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Chandravanshi M, Gogoi P, Kanaujia SP. Structural and thermodynamic correlation illuminates the selective transport mechanism of disaccharide α‐glycosides through ABC transporter. FEBS J 2019; 287:1576-1597. [DOI: 10.1111/febs.15093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 09/04/2019] [Accepted: 10/11/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Monika Chandravanshi
- Department of Biosciences and Bioengineering Indian Institute of Technology Guwahati India
| | - Prerana Gogoi
- Department of Biosciences and Bioengineering Indian Institute of Technology Guwahati India
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2
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Liu J, Liu Z, Jiang C, Mao X. Biochemical Characterization and Substrate Degradation Mode of a Novel α-Agarase from Catenovulum agarivorans. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:10373-10379. [PMID: 31453692 DOI: 10.1021/acs.jafc.9b03073] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Agarose can be hydrolyzed into agarooligosaccharides (AOSs) by α-agarase, which is an important enzyme for efficient saccharification of agarose or preparation of bioactive oligosaccharides from agarose. Although many β-agarases have been reported and characterized, there are only a few studies on α-agarases. Here, we cloned a novel α-agarase named CaLJ96 with a molecular weight of approximately 200 kDa belonging to glycoside hydrolase family 96 from Catenovulum agarivorans. CaLJ96 has good pH stability and exhibits maximum activity at 37 °C and pH 7.0. The hydrolyzed products of agarose by CaLJ96 are analyzed as agarobiose (A2), agarotetraose (A4), and agarohexaose (A6), in which A4 is the dominant product. CaLJ96 can hydrolyze agaropentaose (A5) into A2 and agarotriose (A3) and A6 into A2 and A4 but cannot act on A2, A3, or A4. This is the first report to characterize the α-agarase action on AOSs in detail. Therefore, CaLJ96 has potential for the manufacture of bioactive AOSs.
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Affiliation(s)
- Jie Liu
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Zhen Liu
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Chengcheng Jiang
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Xiangzhao Mao
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
- Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266237 , China
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3
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Gunnoo M, Cazade PA, Orlowski A, Chwastyk M, Liu H, Ta DT, Cieplak M, Nash M, Thompson D. Steered molecular dynamics simulations reveal the role of Ca 2+ in regulating mechanostability of cellulose-binding proteins. Phys Chem Chem Phys 2019; 20:22674-22680. [PMID: 30132772 DOI: 10.1039/c8cp00925b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The conversion of cellulosic biomass into biofuels requires degradation of the biomass into fermentable sugars. The most efficient natural cellulase system for carrying out this conversion is an extracellular multi-enzymatic complex named the cellulosome. In addition to temperature and pH stability, mechanical stability is important for functioning of cellulosome domains, and experimental techniques such as Single Molecule Force Spectroscopy (SMFS) have been used to measure the mechanical strength of several cellulosomal proteins. Molecular dynamics computer simulations provide complementary atomic-resolution quantitative maps of domain mechanical stability for identification of experimental leads for protein stabilization. In this study, we used multi-scale steered molecular dynamics computer simulations, benchmarked against new SMFS measurements, to measure the intermolecular contacts that confer high mechanical stability to a family 3 Carbohydrate Binding Module protein (CBM3) derived from the archetypal Clostridium thermocellum cellulosome. Our data predicts that electrostatic interactions in the calcium binding pocket modulate the mechanostability of the cellulose-binding module, which provides an additional design rule for the rational re-engineering of designer cellulosomes for biotechnology. Our data offers new molecular insights into the origins of mechanostability in cellulose binding domains and gives leads for synthesis of more robust cellulose-binding protein modules. On the other hand, simulations predict that insertion of a flexible strand can promote alternative unfolding pathways and dramatically reduce the mechanostability of the carbohydrate binding module, which gives routes to rational design of tailormade fingerprint complexes for force spectroscopy experiments.
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Affiliation(s)
- Melissabye Gunnoo
- Department of Physics, Bernal Institute, University of Limerick, V94 T9PX, Ireland.
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4
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Dhillon A, Sharma K, Rajulapati V, Goyal A. The multi-ligand binding first family 35 Carbohydrate Binding Module (CBM35) of Clostridium thermocellum targets rhamnogalacturonan I. Arch Biochem Biophys 2018; 654:194-208. [PMID: 30080990 DOI: 10.1016/j.abb.2018.07.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/25/2018] [Accepted: 07/27/2018] [Indexed: 11/24/2022]
Abstract
Carbohydrate Binding Modules (CBMs) targeting cellulose, xylan and mannan have been reported, however, a CBM targeting rhamnogalacturonan I (RG I) has never been identified. We had studied earlier a rhamnogalacturonan lyase (CtRGL) from Clostridium thermocellum that was associated with a family 35 CBM, Rgl-CBM35. In this study we show that Rgl-CBM35 displays binding with β-d-glucuronic acid (β-D-GlcpA), Δ4,5-anhydro-d-galactopyranosyluronic acid (Δ4,5-GalpA), rhamnogalacturonan I, arabinan, galactan, glucuronoxylans and arabinoxylans. Rgl-CBM35 contains a conserved ligand binding site in the loops known for binding β-D-GlcpA and Δ4,5-GalpA moiety of unsaturated RG I and pectic-oligosaccharides. Mutagenesis revealed that Asn118 plays an important role in binding β-D-GlcpA, Δ4,5-GalpA, sugarbeet arabinan and potato galactan at its conserved ligand binding site present in surface exposed loops. EDTA-treated Rgl-CBM35 showed no affinity towards β-D-GlcpA and Δ4,5-GalpA underscoring Ca2+ mediated ligand recognition. Contrastingly, the EDTA-treated Rgl-CBM35 and its mutant N118A displayed affinity for sugarbeet arabinan and potato galactan. The curtailed affinity of Y37A/N118A and R69A/N118A double mutants towards sugarbeet arabinan emphasized the presence of a second ligand binding site. Rgl-CBM35 is the first CBM reported to primarily target RG I and also is the first member of family 35 CBM possessing at least two ligand binding sites.
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Affiliation(s)
- Arun Dhillon
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Kedar Sharma
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Vikky Rajulapati
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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5
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Newmister SA, Li S, Garcia-Borràs M, Sanders JN, Yang S, Lowell AN, Yu F, Smith JL, Williams RM, Houk KN, Sherman DH. Structural basis of the Cope rearrangement and cyclization in hapalindole biogenesis. Nat Chem Biol 2018; 14:345-351. [PMID: 29531360 PMCID: PMC5880276 DOI: 10.1038/s41589-018-0003-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/17/2018] [Indexed: 11/09/2022]
Abstract
Hapalindole alkaloids are a structurally diverse class of cyanobacterial natural products defined by their varied polycyclic ring systems and diverse biological activities. These complex metabolites are generated from a common biosynthetic intermediate by the Stig cyclases in three mechanistic steps: a rare Cope rearrangement, 6-exo-trig cyclization, and electrophilic aromatic substitution. Here we report the structure of HpiC1, a Stig cyclase that catalyzes the formation of 12-epi-hapalindole U in vitro. The 1.5-Å structure revealed a dimeric assembly with two calcium ions per monomer and with the active sites located at the distal ends of the protein dimer. Mutational analysis and computational methods uncovered key residues for an acid-catalyzed [3,3]-sigmatropic rearrangement, as well as specific determinants that control the position of terminal electrophilic aromatic substitution, leading to a switch from hapalindole to fischerindole alkaloids.
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Affiliation(s)
- Sean A Newmister
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Shasha Li
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jacob N Sanders
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Song Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Andrew N Lowell
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Fengan Yu
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Robert M Williams
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA.
- University of Colorado Cancer Center, Aurora, CO, USA.
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
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6
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Aronsson A, Güler F, Petoukhov MV, Crennell SJ, Svergun DI, Linares-Pastén JA, Nordberg Karlsson E. Structural insights of Rm Xyn10A – A prebiotic-producing GH10 xylanase with a non-conserved aglycone binding region. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:292-306. [DOI: 10.1016/j.bbapap.2017.11.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 10/05/2017] [Accepted: 11/12/2017] [Indexed: 02/02/2023]
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7
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Zhang W, Xu J, Liu D, Liu H, Lu X, Yu W. Characterization of an α-agarase from Thalassomonas sp. LD5 and its hydrolysate. Appl Microbiol Biotechnol 2018; 102:2203-2212. [PMID: 29353307 DOI: 10.1007/s00253-018-8762-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 12/19/2017] [Accepted: 01/09/2018] [Indexed: 12/17/2022]
Abstract
It has been a long time since the first α-agarase was discovered. However, only two α-agarases have been cloned and partially characterized so far and the study of α-agarases has lagged far behind that of β-agarases. Here, we report an α-agarase, AgaD, cloned from marine bacterium Thalassomonas sp. LD5. Its cDNA consists of 4401 bp, encoding a protein of 1466 amino acids. Based on amino acid similarity, AgaD is classified into glycoside hydrolase (GH) family GH96. The recombinant enzyme gave a molecular weight of about 180 kDa on SDS-PAGE and 360 kDa on Native-PAGE indicating it acted as a dimer. However, the recombinant enzyme is labile and easy to be fractured into series of small active fragments, of which the smallest one is about 70 kDa, matching the size of catalytic module. The enzyme has maximal activity at 35 °C and pH 7.4, and shows a strong dependence on the presence of calcium ions. AgaD degrades agarose to yield agarotetraose as the predominate end product. However, the hydrolysates are rapidly degraded to odd-numbered oligosaccharides under strong alkaline condition. The spectra of ESI-MS and 1H-NMR proved that the main hydrolysate agarotetraose is degraded into neoagarotriose, bearing the sequence of G-A-G (G, D-galactose; A, 3,6-anhydro-α-L-galactose). Unlike the alkaline condition, the hydrolysates are further hydrolyzed into smaller degree polymerization (DP) of agaro-oligosaccharides (AOS) in dilute strong acid. Therefore, this study provides more insights into the properties for both the α-agarases and the AOS.
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Affiliation(s)
- Weibin Zhang
- School of Medicine and Pharmacy, Key Laboratory of Marine Drugs, Chinese Ministry of Education, Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, 266003, China
| | - Jingnan Xu
- School of Medicine and Pharmacy, Key Laboratory of Marine Drugs, Chinese Ministry of Education, Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, 266003, China
| | - Dan Liu
- School of Medicine and Pharmacy, Key Laboratory of Marine Drugs, Chinese Ministry of Education, Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, 266003, China
| | - Huan Liu
- School of Medicine and Pharmacy, Key Laboratory of Marine Drugs, Chinese Ministry of Education, Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, 266003, China
| | - Xinzhi Lu
- School of Medicine and Pharmacy, Key Laboratory of Marine Drugs, Chinese Ministry of Education, Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, 266003, China.
| | - Wengong Yu
- School of Medicine and Pharmacy, Key Laboratory of Marine Drugs, Chinese Ministry of Education, Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, 266003, China. .,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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8
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Potassium and sodium ions enhance the activity and thermostability of 1,4-α-glucan branching enzyme from Geobacillus thermoglucosidasius in the presence of glycerol. Int J Biol Macromol 2017; 102:712-717. [DOI: 10.1016/j.ijbiomac.2017.04.061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/14/2017] [Accepted: 04/14/2017] [Indexed: 11/22/2022]
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9
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Obeng EM, Budiman C, Ongkudon CM. Identifying additives for cellulase enhancement—A systematic approach. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2017.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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10
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Linares-Pastén JA, Falck P, Albasri K, Kjellström S, Adlercreutz P, Logan DT, Karlsson EN. Three-dimensional structures and functional studies of two GH43 arabinofuranosidases fromWeissellasp. strain 142 andLactobacillus brevis. FEBS J 2017; 284:2019-2036. [DOI: 10.1111/febs.14101] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/13/2017] [Accepted: 05/04/2017] [Indexed: 12/12/2022]
Affiliation(s)
| | - Peter Falck
- Biotechnology; Department of Chemistry; Lund University; Sweden
| | - Khalil Albasri
- Biotechnology; Department of Chemistry; Lund University; Sweden
| | - Sven Kjellström
- Biochemistry and Structural Biology; Department of Chemistry; Lund University; Sweden
| | | | - Derek T. Logan
- Biochemistry and Structural Biology; Department of Chemistry; Lund University; Sweden
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11
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Structural Insight of a Trimodular Halophilic Cellulase with a Family 46 Carbohydrate-Binding Module. PLoS One 2015; 10:e0142107. [PMID: 26562160 PMCID: PMC4643050 DOI: 10.1371/journal.pone.0142107] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 10/16/2015] [Indexed: 01/08/2023] Open
Abstract
Cellulases are the key enzymes used in the biofuel industry. A typical cellulase contains a catalytic domain connected to a carbohydrate-binding module (CBM) through a flexible linker. Here we report the structure of an atypical trimodular cellulase which harbors a catalytic domain, a CBM46 domain and a rigid CBM_X domain between them. The catalytic domain shows the features of GH5 family, while the CBM46 domain has a sandwich-like structure. The catalytic domain and the CBM46 domain form an extended substrate binding cleft, within which several tryptophan residues are well exposed. Mutagenesis assays indicate that these residues are essential for the enzymatic activities. Gel affinity electrophoresis shows that these tryptophan residues are involved in the polysaccharide substrate binding. Also, electrostatic potential analysis indicates that almost the entire solvent accessible surface of CelB is negatively charged, which is consistent with the halophilic nature of this enzyme.
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12
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Leis B, Heinze S, Angelov A, Pham VTT, Thürmer A, Jebbar M, Golyshin PN, Streit WR, Daniel R, Liebl W. Functional Screening of Hydrolytic Activities Reveals an Extremely Thermostable Cellulase from a Deep-Sea Archaeon. Front Bioeng Biotechnol 2015; 3:95. [PMID: 26191525 PMCID: PMC4486847 DOI: 10.3389/fbioe.2015.00095] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/17/2015] [Indexed: 01/27/2023] Open
Abstract
Extreme habitats serve as a source of enzymes that are active under extreme conditions and are candidates for industrial applications. In this work, six large-insert mixed genomic libraries were screened for hydrolase activities in a broad temperature range (8-70°C). Among a variety of hydrolytic activities, one fosmid clone, derived from a library of pooled isolates of hyperthermophilic archaea from deep sea vents, displayed hydrolytic activity on carboxymethyl cellulose substrate plates at 70°C but not at lower temperatures. Sequence analysis of the fosmid insert revealed a gene encoding a novel glycoside hydrolase family 12 (GHF12) endo-1,4-β-glucanase, termed Cel12E. The enzyme shares 45% sequence identity with a protein from the archaeon Thermococcus sp. AM4 and displays a unique multidomain architecture. Biochemical characterization of Cel12E revealed a remarkably thermostable protein, which appears to be of archaeal origin. The enzyme displayed maximum activity at 92°C and was active on a variety of linear 1,4-β-glucans like carboxymethyl cellulose, β-glucan, lichenan, and phosphoric acid swollen cellulose. The protein is able to bind to various insoluble β-glucans. Product pattern analysis indicated that Cel12E is an endo-cleaving β-glucanase. Cel12E expands the toolbox of hyperthermostable archaeal cellulases with biotechnological potential.
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Affiliation(s)
- Benedikt Leis
- Department of Microbiology, School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Simon Heinze
- Department of Microbiology, School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Angel Angelov
- Department of Microbiology, School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Vu Thuy Trang Pham
- Department of Microbiology, School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Andrea Thürmer
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Georg-August University Göttingen, Göttingen, Germany
| | - Mohamed Jebbar
- Laboratoire de Microbiologie des Environnements Extrêmes-UMR 6197 (CNRS-Ifremer-UBO), Institut Universitaire Européen de la Mer, Université de Bretagne Occidentale, Plouzané, France
| | | | - Wolfgang R. Streit
- Fakultät für Mathematik, Informatik und Naturwissenschaften Biologie, Biozentrum Klein Flottbek, Universität Hamburg, Hamburg, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Georg-August University Göttingen, Göttingen, Germany
| | - Wolfgang Liebl
- Department of Microbiology, School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
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13
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Verma AK, Bule P, Ribeiro T, Brás JLA, Mukherjee J, Gupta MN, Fontes CMGA, Goyal A. The family 6 Carbohydrate Binding Module (CtCBM6) of glucuronoxylanase (CtXynGH30) of Clostridium thermocellum binds decorated and undecorated xylans through cleft A. Arch Biochem Biophys 2015; 575:8-21. [PMID: 25857803 DOI: 10.1016/j.abb.2015.03.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 02/24/2015] [Accepted: 03/17/2015] [Indexed: 10/23/2022]
Abstract
CtCBM6 of glucuronoxylan-xylanohydrolase (CtXynGH30) from Clostridium thermocellum was cloned, expressed and purified as a soluble ~14 kDa protein. Quantitative binding analysis with soluble polysaccharides by affinity electrophoresis and ITC revealed that CtCBM6 displays similar affinity towards decorated and undecorated xylans by binding wheat- and rye-arabinoxylans, beechwood-, birchwood- and oatspelt-xylan. Protein melting studies confirmed thermostable nature of CtCBM6 and that Ca(2+) ions did not affect its structure stability and binding affinity significantly. The CtCBM6 structure was modeled and refined and CD spectrum displayed 44% β-strands supporting the predicted structure. CtCBM6 displays a jelly roll β-sandwich fold presenting two potential carbohydrate binding clefts, A and B. The cleft A, is located between two loops connecting β4-β5 and β8-β9 strands. Tyr28 and Phe84 present on these loops make a planar hydrophobic binding surface to accommodate sugar ring of ligand. The cleft B, is located on concave surface of β-sandwich fold. Tyr34 and Tyr104 make a planar hydrophobic platform, which may be inaccessible to ligand due to hindrance by Pro68. Site-directed mutagenesis revealed Tyr28 and Phe84 in cleft A, playing a major role in ligand binding. The results suggest that CtCBM6 interacts with carbohydrates through cleft A, which recognizes equally well both decorated and un-decorated xylans.
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Affiliation(s)
- Anil Kumar Verma
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Pedro Bule
- CIISA-Faculdade de Medicina Veterinária, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - Teresa Ribeiro
- CIISA-Faculdade de Medicina Veterinária, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - Joana L A Brás
- CIISA-Faculdade de Medicina Veterinária, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - Joyeeta Mukherjee
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Munishwar N Gupta
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Carlos M G A Fontes
- CIISA-Faculdade de Medicina Veterinária, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - Arun Goyal
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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14
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Chen CC, Ko TP, Huang JW, Guo RT. Heat- and Alkaline-Stable Xylanases: Application, Protein Structure and Engineering. CHEMBIOENG REVIEWS 2015. [DOI: 10.1002/cben.201400035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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15
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A GH57 4-α-glucanotransferase of hyperthermophilic origin with potential for alkyl glycoside production. Appl Microbiol Biotechnol 2015; 99:7101-13. [DOI: 10.1007/s00253-015-6435-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 01/23/2015] [Accepted: 01/24/2015] [Indexed: 10/24/2022]
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16
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Artificial affinity proteins as ligands of immunoglobulins. Biomolecules 2015; 5:60-75. [PMID: 25647098 PMCID: PMC4384111 DOI: 10.3390/biom5010060] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 12/17/2014] [Accepted: 01/23/2015] [Indexed: 12/17/2022] Open
Abstract
A number of natural proteins are known to have affinity and specificity for immunoglobulins. Some of them are widely used as reagents for detection or capture applications, such as Protein G and Protein A. However, these natural proteins have a defined spectrum of recognition that may not fit specific needs. With the development of combinatorial protein engineering and selection techniques, it has become possible to design artificial affinity proteins with the desired properties. These proteins, termed alternative scaffold proteins, are most often chosen for their stability, ease of engineering and cost-efficient recombinant production in bacteria. In this review, we focus on alternative scaffold proteins for which immunoglobulin binders have been identified and characterized.
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17
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Magnetic cross-linked enzyme aggregates (CLEAs): A novel concept towards carrier free immobilization of lignocellulolytic enzymes. Enzyme Microb Technol 2014; 61-62:17-27. [DOI: 10.1016/j.enzmictec.2014.04.009] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 04/10/2014] [Accepted: 04/17/2014] [Indexed: 11/21/2022]
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18
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Ghosh A, Luís AS, Brás JLA, Pathaw N, Chrungoo NK, Fontes CMGA, Goyal A. Deciphering ligand specificity of a Clostridium thermocellum family 35 carbohydrate binding module (CtCBM35) for gluco- and galacto- substituted mannans and its calcium induced stability. PLoS One 2013; 8:e80415. [PMID: 24324599 PMCID: PMC3855759 DOI: 10.1371/journal.pone.0080415] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 10/02/2013] [Indexed: 11/25/2022] Open
Abstract
This study investigated the role of CBM35 from Clostridium thermocellum (CtCBM35) in polysaccharide recognition. CtCBM35 was cloned into pET28a (+) vector with an engineered His6 tag and expressed in Escherichia coli BL21 (DE3) cells. A homogenous 15 kDa protein was purified by immobilized metal ion chromatography (IMAC). Ligand binding analysis of CtCBM35 was carried out by affinity electrophoresis using various soluble ligands. CtCBM35 showed a manno-configured ligand specific binding displaying significant association with konjac glucomannan (Ka = 14.3×10(4) M(-1)), carob galactomannan (Ka = 12.4×10(4) M(-1)) and negligible association (Ka = 12 µM(-1)) with insoluble mannan. Binding of CtCBM35 with polysaccharides which was calcium dependent exhibited two fold higher association in presence of 10 mM Ca(2+) ion with konjac glucomannan (Ka = 41×10(4) M(-1)) and carob galactomannan (Ka = 30×10(4) M(-1)). The polysaccharide binding was further investigated by fluorescence spectrophotometric studies. On binding with carob galactomannan and konjac glucomannan the conformation of CtCBM35 changed significantly with regular 21 nm peak shifts towards lower quantum yield. The degree of association (K a) with konjac glucomannan and carob galactomannan, 14.3×10(4) M(-1) and 11.4×10(4) M(-1), respectively, corroborated the findings from affinity electrophoresis. The association of CtCBM35with konjac glucomannan led to higher free energy of binding (ΔG) -25 kJ mole(-1) as compared to carob galactomannan (ΔG) -22 kJ mole(-1). On binding CtCBM35 with konjac glucomannan and carob galactomannan the hydrodynamic radius (RH) as analysed by dynamic light scattering (DLS) study, increased to 8 nm and 6 nm, respectively, from 4.25 nm in absence of ligand. The presence of 10 mM Ca(2+) ions imparted stiffer orientation of CtCBM35 particles with increased RH of 4.52 nm. Due to such stiffer orientation CtCBM35 became more thermostable and its melting temperature was shifted to 70°C from initial 50°C.
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Affiliation(s)
- Arabinda Ghosh
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Ana Sofia Luís
- CIISA-Faculdade de Medicina Veterinaria, Avenida da Universidade Técnica, Lisbon, Portugal
| | - Joana L. A. Brás
- CIISA-Faculdade de Medicina Veterinaria, Avenida da Universidade Técnica, Lisbon, Portugal
| | - Neeta Pathaw
- North Eastern Hill University, Shillong, Meghalaya, India
| | | | - Carlos M. G. A. Fontes
- CIISA-Faculdade de Medicina Veterinaria, Avenida da Universidade Técnica, Lisbon, Portugal
| | - Arun Goyal
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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19
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Li C, Ban X, Gu Z, Li Z. Calcium ion contribution to thermostability of cyclodextrin glycosyltransferase is closely related to calcium-binding site CaIII. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:8836-8841. [PMID: 23968201 DOI: 10.1021/jf4024273] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In the study, we investigated the contribution of Ca²⁺ to the thermostability of α-cyclodextrin glycosyltransferase (α-CGTase) from Paenibacillus macerans , which has two calcium-binding sites (CaI and CaII), and β-CGTase from Bacillus circulans , which contains an additional calcium-binding site (CaIII), consisting of Ala315 and Asp577. It was found that the contribution of Ca²⁺ to the thermostability of two CGTases displayed a marked difference. Ca²⁺ affected β-CGTase thermostability significantly. After Ca²⁺ was added to β-CGTase solution to a final concentration of 5 mM followed by incubation for 120 min at 60 °C, residual activity of β-CGTase was 88.3%, which was much higher than that without Ca²⁺. However, Ca²⁺ had a small contribution to α-CGTase thermostability. Furthermore, A315D and D577K mutations at CaIII could significantly change the contribution of Ca²⁺ to β-CGTase thermostability. These results suggested that the contribution of Ca²⁺ to CGTase thermostability was closely related to CaIII.
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Affiliation(s)
- Caiming Li
- State Key Laboratory of Food Science and Technology, and ‡School of Food Science and Technology, Jiangnan University , Wuxi 214122, People's Republic of China
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20
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von Schantz L, Håkansson M, Logan DT, Walse B, Österlin J, Nordberg-Karlsson E, Ohlin M. Structural basis for carbohydrate-binding specificity—A comparative assessment of two engineered carbohydrate-binding modules. Glycobiology 2012; 22:948-61. [DOI: 10.1093/glycob/cws063] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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21
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Montanier C, Flint JE, Bolam DN, Xie H, Liu Z, Rogowski A, Weiner DP, Ratnaparkhe S, Nurizzo D, Roberts SM, Turkenburg JP, Davies GJ, Gilbert HJ. Circular permutation provides an evolutionary link between two families of calcium-dependent carbohydrate binding modules. J Biol Chem 2010; 285:31742-54. [PMID: 20659893 PMCID: PMC2951246 DOI: 10.1074/jbc.m110.142133] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 07/13/2010] [Indexed: 11/06/2022] Open
Abstract
The microbial deconstruction of the plant cell wall is a critical biological process, which also provides important substrates for environmentally sustainable industries. Enzymes that hydrolyze the plant cell wall generally contain non-catalytic carbohydrate binding modules (CBMs) that contribute to plant cell wall degradation. Here we report the biochemical properties and crystal structure of a family of CBMs (CBM60) that are located in xylanases. Uniquely, the proteins display broad ligand specificity, targeting xylans, galactans, and cellulose. Some of the CBM60s display enhanced affinity for their ligands through avidity effects mediated by protein dimerization. The crystal structure of vCBM60, displays a β-sandwich with the ligand binding site comprising a broad cleft formed by the loops connecting the two β-sheets. Ligand recognition at site 1 is, exclusively, through hydrophobic interactions, whereas binding at site 2 is conferred by polar interactions between a protein-bound calcium and the O2 and O3 of the sugar. The observation, that ligand recognition at site 2 requires only a β-linked sugar that contains equatorial hydroxyls at C2 and C3, explains the broad ligand specificity displayed by vCBM60. The ligand-binding apparatus of vCBM60 displays remarkable structural conservation with a family 36 CBM (CBM36); however, the residues that contribute to carbohydrate recognition are derived from different regions of the two proteins. Three-dimensional structure-based sequence alignments reveal that CBM36 and CBM60 are related by circular permutation. The biological and evolutionary significance of the mechanism of ligand recognition displayed by family 60 CBMs is discussed.
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Affiliation(s)
- Cedric Montanier
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - James E. Flint
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - David N. Bolam
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Hefang Xie
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Ziyuan Liu
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Artur Rogowski
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | | | - Supriya Ratnaparkhe
- the Complex Carbohydrate Research Center, The University of Georgia, Athens, Georgia 30602-4712
| | - Didier Nurizzo
- the European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, F-38043 Grenoble Cedex, France
| | - Shirley M. Roberts
- the York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom, and
| | - Johan P. Turkenburg
- the York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom, and
| | - Gideon J. Davies
- the York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom, and
| | - Harry J. Gilbert
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
- the Complex Carbohydrate Research Center, The University of Georgia, Athens, Georgia 30602-4712
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22
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Yeh AP, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Cai X, Carlton D, Chen C, Chiu HJ, Chiu M, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Lam WW, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 Å resolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1287-96. [PMID: 20944224 PMCID: PMC2954218 DOI: 10.1107/s1744309110028228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Accepted: 07/14/2010] [Indexed: 03/06/2023]
Abstract
BT2081 from Bacteroides thetaiotaomicron (GenBank accession code NP_810994.1) is a member of a novel protein family consisting of over 160 members, most of which are found in the different classes of Bacteroidetes. Genome-context analysis lends support to the involvement of this family in carbohydrate metabolism, which plays a key role in B. thetaiotaomicron as a predominant bacterial symbiont in the human distal gut microbiome. The crystal structure of BT2081 at 2.05 Å resolution represents the first structure from this new protein family. BT2081 consists of an N-terminal domain, which adopts a β-sandwich immunoglobulin-like fold, and a larger C-terminal domain with a β-sandwich jelly-roll fold. Structural analyses reveal that both domains are similar to those found in various carbohydrate-active enzymes. The C-terminal β-jelly-roll domain contains a potential carbohydrate-binding site that is highly conserved among BT2081 homologs and is situated in the same location as the carbohydrate-binding sites that are found in structurally similar glycoside hydrolases (GHs). However, in BT2081 this site is partially occluded by surrounding loops, which results in a deep solvent-accessible pocket rather than a shallower solvent-exposed cleft.
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Affiliation(s)
- Andrew P. Yeh
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Polat Abdubek
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Tamara Astakhova
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Herbert L. Axelrod
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Constantina Bakolitsa
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Xiaohui Cai
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Dennis Carlton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Connie Chen
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Hsiu-Ju Chiu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Michelle Chiu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Thomas Clayton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Debanu Das
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Marc C. Deller
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lian Duan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Kyle Ellrott
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Carol L. Farr
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Julie Feuerhelm
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Joanna C. Grant
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Anna Grzechnik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gye Won Han
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Kevin K. Jin
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Heath E. Klock
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Mark W. Knuth
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Piotr Kozbial
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - S. Sri Krishna
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Abhinav Kumar
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Winnie W. Lam
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - David Marciano
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Daniel McMullan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Mitchell D. Miller
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Andrew T. Morse
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Edward Nigoghossian
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Amanda Nopakun
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Linda Okach
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Christina Puckett
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Ron Reyes
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Henry J. Tien
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Christine B. Trame
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Henry van den Bedem
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Dana Weekes
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Tiffany Wooten
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Qingping Xu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Keith O. Hodgson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - John Wooley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Marc-André Elsliger
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ashley M. Deacon
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Adam Godzik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Scott A. Lesley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian A. Wilson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
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23
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Correia MAS, Abbott DW, Gloster TM, Fernandes VO, Prates JAM, Montanier C, Dumon C, Williamson MP, Tunnicliffe RB, Liu Z, Flint JE, Davies GJ, Henrissat B, Coutinho PM, Fontes CMGA, Gilbert HJ. Signature active site architectures illuminate the molecular basis for ligand specificity in family 35 carbohydrate binding module. Biochemistry 2010; 49:6193-205. [PMID: 20496884 DOI: 10.1021/bi1006139] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The deconstruction of the plant cell wall is an important biological process that is attracting considerable industrial interest, particularly in the bioenergy sector. Enzymes that attack the plant cell wall generally contain one or more noncatalytic carbohydrate binding modules (CBMs) that play an important targeting function. While CBMs that bind to the backbones of plant structural polysaccharides have been widely described, modules that recognize components of the vast array of decorations displayed on these polymers have been relatively unexplored. Here we show that a family 35 CBM member (CBM35), designated CtCBM35-Gal, binds to alpha-D-galactose (Gal) and, within the context of the plant cell wall, targets the alpha-1,6-Gal residues of galactomannan but not the beta-D-Gal residues in xyloglucan. The crystal structure of CtCBM35-Gal reveals a canonical beta-sandwich fold. Site-directed mutagenesis studies showed that the ligand is accommodated within the loops that connect the two beta-sheets. Although the ligand binding site of the CBM displays significant structural similarity with calcium-dependent CBM35s that target uronic acids, subtle differences in the conformation of conserved residues in the ligand binding site lead to the loss of metal binding and uronate recognition. A model is proposed in which the orientation of the pair of aromatic residues that interact with the two faces of the Gal pyranose ring plays a pivotal role in orientating the axial O4 atom of the ligand toward Asn140, which is invariant in CBM35. The ligand recognition site of exo-CBM35s (CBM35-Gal and the uronic acid binding CBM35s) appears to overlap with that of CBM35-Man, which binds to the internal regions of mannan, a beta-polymer of mannose. Using site-directed mutagenesis, we show that although there is conservation of several functional residues within the binding sites of endo- and exo-CBM35s, the endo-CBM does not utilize Asn113 (equivalent to Asn140 in CBM35-Gal) in mannan binding, despite the importance of the equivalent residue in ligand recognition across the CBM35 and CBM6 landscape. The data presented in this report are placed within a wider phylogenetic context for the CBM35 family.
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Affiliation(s)
- Márcia A S Correia
- CIISA, Faculdade de Medicina Veterinária, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
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24
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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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25
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Gullfot F, Tan TC, von Schantz L, Karlsson EN, Ohlin M, Brumer H, Divne C. The crystal structure of XG-34, an evolved xyloglucan-specific carbohydrate-binding module. Proteins 2010; 78:785-9. [PMID: 19950365 DOI: 10.1002/prot.22642] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Fredrika Gullfot
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden
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26
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Nielsen MM, Bozonnet S, Seo ES, Mótyán JA, Andersen JM, Dilokpimol A, Abou Hachem M, Gyémánt G, Næsted H, Kandra L, Sigurskjold BW, Svensson B. Two Secondary Carbohydrate Binding Sites on the Surface of Barley α-Amylase 1 Have Distinct Functions and Display Synergy in Hydrolysis of Starch Granules. Biochemistry 2009; 48:7686-97. [DOI: 10.1021/bi900795a] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Morten M. Nielsen
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Sophie Bozonnet
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Copenhagen Valby, Denmark
| | - Eun-Seong Seo
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - János A. Mótyán
- Department of Biochemistry, Faculty of Sciences, University of Debrecen, Debrecen, Hungary H-4010
| | - Joakim M. Andersen
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Adiphol Dilokpimol
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Maher Abou Hachem
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Gyöngyi Gyémánt
- Department of Biochemistry, Faculty of Sciences, University of Debrecen, Debrecen, Hungary H-4010
| | - Henrik Næsted
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Lili Kandra
- Department of Biochemistry, Faculty of Sciences, University of Debrecen, Debrecen, Hungary H-4010
| | - Bent W. Sigurskjold
- Department of Biology, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Copenhagen Valby, Denmark
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27
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Abou-hachem M, Olsson F, Williamson M, Linse S, Crennell S, Hreggvidsson G, Kristjansson J, Holst O, Nordberg Karlsson E. The Modular Organisation and Stability of a Thermostable Family 10 Xylanase. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/1024240310001614315] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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28
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Henshaw J, Horne-Bitschy A, van Bueren AL, Money VA, Bolam DN, Czjzek M, Ekborg NA, Weiner RM, Hutcheson SW, Davies GJ, Boraston AB, Gilbert HJ. Family 6 carbohydrate binding modules in beta-agarases display exquisite selectivity for the non-reducing termini of agarose chains. J Biol Chem 2006; 281:17099-17107. [PMID: 16601125 DOI: 10.1074/jbc.m600702200] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Carbohydrate recognition is central to the biological and industrial exploitation of plant structural polysaccharides. These insoluble polymers are recalcitrant to microbial degradation, and enzymes that catalyze this process generally contain non-catalytic carbohydrate binding modules (CBMs) that potentiate activity by increasing substrate binding. Agarose, a repeat of the disaccharide 3,6-anhydro-alpha-L-galactose-(1,3)-beta-D-galactopyranose-(1,4), is the dominant matrix polysaccharide in marine algae, yet the role of CBMs in the hydrolysis of this important polymer has not previously been explored. Here we show that family 6 CBMs, present in two different beta-agarases, bind specifically to the non-reducing end of agarose chains, recognizing only the first repeat of the disaccharide. The crystal structure of one of these modules Aga16B-CBM6-2, in complex with neoagarohexaose, reveals the mechanism by which the protein displays exquisite specificity, targeting the equatorial O4 and the axial O3 of the anhydro-L-galactose. Targeting of the CBM6 to the non-reducing end of agarose chains may direct the appended catalytic modules to areas of the plant cell wall attacked by beta-agarases where the matrix polysaccharide is likely to be more amenable to further enzymic hydrolysis.
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Affiliation(s)
- Joanna Henshaw
- Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Ami Horne-Bitschy
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
| | - Alicia Lammerts van Bueren
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
| | - Victoria A Money
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, United Kingdom
| | - David N Bolam
- Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Mirjam Czjzek
- Station Biologique de Roscoff, Vegetaux Marins et Biomolecules, UMR7139-CNRS-UPMC, Place George Teissier, B. P. 74, 29682 Roscoff, France
| | - Nathan A Ekborg
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Ronald M Weiner
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Steven W Hutcheson
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Gideon J Davies
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, United Kingdom
| | - Alisdair B Boraston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
| | - Harry J Gilbert
- Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom.
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29
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Najmudin S, Guerreiro CIPD, Carvalho AL, Prates JAM, Correia MAS, Alves VD, Ferreira LMA, Romão MJ, Gilbert HJ, Bolam DN, Fontes CMGA. Xyloglucan is recognized by carbohydrate-binding modules that interact with beta-glucan chains. J Biol Chem 2005; 281:8815-28. [PMID: 16314409 DOI: 10.1074/jbc.m510559200] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Enzyme systems that attack the plant cell wall contain noncatalytic carbohydrate-binding modules (CBMs) that mediate attachment to this composite structure and play a pivotal role in maximizing the hydrolytic process. Although xyloglucan, which includes a backbone of beta-1,4-glucan decorated primarily with xylose residues, is a key component of the plant cell wall, CBMs that bind to this polymer have not been identified. Here we showed that the C-terminal domain of the modular Clostridium thermocellum enzyme CtCel9D-Cel44A (formerly known as CelJ) comprises a novel CBM (designated CBM44) that binds with equal affinity to cellulose and xyloglucan. We also showed that accommodation of xyloglucan side chains is a general feature of CBMs that bind to single cellulose chains. The crystal structures of CBM44 and the other CBM (CBM30) in CtCel9D-Cel44A display a beta-sandwich fold. The concave face of both CBMs contains a hydrophobic platform comprising three tryptophan residues that can accommodate up to five glucose residues. The orientation of these aromatic residues is such that the bound ligand would adopt the twisted conformation displayed by cello-oligosaccharides in solution. Mutagenesis studies confirmed that the hydrophobic platform located on the concave face of both CBMs mediates ligand recognition. In contrast to other CBMs that bind to single polysaccharide chains, the polar residues in the binding cleft of CBM44 play only a minor role in ligand recognition. The mechanism by which these proteins are able to recognize linear and decorated beta-1,4-glucans is discussed based on the structures of CBM44 and the other CBMs that bind single cellulose chains.
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Affiliation(s)
- Shabir Najmudin
- Requimte, Departamento de Química, FCT-UNL, 2829-516 Caparica, Portugal, CIISA-Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
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30
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Bjornsdottir SH, Blondal T, Hreggvidsson GO, Eggertsson G, Petursdottir S, Hjorleifsdottir S, Thorbjarnardottir SH, Kristjansson JK. Rhodothermus marinus: physiology and molecular biology. Extremophiles 2005; 10:1-16. [PMID: 16075163 DOI: 10.1007/s00792-005-0466-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2004] [Accepted: 06/17/2005] [Indexed: 11/24/2022]
Abstract
Rhodothermus marinus has been the subject of many studies in recent years. It is a thermohalophilic bacterium and is the only validly described species in the genus Rhodothermus. It is not closely related to other well-known thermophiles and is the only thermophile within the family Crenotrichaceae. R. marinus has been isolated from several similar but distantly located geothermal habitats, many of which are subject to large fluctuations in environmental conditions. This presumably affects the physiology of R. marinus. Many of its enzymes show optimum activity at temperatures considerably higher than 65 degrees C, the optimum for growth, and some are active over a broad temperature range. Studies have found distinguishing components in the R. marinus electron transport chain as well as in its pool of intracellular solutes, which accumulate during osmotic stress. The species hosts both bacteriophages and plasmids and a functional intein has been isolated from its chromosome. Despite these interesting features and its unknown genetics, interest in R. marinus has been mostly stimulated by its thermostable enzymes, particularly polysaccharide hydrolysing enzymes and enzymes of DNA synthesis which may be useful in industry and in the laboratory. R. marinus has not been amenable to genetic analysis until recently when a system for gene transfer was established. Here, we review the current literature on R. marinus.
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31
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Carvalho AL, Goyal A, Prates JAM, Bolam DN, Gilbert HJ, Pires VMR, Ferreira LMA, Planas A, Romão MJ, Fontes CMGA. The family 11 carbohydrate-binding module of Clostridium thermocellum Lic26A-Cel5E accommodates beta-1,4- and beta-1,3-1,4-mixed linked glucans at a single binding site. J Biol Chem 2004; 279:34785-93. [PMID: 15192099 DOI: 10.1074/jbc.m405867200] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Modular glycoside hydrolases that attack recalcitrant polymers generally contain noncatalytic carbohydrate-binding modules (CBMs), which play a critical role in the action of these enzymes by localizing the appended catalytic domains onto the surface of insoluble polysaccharide substrates. Type B CBMs, which recognize single polysaccharide chains, display ligand specificities that are consistent with the substrates hydrolyzed by the associated catalytic domains. In enzymes that contain multiple catalytic domains with distinct substrate specificities, it is unclear how these different activities influence the evolution of the ligand recognition profile of the appended CBM. To address this issue, we have characterized the properties of a family 11 CBM (CtCBM11) in Clostridium thermocellum Lic26A-Cel5E, an enzyme that contains GH5 and GH26 catalytic domains that display beta-1,4- and beta-1,3-1,4-mixed linked endoglucanase activity, respectively. Here we show that CtCBM11 binds to both beta-1,4- and beta-1,3-1,4-mixed linked glucans, displaying K(a) values of 1.9 x 10(5), 4.4 x 10(4), and 2 x 10(3) m(-1) for Glc-beta1,4-Glc-beta1,4-Glc-beta1,3-Glc, Glc-beta1,4-Glc-beta1,4-Glc-beta1,4-Glc, and Glc-beta1,3-Glc-beta1,4-Glc-beta1,3-Glc, respectively, demonstrating that CBMs can display a preference for mixed linked glucans. To determine whether these ligands are accommodated in the same or diverse sites in CtCBM11, the crystal structure of the protein was solved to a resolution of 1.98 A. The protein displays a beta-sandwich with a concave side that forms a potential binding cleft. Site-directed mutagenesis revealed that Tyr(22), Tyr(53), and Tyr(129), located in the putative binding cleft, play a central role in the recognition of all the ligands recognized by the protein. We propose, therefore, that CtCBM11 contains a single ligand-binding site that displays affinity for both beta-1,4- and beta-1,3-1,4-mixed linked glucans.
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Affiliation(s)
- Ana L Carvalho
- Rede de Química e Technologia/Centro de Química Fina e Biotechnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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32
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Bolam DN, Xie H, Pell G, Hogg D, Galbraith G, Henrissat B, Gilbert HJ. X4 modules represent a new family of carbohydrate-binding modules that display novel properties. J Biol Chem 2004; 279:22953-63. [PMID: 15004012 DOI: 10.1074/jbc.m313317200] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hydrolysis of the plant cell wall by microbial glycoside hydrolases and esterases is the primary mechanism by which stored organic carbon is utilized in the biosphere, and thus these enzymes are of considerable biological and industrial importance. Plant cell wall-degrading enzymes in general display a modular architecture comprising catalytic and non-catalytic modules. The X4 modules in glycoside hydrolases represent a large family of non-catalytic modules whose function is unknown. Here we show that the X4 modules from a Cellvibrio japonicus mannanase (Man5C) and arabinofuranosidase (Abf62A) bind to polysaccharides, and thus these proteins comprise a new family of carbohydrate-binding modules (CBMs), designated CBM35. The Man5C-CBM35 binds to galactomannan, insoluble amorphous mannan, glucomannan, and manno-oligosaccharides but does not interact with crystalline mannan, cellulose, cello-oligosaccharides, or other polysaccharides derived from the plant cell wall. Man5C-CBM35 also potentiates mannanase activity against insoluble amorphous mannan. Abf62A-CBM35 interacts with unsubstituted oat-spelt xylan but not substituted forms of the hemicellulose or xylo-oligosaccharides, and requires calcium for binding. This is in sharp contrast to other xylan-binding CBMs, which interact in a calcium-independent manner with both xylo-oligosaccharides and decorated xylans.
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Affiliation(s)
- David N Bolam
- School of Cell and Molecular Biosciences, University of Newcastle upon Tyne, The Agriculture Building, Newcastle upon Tyne NE1 7RU, United Kingdom
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33
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Abou-Hachem M, Olsson F, Nordberg Karlsson E. Probing the stability of the modular family 10 xylanase from Rhodothermus marinus. Extremophiles 2003; 7:483-91. [PMID: 12942350 DOI: 10.1007/s00792-003-0348-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2003] [Accepted: 07/07/2003] [Indexed: 11/27/2022]
Abstract
The thermophilic bacterium Rhodothermus marinus produces a modular xylanase (Xyn10A) consisting of two N-terminal carbohydrate-binding modules (CBMs), followed by a domain of unknown function, and a catalytic module flanked by a fifth domain. Both Xyn10A CBMs bind calcium ions, and this study explores the effect of these ions on the stability of the full-length enzyme. Xyn10A and truncated forms thereof were produced and their thermostabilities were evaluated under different calcium loads. Studies performed using differential scanning calorimetry showed that the unfolding temperature of the Xyn10A was significantly dependent on the presence of Ca2+, and that the third domain of the enzyme binds at least one Ca2+. Thermal inactivation studies confirmed the role of tightly bound Ca2+ in stabilizing the enzyme, but showed that the presence of a large excess of this ion results in reduced kinetic stability. The truncated forms of Xyn10A were less stable than the full-length enzyme, indicative of module/domain thermostabilizing interactions. Finally, possible roles of the two domains of unknown function are discussed in the light of this study. This is the first report on the thermostabilizing role of calcium on a modular family 10 xylanase that displays multiple calcium binding in three of its five domains/modules.
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Affiliation(s)
- Maher Abou-Hachem
- Department of Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
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34
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Devillard E, Bera-Maillet C, Flint HJ, Scott KP, Newbold CJ, Wallace RJ, Jouany JP, Forano E. Characterization of XYN10B, a modular xylanase from the ruminal protozoan Polyplastron multivesiculatum, with a family 22 carbohydrate-binding module that binds to cellulose. Biochem J 2003; 373:495-503. [PMID: 12693992 PMCID: PMC1223500 DOI: 10.1042/bj20021784] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2002] [Revised: 04/04/2003] [Accepted: 04/14/2003] [Indexed: 11/17/2022]
Abstract
A new xylanase gene, xyn10B, was isolated from the ruminal protozoan Polyplastron multivesiculatum and the gene product was characterized. XYN10B is the first protozoan family 10 glycoside hydrolase characterized so far and is a modular enzyme comprising a family 22 carbohydrate-binding module (CBM) preceding the catalytic domain. The CBM22 was shown to be a true CBM. It showed high affinity for soluble arabinoxylan and is the first example of a CBM22 that binds strongly to celluloses of various crystallinities. The enzymic properties of XYN10B were also analysed. Its optimal temperature and pH for activity were 39 degrees C and 7.0 respectively; these values being close to those of the ruminal ecosystem. The phylogenetic relationships between the XYN10B CBM22 or catalytic domain and related sequences from ruminal and non-ruminal bacteria and eukaryotes are reported. The xyn10B gene is shown to lack introns.
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Affiliation(s)
- Estelle Devillard
- Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK
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35
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Abstract
Hemicellulases are a diverse group of enzymes that hydrolyze hemicelluloses--one of the most abundant groups of polysaccharide in nature. These enzymes have many biotechnological applications and their structure/function relationships are a subject of intense research. During the past year, new high-resolution structures of catalytic and non-catalytic domains of hemicellulases have been elucidated, and, together with biochemical studies, they reveal the principles of catalysis and specificity for these enzymes.
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Affiliation(s)
- Dalia Shallom
- Department of Food Engineering and Biotechnology and Institute of Catalysis, Science and Technology, Technion, Haifa 32000, Israel
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