreover, it has attractive features from the point of view of utilization in the paper pulp, animal feed and baking industries since it is an alkali-thermostable protein. In this study, XylnA was purified from the native host source and crystallized by the hanging-drop vapour-diffusion method. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 174.5, b = 54.7, c = 131.5 A, beta = 131.2 degrees, and diffract to better than 2.2 A resolution.
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Affiliation(s)
- K. Manikandan
- Department of Physics, Indian Institute of Science, Bangalore 560 012, India
| | - Amit Bhardwaj
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India
| | - Amit Ghosh
- Institute of Microbial Technology, Sector 39-A, Chandigarh 160 036, India
| | - V. S. Reddy
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India
| | - S. Ramakumar
- Department of Physics, Indian Institute of Science, Bangalore 560 012, India
- Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012, India
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47
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De Lemos Esteves F, Gouders T, Lamotte-Brasseur J, Rigali S, Frère JM. Improving the alkalophilic performances of the Xyl1 xylanase from Streptomyces sp. S38: structural comparison and mutational analysis. Protein Sci 2005; 14:292-302. [PMID: 15659364 PMCID: PMC2253399 DOI: 10.1110/ps.04978705] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Endo-beta-1,4-xylanases of the family 11 glycosyl-hydrolases are catalytically active over a wide range of pH. Xyl1 from Streptomyces sp. S38 belongs to this family, and its optimum pH for enzymatic activity is 6. Xyn11 from Bacillus agaradhaerens and XylJ from Bacillus sp. 41M-1 share 85% sequence identity and have been described as highly alkalophilic enzymes. In an attempt to better understand the alkalophilic adaptation of xylanases, the three-dimensional structures of Xyn11 and Xyl1 were compared. This comparison highlighted an increased number of salt-bridges and the presence of more charged residues in the catalytic cleft as well as an eight-residue-longer loop in the alkalophilic xylanase Xyn11. Some of these charges were introduced in the structure of Xyl1 by site-directed mutagenesis with substitutions Y16D, S18E, G50R, N92D, A135Q, E139K, and Y186E. Furthermore, the eight additional loop residues of Xyn11 were introduced in the homologous loop of Xyl1. In addition, the coding sequence of the XylJ catalytic domain was synthesized by recursive PCR, expressed in a Streptomyces host, purified, and characterized together with the Xyl1 mutants. The Y186E substitution inactivated Xyl1, but the activity was restored when this mutation was combined with the G50R or S18E substitutions. Interestingly, the E139K mutation raised the optimum pH of Xyl1 from 6 to 7.5 but had no effect when combined with the N92D substitution. Modeling studies identified the possible formation of an interaction between the introduced lysine and the substrate, which could be eliminated by the formation of a putative salt-bridge in the N92D/E139K mutant.
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MESH Headings
- Amino Acid Sequence
- Bacillus/enzymology
- Catalytic Domain
- Cloning, Molecular
- DNA Mutational Analysis
- Endo-1,4-beta Xylanases/chemistry
- Endo-1,4-beta Xylanases/genetics
- Endo-1,4-beta Xylanases/physiology
- Hydrogen-Ion Concentration
- Models, Molecular
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Mutation
- Polymerase Chain Reaction
- Protein Conformation
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Recombination, Genetic
- Salts/chemistry
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Streptomyces/enzymology
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Affiliation(s)
- Frédéric De Lemos Esteves
- Centre d'Ingénierie des Protéines, Institut de Chimie, B6a, Université de Liège, Sart Tilman, B-4000 Liège, Belgium.
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48
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Murray KB, Taylor WR, Thornton JM. Toward the detection and validation of repeats in protein structure. Proteins 2005; 57:365-80. [PMID: 15340924 DOI: 10.1002/prot.20202] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We present a method called DAVROS to detect, localize, and validate repeating motifs in protein structure allowing for insertions and deletions. DAVROS uses the score matrix from a structural alignment program (SAP) to search for repeating motifs using an algorithm based on concepts from signal processing and the statistical properties of the alignments. The method was tested against a nonredundant Protein Data Bank, and each chain was assigned a score. For the top 50 chains ranked by score, 70% contain repeating motifs detected without error. These represent 14 types of fold covering alpha, beta, and alphabeta protein classes. A second data set comprising protein chains in different sequence families for triosephosphate isomerase (TIM) barrel, leucine-rich repeat (LRR), trefoil, and alpha-alpha barrel folds was used to assess the ability of DAVROS to detect all motifs within a specific fold. For the second test set, the percentage of motifs detected was highest for the LRR chains (88.7%) and least for the TIM barrels (60%). This variability results from the regularity of the LRR motif compared to the alphabeta units of the TIM barrel, which generally have many more indels. These reduce the strength of the repeat signal in the SAP matrix, making repeat detection more difficult.
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Affiliation(s)
- Kevin B Murray
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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49
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Fujimoto Z, Usui K, Kondo Y, Yasui K, Kawai K, Suzuki T. Crystallization and preliminary X-ray crystallographic studies of XynX, a family 10 xylanase from Aeromonas punctata ME-1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:255-7. [PMID: 16511010 PMCID: PMC1952265 DOI: 10.1107/s1744309105002058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Accepted: 01/20/2005] [Indexed: 11/10/2022]
Abstract
Xylanases catalyze the hydrolysis of beta-1,4-glycosidic linkages within the xylan backbone. XynX is a xylanase from Aeromonas punctata ME-1 and belongs to glycoside hydrolase family 10. While most xylanases show endo-type catalytic activities, XynX shows exo-like catalytic activities, selectively producing xylobiose from birchwood xylan. In this study, XynX was crystallized by the hanging-drop vapour-diffusion method. The crystals belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 79.0, b = 88.6, c = 93.2 A, and diffracted to beyond 1.8 A resolution.
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Affiliation(s)
- Zui Fujimoto
- Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan.
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50
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Collins T, Gerday C, Feller G. Xylanases, xylanase families and extremophilic xylanases. FEMS Microbiol Rev 2005; 29:3-23. [PMID: 15652973 DOI: 10.1016/j.femsre.2004.06.005] [Citation(s) in RCA: 1023] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2003] [Revised: 06/10/2004] [Accepted: 06/14/2004] [Indexed: 11/28/2022] Open
Abstract
Xylanases are hydrolytic enzymes which randomly cleave the beta 1,4 backbone of the complex plant cell wall polysaccharide xylan. Diverse forms of these enzymes exist, displaying varying folds, mechanisms of action, substrate specificities, hydrolytic activities (yields, rates and products) and physicochemical characteristics. Research has mainly focused on only two of the xylanase containing glycoside hydrolase families, namely families 10 and 11, yet enzymes with xylanase activity belonging to families 5, 7, 8 and 43 have also been identified and studied, albeit to a lesser extent. Driven by industrial demands for enzymes that can operate under process conditions, a number of extremophilic xylanases have been isolated, in particular those from thermophiles, alkaliphiles and acidiphiles, while little attention has been paid to cold-adapted xylanases. Here, the diverse physicochemical and functional characteristics, as well as the folds and mechanisms of action of all six xylanase containing families will be discussed. The adaptation strategies of the extremophilic xylanases isolated to date and the potential industrial applications of these enzymes will also be presented.
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Affiliation(s)
- Tony Collins
- Laboratory of Biochemistry, Institute of Chemistry B6, University of Liège, B-4000 Liège, Belgium.
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