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Sun F, Palayam M, Shabek N. Structure of maize BZR1-type β-amylase BAM8 provides new insights into its noncatalytic adaptation. J Struct Biol 2022; 214:107885. [PMID: 35961473 DOI: 10.1016/j.jsb.2022.107885] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/05/2022] [Accepted: 08/06/2022] [Indexed: 11/28/2022]
Abstract
Plant β-amylase (BAM) proteins play an essential role in growth, development, stress response, and hormone regulation. Despite their typical (β/α)8 barrel structure as active catalysts in starch breakdown, catalytically inactive BAMs are implicated in diverse yet elusive functions in plants. The noncatalytic BAM7/8 contain N-terminal BZR1 domains and were shown to be involved in the regulation of brassinosteroid signaling and possibly serve as sensors of yet an uncharacterized metabolic signal. While the structures of several catalytically active BAMs have been reported, structural characterization of the catalytically inactive BZR1-type BAMs remain unknown. Here, we determine the crystal structure of β-amylase domain of Zea mays BAM8/BES1/BZR1-5 and provide comprehensive insights into its noncatalytic adaptation. Using structural-guided comparison combined with biochemical analysis and molecular dynamics simulations, we revealed conformational changes in multiple distinct highly conserved regions resulting in rearrangement of the binding pocket. Altogether, this study adds a new layer of understanding to starch breakdown mechanism and elucidates the acquired adjustments of noncatalytic BZR1-type BAMs as putative regulatory domains and/or metabolic sensors in plants.
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Affiliation(s)
- Fuai Sun
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Malathy Palayam
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Nitzan Shabek
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA.
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2
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Ravenburg CM, Riney MB, Monroe JD, Berndsen CE. The BAM7 gene in Zea mays encodes a protein with similar structural and catalytic properties to Arabidopsis BAM2. Acta Crystallogr D Struct Biol 2022; 78:560-570. [PMID: 35503205 PMCID: PMC9063847 DOI: 10.1107/s2059798322002169] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/23/2022] [Indexed: 11/10/2022] Open
Abstract
Starch accumulates in the plastids of green plant tissues during the day to provide carbon for metabolism at night. Starch hydrolysis is catalyzed by members of the β-amylase (BAM) family, which in Arabidopsis thaliana (At) includes nine structurally and functionally diverse members. One of these enzymes, AtBAM2, is a plastid-localized enzyme that is unique among characterized β-amylases since it is tetrameric and exhibits sigmoidal kinetics. Sequence alignments show that the BAM domains of AtBAM7, a catalytically inactive, nuclear-localized transcription factor with an N-terminal DNA-binding domain, and AtBAM2 are more closely related to each other than they are to any other AtBAM. Since the BAM2 gene is found in more ancient lineages, it was hypothesized that the BAM7 gene evolved from BAM2. However, analysis of the genomes of 48 flowering plants revealed 12 species that appear to possess a BAM7 gene but lack a BAM2 gene. Upon closer inspection, these BAM7 proteins have a greater percent identity to AtBAM2 than to AtBAM7, and they share all of the AtBAM2 functional residues that BAM7 proteins normally lack. It is hypothesized that these genes may encode BAM2-like proteins although they are currently annotated as BAM7-like genes. To test this hypothesis, a cDNA for the short form of corn BAM7 (ZmBAM7-S) was designed for expression in Escherichia coli. Small-angle X-ray scattering data indicate that ZmBAM7-S has a tetrameric solution structure that is more similar to that of AtBAM2 than to that of AtBAM1. In addition, partially purified ZmBAM7-S is catalytically active and exhibits sigmoidal kinetics. Together, these data suggest that some BAM7 genes may encode a functional BAM2. Exploring and understanding the β-amylase gene structure could have an impact on the current annotation of genes.
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Affiliation(s)
- Claire M. Ravenburg
- Department of Biology, James Madison University, 951 Carrier Drive, MSC 7801, Harrisonburg, VA 22807, USA
| | - McKayla B. Riney
- Department of Chemistry and Biochemistry, James Madison University, 901 Carrier Drive, MSC 4501, Harrisonburg, VA 22807, USA
| | - Jonathan D. Monroe
- Department of Biology, James Madison University, 951 Carrier Drive, MSC 7801, Harrisonburg, VA 22807, USA
| | - Christopher E. Berndsen
- Department of Chemistry and Biochemistry, James Madison University, 901 Carrier Drive, MSC 4501, Harrisonburg, VA 22807, USA
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3
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Yang W, van Dijk M, Primavera C, Dekker C. FIB-milled plasmonic nanoapertures allow for long trapping times of individual proteins. iScience 2021; 24:103237. [PMID: 34746702 PMCID: PMC8551080 DOI: 10.1016/j.isci.2021.103237] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/15/2021] [Accepted: 10/04/2021] [Indexed: 11/18/2022] Open
Abstract
We have developed a fabrication methodology for label-free optical trapping of individual nanobeads and proteins in inverted-bowtie-shaped plasmonic gold nanopores. Arrays of these nanoapertures can be reliably produced using focused ion beam (FIB) milling with gap sizes of 10–20 nm, single-nanometer variation, and with a remarkable stability that allows for repeated use. We employ an optical readout where the presence of the protein entering the trap is marked by an increase in the transmission of light through the nanoaperture from the shift of the plasmonic resonance. In addition, the optical trapping force of the plasmonic nanopores allows 20-nm polystyrene beads and proteins, such as beta-amylase and Heat Shock Protein (HSP90), to be trapped for very long times (approximately minutes). On demand, we can release the trapped molecule for another protein to be interrogated. Our work opens up new routes to acquire information on the conformation and dynamics of individual proteins. We demonstrate fabrication of arrays of inverted-bowtie-shaped plasmonic gold nanopores Arrays (>64) of bowties with 10 to 20-nm size gap and single-nanometer variation can be produced We optically tweeze and detect single 20-nm polystyrene beads and individual proteins Our system allows for long observations (approximately minutes) of protein dynamics
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Affiliation(s)
- Wayne Yang
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Madeleine van Dijk
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Christian Primavera
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Cees Dekker
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
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Banda L, Kyallo M, Domelevo Entfellner JB, Moyo M, Swanckaert J, Mwanga RO, Onyango A, Magiri E, Gemenet DC, Yao N, Pelle R, Muzhingi T. Analysis of β-amylase gene ( Amyβ) variation reveals allele association with low enzyme activity and increased firmness in cooked sweetpotato ( Ipomoea batatas) from East Africa. JOURNAL OF AGRICULTURE AND FOOD RESEARCH 2021; 4:100121. [PMID: 34085050 PMCID: PMC8135125 DOI: 10.1016/j.jafr.2021.100121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/04/2021] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
β-amylase is a thermostable enzyme that hydrolyses starch during cooking of sweetpotato (Ipomoea batatas) storage roots, thereby influencing eating quality. Its activity is known to vary amongst genotypes but the genetic diversity of the beta-amylase gene (Amyβ) is not well studied. Amyβ has a highly conserved region between exon V and VI, forming part of the enzyme's active site. To determine the gene diversity, a 2.3 kb fragment, including the conserved region of the Amyβ gene was sequenced from 25 sweetpotato genotypes. The effect of sequence variation on gene expression, enzyme activity, and firmness in cooked roots was determined. Six genotypes carrying several SNPs within exon V, linked with an AT or ATGATA insertion in intron V were unique and clustered together. The genotypes also shared an A336E substitution in the amino acid sequence, eight residues upstream of a substrate-binding Thr344. The genotypes carrying this allele exhibited low gene expression and low enzyme activity. Enzyme activity was negatively correlated with firmness (R = -0.42) in cooked roots. This is the first report of such an allele, associated with low enzyme activity. These results suggest that genetic variation within the AmyB locus can be utilized to develop markers for firmness in sweetpotato breeding.
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Affiliation(s)
- Linly Banda
- Pan African University Institute of Basic Sciences, Technology, and Innovation, Department of Molecular Biology and Biotechnology, P.O. Box 62000, 00200, Nairobi, Kenya
- National University of Science and Technology, Department of Applied Biology and Biochemistry, P.O. Box AC 939, Ascot, Bulawayo, Zimbabwe
| | - Martina Kyallo
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, 00100, Nairobi, Kenya
| | - Jean-Baka Domelevo Entfellner
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, 00100, Nairobi, Kenya
| | - Mukani Moyo
- International Potato Center, Sub-Saharan Africa Regional Office, ILRI Campus, P.O. Box 25171, 00603, Nairobi, Kenya
| | - Jolien Swanckaert
- International Potato Center, Ntinda II Road, Plot 47, P.O. Box 22274, Kampala, Uganda
| | - Robert O.M. Mwanga
- International Potato Center, Ntinda II Road, Plot 47, P.O. Box 22274, Kampala, Uganda
| | - Arnold Onyango
- Jomo Kenyatta University of Agriculture and Technology, Department of Food Science, P.O. Box 62000, 00200, Nairobi, Kenya
| | - Esther Magiri
- Dedan Kimathi University of Technology, Private Bag 10143 Dedan Kimathi, Nyeri, Kenya
| | - Dorcus C. Gemenet
- Kenya Excellence in Breeding Platform, CIMMYT, ICRAF Campus, P.O. Box 1041-00621, Nairobi, Kenya
| | - Nasser Yao
- Alliance Bioversity International-CIAT, CIAT Africa Office, P.O. Box 823, 00621, Nairobi, Kenya
| | - Roger Pelle
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, 00100, Nairobi, Kenya
| | - Tawanda Muzhingi
- International Potato Center, Sub-Saharan Africa Regional Office, ILRI Campus, P.O. Box 25171, 00603, Nairobi, Kenya
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Campus Box 7624 Raleigh, NC, 27695, USA
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5
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Zhang Z, Shigematsu H, Shimizu T, Ohto U. Improving particle quality in cryo-EM analysis using a PEGylation method. Structure 2021; 29:1192-1199.e4. [PMID: 34048698 DOI: 10.1016/j.str.2021.05.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 02/22/2021] [Accepted: 05/07/2021] [Indexed: 01/30/2023]
Abstract
Cryo-electron microscopy (cryo-EM) is widely used for structural biology studies and has been developed extensively in recent years. However, its sample vitrification process is a major limitation because it causes severe particle aggregation and/or denaturation. This effect is thought to occur because particles tend to stick to the "deadly" air-water interface during vitrification. Here, we report a method for PEGylation of proteins that can efficiently protect particles against such problems during vitrification. This method alleviates the laborious process of fine-tuning the vitrification conditions, allowing for analysis of samples that would otherwise be discarded.
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Affiliation(s)
- Zhikuan Zhang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | | | - Toshiyuki Shimizu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Umeharu Ohto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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Liang G, He H, Nai G, Feng L, Li Y, Zhou Q, Ma Z, Yue Y, Chen B, Mao J. Genome-wide identification of BAM genes in grapevine (Vitis vinifera L.) and ectopic expression of VvBAM1 modulating soluble sugar levels to improve low-temperature tolerance in tomato. BMC PLANT BIOLOGY 2021; 21:156. [PMID: 33771117 PMCID: PMC8004407 DOI: 10.1186/s12870-021-02916-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 03/04/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Low temperature (LT) is one of the main limiting factors that affect growth and development in grape. Increasing soluble sugar and scavenging reactive oxygen species (ROS) play critical roles in grapevine resistance to cold stress. However, the mechanism of β-amylase (BAM) involved in the regulation of sugar levels and antioxidant enzyme activities in response to cold stress is unclear. RESULTS In this study, six BAM genes were identified and clustered into four groups. Multiple sequence alignment and gene structure analysis showed that VvBAM6 lacked the Glu380 residue and contained only an exon. The transcript abundance of VvBAM1 and VvBAM3 significantly increased as temperature decreased. After LT stress, VvBAM1 was highly expressed in the leaves, petioles, stems, and roots of overexpressing tomato lines. The total amylase and BAM activities increased by 6.5- and 6.01-fold in transgenic plants compared with those in wild-type tomato plants (WT) subjected to LT, respectively. The glucose and sucrose contents in transgenic plants were significantly higher than those in WT plants, whereas the starch contents in the former decreased by 1.5-fold compared with those in the latter under LT stress. The analysis of transcriptome sequencing data revealed that 541 genes were upregulated, and 663 genes were downregulated in transgenic plants. One sugar transporter protein gene (SlSTP10), two peroxidase (POD)-related genes (SlPER7 and SlPER5), and one catalase (CAT)-related gene (SlCAT1) were upregulated by 8.6-, 3.6-, 3.0-, and 2.3-fold in transgenic plants after LT stress, respectively. CONCLUSIONS Our results suggest that VvBAM1 overexpression promotes ROS scavenging and improves cold tolerance ability by modulating starch hydrolysis to affect soluble sugar levels in tomato plants.
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Affiliation(s)
- Guoping Liang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Honghong He
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Guojie Nai
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Lidan Feng
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Yanmei Li
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Qi Zhou
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Zonghuan Ma
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Yuan Yue
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Baihong Chen
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China.
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7
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Agrawal DC, Yadav A, Khan MA, Kundu S, Kayastha AM. Denaturant Induced Equilibrium Unfolding and Conformational Transitional Studies of Germinated Fenugreek β-Amylase Revealed Molten Globule like State at Low pH. Protein Pept Lett 2020; 27:1046-1057. [PMID: 32242773 DOI: 10.2174/0929866527666200403082721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/22/2020] [Accepted: 02/24/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND β-Amylase (EC 3.2.1.2) is a maltogenic enzyme, which releases β-maltose from the non-reducing end of the substrates. The enzyme plays important roles for the production of vaccine, maltiol and maltose rich syrups. Apart from these applications the enzyme protects cells from abiotic as well as oxidative damage. The enzyme is βwell characterized in βplants and microbes and crystal structures of β-amylases βhave been βobtained from sweet potato, soybean and Bacillus cereus. OBJECTIVE Find out correlation between structural and functional stability induced by change in pH, temperature and chaotropes. METHODS Activity, intrinsic fluorescence, extrinsic fluorescence, near- and far- ultraviolet circular dichroism spectroscopic measurements were performed. RESULTS Peaks about 208 nm and 222 nm obtained by near-ultraviolet circular dichroism correspond to α-helix whereas peak at 215 nm shows presence of β-sheet. At pH 2.0, absence of tertiary structures, exposed of hydrophobic regions and presence of substantial secondary structures, revealed the existence of molten globule like state. Temperature induced denaturation studies showed that the enzyme was stable up to 75 ºC and the process was found to be irreversible in nature. Chaotropes dependent equilibrium unfolding studies revealed that at low concentration of chaotropes, ellipticity and intrinsic fluorescence βintensity were βdecreased βwhereas βenzymatic activity remained unchanged, which revealed fenugreek β-amylase is multi-domains enzyme and catalytic βdomain βis more βstable compare to non-catalytic domain. Moreover, the transition was sigmoidal and non-coincidental. CONCLUSION Results indicate the probable existence of intermediate states that might perform significant role in physiological process and biotechnological applications.
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Affiliation(s)
- Dinesh Chand Agrawal
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Anjali Yadav
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Mohd Asim Khan
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Arvind M Kayastha
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
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Chandrasekharan NP, Ravenburg CM, Roy IR, Monroe JD, Berndsen CE. Solution structure and assembly of β-amylase 2 from Arabidopsis thaliana. Acta Crystallogr D Struct Biol 2020; 76:357-365. [PMID: 32254060 PMCID: PMC7137110 DOI: 10.1107/s2059798320002016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/12/2020] [Indexed: 11/11/2022] Open
Abstract
Starch is a key energy-storage molecule in plants that requires controlled synthesis and breakdown for effective plant growth. β-Amylases (BAMs) hydrolyze starch into maltose to help to meet the metabolic needs of the plant. In the model plant Arabidopsis thaliana there are nine BAMs, which have apparently distinct functional and domain structures, although the functions of only a few of the BAMs are known and there are no 3D structures of BAMs from this organism. Recently, AtBAM2 was proposed to form a tetramer based on chromatography and activity assays of mutants; however, there was no direct observation of this tetramer. Here, small-angle X-ray scattering data were collected from AtBAM2 and its N-terminal truncations to describe the structure and assembly of the tetramer. Comparison of the scattering of the AtBAM2 tetramer with data collected from sweet potato (Ipomoea batatas) BAM5, which is also reported to form a tetramer, showed there were differences in the overall assembly. Analysis of the N-terminal truncations of AtBAM2 identified a loop sequence found only in BAM2 orthologs that appears to be critical for AtBAM2 tetramer assembly as well as for activity.
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Affiliation(s)
- Nithesh P. Chandrasekharan
- Department of Chemistry and Biochemistry, James Madison University, 901 Carrier Drive, MSC 4501, Harrisonburg, VA 22807, USA
| | - Claire M. Ravenburg
- Department of Biology, James Madison University, 951 Carrier Drive, MSC 7801, Harrisonburg, VA 22807, USA
| | - Ian R. Roy
- Department of Health Sciences, James Madison University, 235 Martin Luther King Jr Way, MSC 4301, Harrisonburg, VA 22807, USA
| | - Jonathan D. Monroe
- Department of Biology, James Madison University, 951 Carrier Drive, MSC 7801, Harrisonburg, VA 22807, USA
| | - Christopher E. Berndsen
- Department of Chemistry and Biochemistry, James Madison University, 901 Carrier Drive, MSC 4501, Harrisonburg, VA 22807, USA
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9
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Winogradoff D, John S, Aksimentiev A. Protein unfolding by SDS: the microscopic mechanisms and the properties of the SDS-protein assembly. NANOSCALE 2020; 12:5422-5434. [PMID: 32080694 PMCID: PMC7291819 DOI: 10.1039/c9nr09135a] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The effects of detergent sodium dodecyl sulfate (SDS) on protein structure and dynamics are fundamental to the most common laboratory technique used to separate proteins and determine their molecular weights: polyacrylamide gel electrophoresis. However, the mechanism by which SDS induces protein unfolding and the microstructure of protein-SDS complexes remain largely unknown. Here, we report a detailed account of SDS-induced unfolding of two proteins-I27 domain of titin and β-amylase-obtained through all-atom molecular dynamics simulations. Both proteins were found to spontaneously unfold in the presence of SDS at boiling water temperature on the time scale of several microseconds. The protein unfolding was found to occur via two distinct mechanisms in which specific interactions of individual SDS molecules disrupt the protein's secondary structure. In the final state of the unfolding process, the proteins are found to wrap around SDS micelles in a fluid necklace-and-beads configuration, where the number and location of bound micelles changes dynamically. The global conformation of the protein was found to correlate with the number of SDS micelles bound to it, whereas the number of SDS molecules directly bound to the protein was found to define the relaxation time scale of the unfolded protein. Our microscopic characterization of SDS-protein interactions sets the stage for future refinement of SDS-enabled protein characterization methods, including protein fingerprinting and sequencing using a solid-state nanopore.
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Affiliation(s)
- David Winogradoff
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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10
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Agrawal DC, Dwevedi A, Kayastha AM. Biochemical and thermodynamic characterization of de novo synthesized β-amylase from fenugreek. Int J Biol Macromol 2019; 130:786-797. [DOI: 10.1016/j.ijbiomac.2019.02.162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/02/2019] [Accepted: 02/28/2019] [Indexed: 11/16/2022]
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11
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Thalmann M, Coiro M, Meier T, Wicker T, Zeeman SC, Santelia D. The evolution of functional complexity within the β-amylase gene family in land plants. BMC Evol Biol 2019; 19:66. [PMID: 30819112 PMCID: PMC6394054 DOI: 10.1186/s12862-019-1395-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/20/2019] [Indexed: 02/02/2023] Open
Abstract
Background β-Amylases (BAMs) are a multigene family of glucan hydrolytic enzymes playing a key role not only for plant biology but also for many industrial applications, such as the malting process in the brewing and distilling industries. BAMs have been extensively studied in Arabidopsis thaliana where they show a surprising level of complexity in terms of specialization within the different isoforms as well as regulatory functions played by at least three catalytically inactive members. Despite the importance of BAMs and the fact that multiple BAM proteins are also present in other angiosperms, little is known about their phylogenetic history or functional relationship. Results Here, we examined 961 β-amylase sequences from 136 different algae and land plant species, including 66 sequenced genomes and many transcriptomes. The extraordinary number and the diversity of organisms examined allowed us to reconstruct the main patterns of β-amylase evolution in land plants. We identified eight distinct clades in angiosperms, which results from extensive gene duplications and sub- or neo-functionalization. We discovered a novel clade of BAM, absent in Arabidopsis, which we called BAM10. BAM10 emerged before the radiation of seed plants and has the feature of an inactive enzyme. Furthermore, we report that BAM4 – an important protein regulating Arabidopsis starch metabolism – is absent in many relevant starch-accumulating crop species, suggesting that starch degradation may be differently regulated between species. Conclusions BAM proteins originated sometime more than 400 million years ago and expanded together with the differentiation of plants into organisms of increasing complexity. Our phylogenetic analyses provide essential insights for future functional studies of this important class of storage glucan hydrolases and regulatory proteins. Electronic supplementary material The online version of this article (10.1186/s12862-019-1395-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthias Thalmann
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland.,Present address: John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mario Coiro
- Department of Systematic and Evolutionary Botany, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
| | - Tiago Meier
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
| | - Samuel C Zeeman
- Department of Biology, ETH Zürich, Universitätstr. 2, CH-8092, Zurich, Switzerland
| | - Diana Santelia
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland. .,Present address: ETH Zürich, Institute of Integrative Biology, Universitätstrasse 16, 8092, Zürich, Switzerland.
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Monroe JD, Storm AR. Review: The Arabidopsis β-amylase (BAM) gene family: Diversity of form and function. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 276:163-170. [PMID: 30348315 DOI: 10.1016/j.plantsci.2018.08.016] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/27/2018] [Accepted: 08/24/2018] [Indexed: 05/04/2023]
Abstract
Multi-gene families present a rich research area to study how related proteins evolve to acquire new structures and functions. The β-amylase (BAM) gene family is named for catalytic members' ability to hydrolyze starch into maltose units. However, the family also contains proteins that are catalytically inactive, have additional domains, or are not localized with a starch substrate. Here we review the current knowledge of each of the nine Arabidopsis BAMs, including information on their localization, structural features, expression patterns, regulation and potential functions. We also discuss unique characteristics of studying multi-gene families, such as the consideration of different kinetic parameters when performing assays on leaf extracts, and suggest approaches that may be fruitful in learning more about their unique functions.
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Affiliation(s)
- Jonathan D Monroe
- Department of Biology, James Madison University, Harrisonburg, VA 22807, United States.
| | - Amanda R Storm
- Department of Biology, Western Carolina University, Cullowhee, NC 28723, United States.
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Monroe JD, Pope LE, Breault JS, Berndsen CE, Storm AR. Quaternary Structure, Salt Sensitivity, and Allosteric Regulation of β-AMYLASE2 From Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2018; 9:1176. [PMID: 30154813 PMCID: PMC6102588 DOI: 10.3389/fpls.2018.01176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/23/2018] [Indexed: 06/08/2023]
Abstract
The β-amylase family in Arabidopsis thaliana has nine members, four of which are both plastid-localized and, based on active-site sequence conservation, potentially capable of hydrolyzing starch to maltose. We recently reported that one of these enzymes, BAM2, is catalytically active in the presence of physiological levels of KCl, exhibits sigmoidal kinetics with a Hill coefficient of over 3, is tetrameric, has a putative secondary binding site (SBS) for starch, and is highly co-expressed with other starch metabolizing enzymes. Here we generated a tetrameric homology model of Arabidopsis BAM2 that is a dimer of dimers in which the putative SBSs of two subunits form a deep groove between the subunits. To validate this model and identify key residues, we generated a series of mutations and characterized the purified proteins. (1) Three point mutations in the putative subunit interfaces disrupted tetramerization; two that interfered with the formation of the starch-binding groove were largely inactive, whereas a third mutation prevented pairs of dimers from forming and was active. (2) The model revealed that a 30-residue N-terminal acidic region, not found in other BAMs, appears to form part of the putative starch-binding groove. A mutant lacking this acidic region was active and did not require KCl for activity. (3) A conserved tryptophan residue in the SBS is necessary for activation and may form π-bonds with sugars in starch. (4) Sequence alignments revealed a conserved serine residue next to one of the catalytic glutamic acid residues, that is a conserved glycine in all other active BAMs. The serine side chain points away from the active site and toward the putative starch-binding groove. Mutating the serine in BAM2 to a glycine resulted in an enzyme with a VMax similar to that of the wild type enzyme but with a 7.5-fold lower KM for soluble starch. Interestingly, the mutant no longer exhibited sigmoidal kinetics, suggesting that allosteric communication between the putative SBS and the active site was disrupted. These results confirm the unusual structure and function of this widespread enzyme, and suggest that our understanding of starch degradation in plants is incomplete.
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Affiliation(s)
- Jonathan D. Monroe
- Department of Biology, James Madison University, Harrisonburg, VA, United States
| | - Lauren E. Pope
- Department of Biology, James Madison University, Harrisonburg, VA, United States
| | - Jillian S. Breault
- Department of Biology, James Madison University, Harrisonburg, VA, United States
| | - Christopher E. Berndsen
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA, United States
| | - Amanda R. Storm
- Department of Biology, Western Carolina University, Cullowhee, NC, United States
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Schwenger A, Jurkowski TP, Richert C. Capturing and Stabilizing Folded Proteins in Lattices Formed with Branched Oligonucleotide Hybrids. Chembiochem 2018; 19:1523-1530. [DOI: 10.1002/cbic.201800145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Alexander Schwenger
- Institut für Organische ChemieUniversität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Tomasz P. Jurkowski
- Institut für Biochemie und Technische BiochemieUniversität Stuttgart Allmandring 31 70569 Stuttgart Germany
| | - Clemens Richert
- Institut für Organische ChemieUniversität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
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15
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Niu C, Zheng F, Li Y, Liu C, Li Q. Process optimization of the extraction condition of β‐amylase from brewer's malt and its application in the maltose syrup production. Biotechnol Appl Biochem 2018; 65:639-647. [DOI: 10.1002/bab.1650] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/28/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Chengtuo Niu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi People's Republic of China
- Laboratory of Brewing Science and Technology, School of Biotechnology Jiangnan University Wuxi People's Republic of China
| | - Feiyun Zheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi People's Republic of China
- Laboratory of Brewing Science and Technology, School of Biotechnology Jiangnan University Wuxi People's Republic of China
| | - Yongxian Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi People's Republic of China
- Laboratory of Brewing Science and Technology, School of Biotechnology Jiangnan University Wuxi People's Republic of China
| | - Chunfeng Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi People's Republic of China
- Laboratory of Brewing Science and Technology, School of Biotechnology Jiangnan University Wuxi People's Republic of China
| | - Qi Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi People's Republic of China
- Laboratory of Brewing Science and Technology, School of Biotechnology Jiangnan University Wuxi People's Republic of China
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Vajravijayan S, Pletnev S, Mani N, Pletneva N, Nandhagopal N, Gunasekaran K. Structural insights on starch hydrolysis by plant β-amylase and its evolutionary relationship with bacterial enzymes. Int J Biol Macromol 2018; 113:329-337. [PMID: 29481953 DOI: 10.1016/j.ijbiomac.2018.02.138] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 02/14/2018] [Accepted: 02/22/2018] [Indexed: 11/17/2022]
Abstract
The conversion of starch to maltose is catalysed in plants by β-amylase. The enzymatic mechanism has been well-characterized for the soybean and barley enzymes, which utilise a glutamic acid-glutamate pair. In the present study, we present a surprise observation of maltotetraose at the active site, the presence of which elucidates the clear role of Thr344 as a conformational "switch" between substrate binding and product release during hydrolysis. This observation is confirmed by the selection of maltotetraose by the crystallized enzyme although that carbohydrate was present in only trace amounts. The conformation of the residues in the substrate-binding site changed upon substrate binding, leading to the movement of threonine, glutamic acid, and the loop conformation, elucidating a missing link in the existing mechanism. By aligning our substrate-free and maltotetraose-bound structures with other existing structures, the sequence of events from substrate binding to hydrolysis can be visualized. Apart from this, the evolutionary relationship among β-amylases of bacterial and amyloplastic origin could be established. The presence of a sugar-binding domain in the bacterial enzyme and its absence in the plant counterpart could be attributed to a carbohydrate-rich environment. Interestingly, cladogram analysis indicates the presence of N-terminal additions in some plant β-amylases. Based on sequence similarity, we postulate that the role of such additions is important for the regulation of enzymatic activity, particularly under stress conditions.
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Affiliation(s)
- S Vajravijayan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India
| | - S Pletnev
- Macromolecular Crystallography Laboratory, National Cancer Institute, and Basic Science Program, Leidos Biomedical Research Inc., Argonne, IL 60439, USA
| | - N Mani
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India
| | - N Pletneva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - N Nandhagopal
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India.
| | - K Gunasekaran
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India.
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17
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He L, Park SH, Hai Dang ND, Duong HX, Duong TPC, Tran PL, Park JT, Ni L, Park KH. Characterization and thermal inactivation kinetics of highly thermostable ramie leaf β-amylase. Enzyme Microb Technol 2017; 101:17-23. [DOI: 10.1016/j.enzmictec.2017.02.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 02/19/2017] [Accepted: 02/24/2017] [Indexed: 11/29/2022]
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18
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Hou J, Zhang H, Liu J, Reid S, Liu T, Xu S, Tian Z, Sonnewald U, Song B, Xie C. Amylases StAmy23, StBAM1 and StBAM9 regulate cold-induced sweetening of potato tubers in distinct ways. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2317-2331. [PMID: 28369567 PMCID: PMC5447890 DOI: 10.1093/jxb/erx076] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Cold-induced sweetening (CIS) in potato is detrimental to the quality of processed products. Conversion of starch to reducing sugars (RS) by amylases is considered one of the main pathways in CIS but is not well studied. The amylase genes StAmy23, StBAM1, and StBAM9 were studied for their functions in potato CIS. StAmy23 is localized in the cytoplasm, whereas StBAM1 and StBAM9 are targeted to the plastid stroma and starch granules, respectively. Genetic transformation of these amylases in potatoes by RNA interference showed that β-amylase activity could be decreased in cold-stored tubers by silencing of StBAM1 and collective silencing of StBAM1 and StBAM9. However, StBAM9 silencing did not decrease β-amylase activity. Silencing StBAM1 and StBAM9 caused starch accumulation and lower RS, which was more evident in simultaneously silenced lines, suggesting functional redundancy. Soluble starch content increased in RNAi-StBAM1 lines but decreased in RNAi-StBAM9 lines, suggesting that StBAM1 may regulate CIS by hydrolysing soluble starch and StBAM9 by directly acting on starch granules. Moreover, StBAM9 interacted with StBAM1 on the starch granules. StAmy23 silencing resulted in higher phytoglycogen and lower RS accumulation in cold-stored tubers, implying that StAmy23 regulates CIS by degrading cytosolic phytoglycogen. Our findings suggest that StAmy23, StBAM1, and StBAM9 function in potato CIS with varying levels of impact.
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Affiliation(s)
- Juan Hou
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture, Wuhan 430070, People's Republic of China
- National Center for Vegetable Improvement (Central China), Wuhan 430070, People's Republic of China
- Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Huiling Zhang
- Huazhong Agricultural University, Wuhan 430070, People's Republic of China
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Wuhan 430070, People's Republic of China
- College of Forestry, Henan University of Science and Technology, Luoyang 471003, People's Republic of China
| | - Jun Liu
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture, Wuhan 430070, People's Republic of China
- National Center for Vegetable Improvement (Central China), Wuhan 430070, People's Republic of China
- Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Stephen Reid
- Biochemistry Division, Department of Biology, Friedrich-Alexander-University Erlangen-Nuernberg, 91058 Erlangen, Germany
| | - Tengfei Liu
- National Center for Vegetable Improvement (Central China), Wuhan 430070, People's Republic of China
- Huazhong Agricultural University, Wuhan 430070, People's Republic of China
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Wuhan 430070, People's Republic of China
| | - Shijing Xu
- National Center for Vegetable Improvement (Central China), Wuhan 430070, People's Republic of China
- Huazhong Agricultural University, Wuhan 430070, People's Republic of China
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Wuhan 430070, People's Republic of China
| | - Zhendong Tian
- National Center for Vegetable Improvement (Central China), Wuhan 430070, People's Republic of China
- Huazhong Agricultural University, Wuhan 430070, People's Republic of China
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Wuhan 430070, People's Republic of China
| | - Uwe Sonnewald
- Biochemistry Division, Department of Biology, Friedrich-Alexander-University Erlangen-Nuernberg, 91058 Erlangen, Germany
| | - Botao Song
- National Center for Vegetable Improvement (Central China), Wuhan 430070, People's Republic of China
- Huazhong Agricultural University, Wuhan 430070, People's Republic of China
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Wuhan 430070, People's Republic of China
| | - Conghua Xie
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture, Wuhan 430070, People's Republic of China
- National Center for Vegetable Improvement (Central China), Wuhan 430070, People's Republic of China
- Huazhong Agricultural University, Wuhan 430070, People's Republic of China
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Costa L, Andriatis A, Brennich M, Teulon JM, Chen SWW, Pellequer JL, Round A. Combined small angle X-ray solution scattering with atomic force microscopy for characterizing radiation damage on biological macromolecules. BMC STRUCTURAL BIOLOGY 2016; 16:18. [PMID: 27788689 PMCID: PMC5081678 DOI: 10.1186/s12900-016-0068-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/06/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND Synchrotron radiation facilities are pillars of modern structural biology. Small-Angle X-ray scattering performed at synchrotron sources is often used to characterize the shape of biological macromolecules. A major challenge with high-energy X-ray beam on such macromolecules is the perturbation of sample due to radiation damage. RESULTS By employing atomic force microscopy, another common technique to determine the shape of biological macromolecules when deposited on flat substrates, we present a protocol to evaluate and characterize consequences of radiation damage. It requires the acquisition of images of irradiated samples at the single molecule level in a timely manner while using minimal amounts of protein. The protocol has been tested on two different molecular systems: a large globular tetremeric enzyme (β-Amylase) and a rod-shape plant virus (tobacco mosaic virus). Radiation damage on the globular enzyme leads to an apparent increase in molecular sizes whereas the effect on the long virus is a breakage into smaller pieces resulting in a decrease of the average long-axis radius. CONCLUSIONS These results show that radiation damage can appear in different forms and strongly support the need to check the effect of radiation damage at synchrotron sources using the presented protocol.
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Affiliation(s)
- Luca Costa
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, Grenoble, 38000 France
- Present Address: CBS, Centre de Biochimie Structurale, CNRS UMR 5048-INSERM UMR 1054, 29, Rue de Navacelles, Montpellier, 34090 France
| | - Alexander Andriatis
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, Grenoble, 38000 France
- MIT, 77 Massachusetts Ave., Cambridge, 02139 MA USA
| | - Martha Brennich
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, Grenoble, 38000 France
| | - Jean-Marie Teulon
- Univ. Grenoble Alpes, 71 Avenue des Martyrs, Grenoble, 38044 France
- CNRS, IBS, 71 Avenue des Martyrs, Grenoble, 38044 France
- CEA, IBS, 71 Avenue des Martyrs, Grenoble, France
| | - Shu-wen W. Chen
- Univ. Grenoble Alpes, 71 Avenue des Martyrs, Grenoble, 38044 France
- CNRS, IBS, 71 Avenue des Martyrs, Grenoble, 38044 France
- CEA, IBS, 71 Avenue des Martyrs, Grenoble, France
| | - Jean-Luc Pellequer
- Univ. Grenoble Alpes, 71 Avenue des Martyrs, Grenoble, 38044 France
- CNRS, IBS, 71 Avenue des Martyrs, Grenoble, 38044 France
- CEA, IBS, 71 Avenue des Martyrs, Grenoble, France
| | - Adam Round
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, Grenoble, 38000 France
- Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 Avenue des Martyrs, Grenoble, 38000 France
- Faculty of Natural Sciences, Keele University, Keele, Staffordshire UK
- Present Address: European XFEL GmbH, Holzkoppel 4, Schenefeld, 22869 Germany
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20
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Choi H, Kim HJ, Matsuura A, Mikami B, Yoon HJ, Lee HH. Structural and functional studies of a metallo-β-lactamase unveil a new type of structurally encoded nickel-containing heterodinuclear site. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:2054-65. [PMID: 26457429 DOI: 10.1107/s1399004715014807] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 08/06/2015] [Indexed: 11/10/2022]
Abstract
The selection of correct metal ions with high fidelity against competing cellular cations is crucial for the function of many metalloenzymes; however, the understanding of the principles that govern metal selectivity is still incomplete. In this study, the crystal structure of the Tm1162 protein from Thermotoga maritima, a metallo-β-lactamase, is reported. Several crystal structures of wild-type Tm1162 and its mutants were solved. Homologues of Tm1162 are widely distributed in bacteria and archaea, including several human pathogens. The monomer possesses an αβ/βα fold, with the core β-strands having the β-sheet sandwich structure common to the metallo-β-lactamase superfamily. Tm1162 exists as a trimer in the crystal and this trimeric unit is likely to be present in solution. In the trimer, three active sites reside at the interface between subunits, suggesting that the oligomeric assembly is crucial for catalysis. A new type of structurally encoded heterodinuclear site has been identified by confirming the identity of nickel-containing heteronuclear sites in Tm1162 via X-ray absorption spectroscopy and anomalous difference Fourier maps. The second coordination sphere, including His8 and Glu73, maintains the side-chain orientations of histidines and stabilizes the metal-binding site. Nickel coordination was crucial for the oligomerization of Tm1162. The nickel-dependent and manganese-dependent β-lactamase and phosphodiesterase activities of Tm1162 have also been characterized.
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Affiliation(s)
- Hwajung Choi
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Hee Jung Kim
- Department of Bio and Nano Chemistry, Kookmin University, Seoul 136-702, Republic of Korea
| | - Atsushi Matsuura
- Department of Bio and Nano Chemistry, Kookmin University, Seoul 136-702, Republic of Korea
| | - Bunzo Mikami
- Laboratory of Quality Design and Exploitation, Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Kyoto 611-0011, Japan
| | - Hye Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
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21
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Unexpected mode of action of sweet potato β-amylase on maltooligomer substrates. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1976-81. [DOI: 10.1016/j.bbapap.2013.06.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 06/18/2013] [Accepted: 06/21/2013] [Indexed: 11/18/2022]
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22
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Rejzek M, Stevenson CE, Southard AM, Stanley D, Denyer K, Smith AM, Naldrett MJ, Lawson DM, Field RA. Chemical genetics and cereal starch metabolism: structural basis of the non-covalent and covalent inhibition of barley β-amylase. MOLECULAR BIOSYSTEMS 2010; 7:718-30. [PMID: 21085740 DOI: 10.1039/c0mb00204f] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
There are major issues regarding the proposed pathway for starch degradation in germinating cereal grain. Given the commercial importance but genetic intractability of the problem, we have embarked on a program of chemical genetics studies to identify and dissect the pathway and regulation of starch degradation in germinating barley grains. As a precursor to in vivo studies, here we report systematic analysis of the reversible and irreversible inhibition of the major β-amylase of the grain endosperm (BMY1). The molecular basis of inhibitor action was defined through high resolution X-ray crystallography studies of unliganded barley β-amylase, as well as its complexes with glycone site binder disaccharide iminosugar G1M, irreversible inhibitors α-epoxypropyl and α-epoxybutyl glucosides, which target the enzyme's catalytic residues, and the aglycone site binders acarbose and α-cyclodextrin.
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Affiliation(s)
- Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
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23
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Dziedzoave N, Graffham A, Westby A, Otoo J, Komlaga G. Influence of variety and growth environment on β-amylase activity of flour from sweet potato (Ipomea batatas). Food Control 2010. [DOI: 10.1016/j.foodcont.2009.05.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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24
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Li J, Francisco P, Zhou W, Edner C, Steup M, Ritte G, Bond CS, Smith SM. Catalytically-inactive beta-amylase BAM4 required for starch breakdown in Arabidopsis leaves is a starch-binding-protein. Arch Biochem Biophys 2009; 489:92-8. [PMID: 19664588 DOI: 10.1016/j.abb.2009.07.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Revised: 07/23/2009] [Accepted: 07/31/2009] [Indexed: 12/15/2022]
Abstract
Of the four chloroplast beta-amylase (BAM) proteins identified in Arabidopsis, BAM3 and BAM4 were previously shown to play the major roles in leaf starch breakdown, although BAM4 apparently lacks key active site residues and beta-amylase activity. Here we tested multiple BAM4 proteins with different N-terminal sequences with a range of glucan substrates and assay methods, but detected no alpha-1,4-glucan hydrolase activity. BAM4 did not affect BAM1, BAM2 or BAM3 activity even when added in 10-fold excess, nor the BAM3-catalysed release of maltose from isolated starch granules in the presence of glucan water dikinase. However, BAM4 binds to amylopectin and to amylose-Sepharose whereas BAM2 has very low beta-amylase activity and poor glucan binding. The low activity of BAM2 may be explained by poor glucan binding but absence of BAM4 activity is not. These results suggest that BAM4 facilitates starch breakdown by a mechanism involving direct interaction with starch or other alpha-1,4-glucan.
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Affiliation(s)
- Jing Li
- Centres of Excellence for Plant Metabolomics, Plant Energy Biology, Crawley, WA 6009, Australia
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25
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Fulton DC, Stettler M, Mettler T, Vaughan CK, Li J, Francisco P, Gil M, Reinhold H, Eicke S, Messerli G, Dorken G, Halliday K, Smith AM, Smith SM, Zeeman SC. Beta-AMYLASE4, a noncatalytic protein required for starch breakdown, acts upstream of three active beta-amylases in Arabidopsis chloroplasts. THE PLANT CELL 2008; 20:1040-58. [PMID: 18390594 PMCID: PMC2390740 DOI: 10.1105/tpc.107.056507] [Citation(s) in RCA: 233] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Revised: 02/21/2008] [Accepted: 03/20/2008] [Indexed: 05/17/2023]
Abstract
This work investigated the roles of beta-amylases in the breakdown of leaf starch. Of the nine beta-amylase (BAM)-like proteins encoded in the Arabidopsis thaliana genome, at least four (BAM1, -2, -3, and -4) are chloroplastic. When expressed as recombinant proteins in Escherichia coli, BAM1, BAM2, and BAM3 had measurable beta-amylase activity but BAM4 did not. BAM4 has multiple amino acid substitutions relative to characterized beta-amylases, including one of the two catalytic residues. Modeling predicts major differences between the glucan binding site of BAM4 and those of active beta-amylases. Thus, BAM4 probably lost its catalytic capacity during evolution. Total beta-amylase activity was reduced in leaves of bam1 and bam3 mutants but not in bam2 and bam4 mutants. The bam3 mutant had elevated starch levels and lower nighttime maltose levels than the wild type, whereas bam1 did not. However, the bam1 bam3 double mutant had a more severe phenotype than bam3, suggesting functional overlap between the two proteins. Surprisingly, bam4 mutants had elevated starch levels. Introduction of the bam4 mutation into the bam3 and bam1 bam3 backgrounds further elevated the starch levels in both cases. These data suggest that BAM4 facilitates or regulates starch breakdown and operates independently of BAM1 and BAM3. Together, our findings are consistent with the proposal that beta-amylase is a major enzyme of starch breakdown in leaves, but they reveal unexpected complexity in terms of the specialization of protein function.
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Affiliation(s)
- Daniel C Fulton
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
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Abstract
An overview presentation is made on the current global status of fungal beta3-amylases, their characteristics and applications in various industries. Among the few available report on beta-amylase producing fungal strains, many showed a preference for a cultivation temperature of 28 degrees C, acidic pH and soluble starch as an inducer of enzyme synthesis. In some fungal strains, alpha-amylase and alpha-glucosidases were found to be present as major contaminating enzymes. Although the existence of a few starch digesting and raw starch adsorbing fungal strains were reported, detailed study on molecular biology of corresponding fungal genes was not available.
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Affiliation(s)
- Rina Rani Ray
- Department of Zoology, Barasat Government College, Barasat, North 24 pgns., West Bengal, India
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27
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Hirata A, Adachi M, Utsumi S, Mikami B. Engineering of the pH optimum of Bacillus cereus beta-amylase: conversion of the pH optimum from a bacterial type to a higher-plant type. Biochemistry 2004; 43:12523-31. [PMID: 15449941 DOI: 10.1021/bi049173h] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The optimum pH of Bacillus cereus beta-amylase (BCB, pH 6.7) differs from that of soybean beta-amylase (SBA, pH 5.4) due to the substitution of a few amino acid residues near the catalytic base residue (Glu 380 in SBA and Glu 367 in BCB). To explore the mechanism for controlling the optimum pH of beta-amylase, five mutants of BCB (Y164E, Y164F, Y164H, Y164Q, and Y164Q/T47M/Y164E/T328N) were constructed and characterized with respect to enzymatic properties and X-ray structural crystal analysis. The optimum pH of the four single mutants shifted to 4.2-4.8, approximately 2 pH units and approximately 1 pH unit lower than those of BCB and SBA, respectively, and their k(cat) values decreased to 41-3% of that of the wild-type enzyme. The X-ray crystal analysis of the enzyme-maltose complexes showed that Glu 367 of the wild type is surrounded by two water molecules (W1 and W2) that are not found in SBA. W1 is hydrogen-bonded to both side chains of Glu 367 and Tyr 164. The mutation of Tyr 164 to Glu and Phe resulted in the disruption of the hydrogen bond between Tyr 164 Oeta and W1 and the introduction of two additional water molecules near position 164. In contrast, the triple mutant of BCB with a slightly decreased pH optimum at pH 6.0 has no water molecules (W1 and W2) around Glu 367. These results suggested that a water-mediated hydrogen bond network (Glu 367...W1...Tyr 164...Thr 328) is the primary requisite for the increased pH optimum of wild-type BCB. This strategy is completely different from that of SBA, in which a hydrogen bond network (Glu 380...Thr 340...Glu 178) reduces the optimum pH in a hydrophobic environment.
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Affiliation(s)
- Akira Hirata
- Laboratory of Food Quality Design and Development, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
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Hirata A, Adachi M, Sekine A, Kang YN, Utsumi S, Mikami B. Structural and enzymatic analysis of soybean beta-amylase mutants with increased pH optimum. J Biol Chem 2004; 279:7287-95. [PMID: 14638688 DOI: 10.1074/jbc.m309411200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Comparison of the architecture around the active site of soybean beta-amylase and Bacillus cereus beta-amylase showed that the hydrogen bond networks (Glu380-(Lys295-Met51) and Glu380-Asn340-Glu178) in soybean beta-amylase around the base catalytic residue, Glu380, seem to contribute to the lower pH optimum of soybean beta-amylase. To convert the pH optimum of soybean beta-amylase (pH 5.4) to that of the bacterial type enzyme (pH 6.7), three mutants of soybean beta-amylase, M51T, E178Y, and N340T, were constructed such that the hydrogen bond networks were removed by site-directed mutagenesis. The kinetic analysis showed that the pH optimum of all mutants shifted dramatically to a neutral pH (range, from 5.4 to 6.0-6.6). The Km values of the mutants were almost the same as that of soybean beta-amylase except in the case of M51T, while the Vmax values of all mutants were low compared with that of soybean beta-amylase. The crystal structure analysis of the wild type-maltose and mutant-maltose complexes showed that the direct hydrogen bond between Glu380 and Asn340 was completely disrupted in the mutants M51T, E178Y, and N340T. In the case of M51T, the hydrogen bond between Glu380 and Lys295 was also disrupted. These results indicated that the reduced pKa value of Glu380 is stabilized by the hydrogen bond network and is responsible for the lower pH optimum of soybean beta-amylase compared with that of the bacterial beta-amylase.
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Affiliation(s)
- Akira Hirata
- Laboratory of Food Quality Design and Development, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
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Díaz A, Sieiro C, Villa TG. Production and partial characterization of a beta-amylase by Xanthophyllomyces dendrorhous. Lett Appl Microbiol 2003; 36:203-7. [PMID: 12641711 DOI: 10.1046/j.1472-765x.2003.01289.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS The characterization of a beta-amylase produced by Xanthophyllomyces dendrorhous. METHODS AND RESULTS Growth in different culture media showed that X. dendrorhous produces an amylase whose synthesis is repressed by the carbon source and induced by starch and maltose. Enzymatic assays using substrates with different degrees of polymerization together with viscosity experiments revealed that the enzyme was beta-amylase. According to the biochemical characterization, the enzyme has a molecular weight of 240 kDa and a Km of 1.35 mg ml-1. The optimum pH and temperature were 5.5 and 50 degrees C, respectively. Using different inhibitors of the enzymatic activity it was shown that cysteine, tryptophan and serine are essential amino acids for catalysis. CONCLUSIONS Xanthophyllomyces dendrorhous CECT1690 synthesizes and secretes beta-amylase that could be a by-product, in addition to carotenoid pigments, in the fermentation downstream. SIGNIFICANCE AND IMPACT OF THE STUDY The beta-amylase produced by X. dendrorhous may have certain industrial applications.
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Affiliation(s)
- A Díaz
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
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Tanaka N, Kajimoto S, Mitani D, Kunugi S. Effects of guanidine hydrochloride and high pressure on subsite flexibility of beta-amylase. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1596:318-25. [PMID: 12007611 DOI: 10.1016/s0167-4838(02)00217-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigated the effects of guanidine hydrochloride (GuHCl) and high pressure on the conformational flexibility of the active site of sweet potato beta-amylase by monitoring the sulfhydryl reaction and the enzymatic activity. The reactivity of Cys345 at the active site, one of six inert half cystine residues of this enzyme, was enhanced by GuHCl at concentrations below 0.5 M. A GuHCl-induced change of the active site was also observed through an intensity change in the near-UV circular dichroism (CD) spectrum. On the other hand, the native conformation of sweet potato beta-amylase observed through fluorescence polarization, far-UV CD spectrum and intrinsic fluorescence was not influenced by GuHCl at concentrations below 0.5 M. Therefore, Cys345 reaction caused by GuHCl was due to an alteration of the local conformation of the active site. GuHCl-induced reaction of Cys345, located in the vicinity of subsites 3 and 4, is attributed to enhanced subsite flexibility, which is responsible for substrate slipping in a single-chain attack mechanism. Due to the flexible conformation, the local region of the subsite is more susceptible to GuHCl perturbation than the molecule overall. The enzymatic activity of sweet potato beta-amylase was reversibly inhibited by GuHCl at concentrations below 0.5 M, and kinetic analysis of the enzymatic mechanism showed that GuHCl decreases the kcat value. High pressure below 400 MPa also inactivated sweet potato beta-amylase with an increase in Cys345 reactivity. These findings indicated that excessively enhanced subsite flexibility reduced the enzymatic activity of sweet potato beta-amylase.
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Affiliation(s)
- Naoki Tanaka
- Department of Polymer Science and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo, 606-8585, Kyoto, Japan.
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31
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Van Damme EJ, Hu J, Barre A, Hause B, Baggerman G, Rougé P, Peumans WJ. Purification, characterization, immunolocalization and structural analysis of the abundant cytoplasmic beta-amylase from Calystegia sepium (hedge bindweed) rhizomes. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:6263-73. [PMID: 11733023 DOI: 10.1046/j.0014-2956.2001.02584.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
An abundant catalytically active beta-amylase (EC 3.2.1.2) was isolated from resting rhizomes of hedge bindweed (Calystegia sepium). Biochemical analysis of the purified protein, molecular modeling, and cloning of the corresponding gene indicated that this enzyme resembles previously characterized plant beta-amylases with regard to its amino-acid sequence, molecular structure and catalytic activities. Immunolocalization demonstrated that the beta-amylase is exclusively located in the cytoplasm. It is suggested that the hedge bindweed rhizome beta-amylase is a cytoplasmic vegetative storage protein.
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Affiliation(s)
- E J Van Damme
- Laboratory for Phytopathology and Plant Protection, Katholieke Universiteit Leuven, Leuven, Belgium.
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Mikami B, Yoon HJ, Yoshigi N. The crystal structure of the sevenfold mutant of barley beta-amylase with increased thermostability at 2.5 A resolution. J Mol Biol 1999; 285:1235-43. [PMID: 9918723 DOI: 10.1006/jmbi.1998.2379] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The three-dimensional structure of the sevenfold mutant of barley beta-amylase (BBA-7s) with increased thermostability was determined by X-ray crystallography. The enzyme was purified as a single component and crystallized by a hanging drop method in the presence of 14 % PEG 6000. The crystals belong to space group P43212 with cell dimensions a=b=72.11 A, c=250.51 A. The diffraction data up to 2.5 A were collected after soaking the crystal in 100 mM maltose with Rsym of 8.6 %. The structure was determined by a molecular replacement method using soybean beta-amylase (SBA) as a search model and refined to an R-factor of 18.7 %. The final model included 500 amino acid residues, 141 water molecules and three glucose residues, which were located at subsites 1-2 and 4 in the active site. The r.m.s. distance of 485 Calpha atoms between BBA-7s and SBA was 0.62 A. Out of the seven mutated amino acids, four (Ser295Ala, Ile297Val, Ser351Pro and Ala376Ser) were substitutions from the common residues with SBA to the thermostable forms. A comparison of the structures of BBA-7s and SBA indicated that the side-chain of Ser376 makes new hydrogen bonds to the main-chain of an adjacent beta-strand, and that the side-chains of Val297 reduce an unfavorable interaction between the side-chains of Ala314. The mutation of Ser295Ala breaks the hydrogen bond between Ser295 OG and Tyr195 OH, which seems to be the reason for the unoccupied glucose residue at subsite 3. The tandem mutations at 350-352 including substitutions to two Pro residues suggested the reduction of main-chain entropy in the unfolded structure of this solvent-exposed protruded loop.
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Affiliation(s)
- B Mikami
- Kyoto University, Uji, Kyoto, 611, Japan.
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Pujadas G, Ramírez FM, Valero R, Palau J. Evolution of β-amylase: Patterns of variation and conservation in subfamily sequences in relation to parsimony mechanisms. Proteins 1998. [DOI: 10.1002/(sici)1097-0134(199608)25:4<456::aid-prot6>3.0.co;2-b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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34
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Adachi M, Mikami B, Katsube T, Utsumi S. Crystal structure of recombinant soybean beta-amylase complexed with beta-cyclodextrin. J Biol Chem 1998; 273:19859-65. [PMID: 9677422 DOI: 10.1074/jbc.273.31.19859] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In order to study the interaction of soybean beta-amylase with substrate, we solved the crystal structure of beta-cyclodextrin-enzyme complex and compared it with that of alpha-cyclodextrin-enzyme complex. The enzyme was expressed in Escherichia coli at a high level as a soluble and catalytically active protein. The purified recombinant enzyme had properties nearly identical to those of native soybean beta-amylase and formed the same crystals as the native enzyme. The crystal structure of recombinant enzyme complexed with beta-cyclodextrin was refined at 2. 07-A resolution with a final crystallographic R value of 15.8% (Rfree = 21.1%). The root mean square deviation in the position of C-alpha atoms between this recombinant enzyme and the native enzyme was 0.22 A. These results indicate that the expression system established here is suitable for studying structure-function relationships of beta-amylase. The conformation of the bound beta-cyclodextrin takes an ellipsoid shape in contrast to the circular shape of the bound alpha-cyclodextrin. The cyclodextrins shared mainly two glucose binding sites, 3 and 4. The glucose residue 4 was slightly shifted from the maltose binding site. This suggests that the binding site of the cyclodextrins is important for its holding of a cleaved substrate, which enables the multiple attack mechanism of beta-amylase.
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Affiliation(s)
- M Adachi
- Research Institute for Food Science, Kyoto University, Uji Kyoto 611-0011, Japan
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35
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Janecek S. alpha-Amylase family: molecular biology and evolution. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1997; 67:67-97. [PMID: 9401418 DOI: 10.1016/s0079-6107(97)00015-1] [Citation(s) in RCA: 146] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Pujadas G, Ramírez FM, Valero R, Palau J. Evolution of beta-amylase: patterns of variation and conservation in subfamily sequences in relation to parsimony mechanisms. Proteins 1996; 25:456-72. [PMID: 8865341 DOI: 10.1002/prot.6] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Soybean and sweet potato beta-amylases are structured as alpha/beta barrels and the same kind of folding may account for all known beta-amylases. We provide a comprehensive analysis of both protein and DNA (coding region) sequences of beta-amylases. The aim of the study is to contribute to the knowledge of the evolutionary molecular relationships among all known beta-amylases. Our approach combines the identification of the putative eightfold structural core formed by beta-strands with a complete multi-alignment analysis of all known sequences. Comparing putative beta-amylase (alpha/beta)8 cores from plants and microorganisms, two differentiated versions of residues at the packing sites, and a unique set of eight identical residues at the C-terminal catalytical site are observed, indicating early evolutionary divergence and absence of localized three-dimensional evolution, respectively. A new analytical approach has been developed in order to work out conserved motifs for beta-amylases, mostly related with the enzyme activity. This approach appears useful as a new routine to find sets of motifs (each set being known as a fingerprint) in protein families. We demonstrate that the evolutionary mechanism for beta-amylases is a combination of parsimonious divergence at three distinguishable rates in relation to the functional signatures, the barrel scaffold, and alpha-helix-containing loops.
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Affiliation(s)
- G Pujadas
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Catalonia, Spain
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Wiesmann C, Beste G, Hengstenberg W, Schulz GE. The three-dimensional structure of 6-phospho-beta-galactosidase from Lactococcus lactis. Structure 1995; 3:961-8. [PMID: 8535789 DOI: 10.1016/s0969-2126(01)00230-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND The enzyme 6-phospho-beta-galactosidase hydrolyzes phospholactose, the product of a phosphor-enolpyruvate-dependent phosphotransferase system. It belongs to glycosidase family 1 and no structure has yet been published for a member of this family. RESULTS The crystal structure of 6-phospho-beta-galactosidase was determined at 2.3 A resolution by multiple isomorphous replacement, using the wild-type enzyme and a designed cysteine mutant. A second crystal form, found with the mutant enzyme, was solved by molecular replacement, yielding the conformation of two chain loops that are invisible in the first crystal form. The active center, located through catalytic residues identified in previous studies, cannot be accessed by the substrate if the two loops are in their defined conformation. The enzyme contains a (beta alpha)8 barrel and the relationship of its chain fold to that of other glycosidases has been quantified. As a side issue, we observed that a cysteine point mutant designed for X-ray analysis crystallized mainly as a symmetric dimer around an intermolecular disulfide bridge formed by the newly introduced cysteine. CONCLUSIONS The presented analysis provides a basis on which to model all other family 1 members and thereby will help in elucidating the catalytic mechanisms of these sequence-related enzymes. Moreover, this enzyme belongs to a superfamily of glycosidases sharing a (beta alpha)8 barrel with catalytic glutamates/aspartates at the ends of the fourth and the seventh strands of the beta barrel.
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Affiliation(s)
- C Wiesmann
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Freiburg, Germany
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Mutational analysis of catalytic mechanism and specificity in amylolytic enzymes. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/s0921-0423(06)80099-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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