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Díaz-Pérez AL, Díaz-Pérez C, Gaona-García RY, Hernández-Santoyo A, Lázaro-Mixteco PE, Reyes-De La Cruz H, Campos-García J. Study of peripheral domains in structure-function of isocitrate lyase (ICL) from Pseudomonas aeruginosa. World J Microbiol Biotechnol 2023; 39:339. [PMID: 37821748 DOI: 10.1007/s11274-023-03768-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/15/2023] [Indexed: 10/13/2023]
Abstract
The capacity of Pseudomonas aeruginosa to assimilate nutrients is essential for niche colonization and contributes to its pathogenicity. Isocitrate lyase (ICL), the first enzyme of the glyoxylate cycle, redirects isocitrate from the tricarboxylic acid cycle to render glyoxylate and succinate. P. aeruginosa ICL (PaICL) is regarded as a virulence factor due to its role in carbon assimilation during infection. The AceA/ICL protein family shares the catalytic domain I, triosephosphate isomerase barrel (TIM-barrel). The carboxyl terminus of domain I is essential for Escherichia coli ICL (EcICL) of subfamily 1. PaICL, which belongs to subfamily 3, has domain II inserted at the periphery of domain I, which is believed to participate in enzyme oligomerization. In addition, PaICL has the α13-loop-α14 (extended motif), which protrudes from the enzyme core, being of unknown function. This study investigates the role of domain II, the extended motif, and the carboxyl-terminus (C-ICL) and amino-terminus (N-ICL) regions in the function of the PaICL enzyme, also as their involvement in the virulence of P. aeruginosa PAO1. Deletion of domain II and the extended motif results in enzyme inactivation and structural instability of the enzyme. The His6-tag fusion at the C-ICL protein produced a less efficient enzyme than fusion at the N-ICL, but without affecting the acetate assimilation or virulence. The PaICL homotetrameric structure of the enzyme was more stable in the N-His6-ICL than in the C-His6-ICL, suggesting that the C-terminus is critical for the ICL quaternary conformation. The ICL-mutant A39 complemented with the recombinant proteins N-His6-ICL or C-His6-ICL were more virulent than the WT PAO1 strain. The findings indicate that the domain II and the extended motif are essential for the ICL structure/function, and the C-terminus is involved in its quaternary structure conformation, confirming that in P. aeruginosa, the ICL is essential for acetate assimilation and virulence.
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Affiliation(s)
- Alma Laura Díaz-Pérez
- Lab. de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. U-3, Ciudad Universitaria, 58030, Morelia, Mich., Mexico
| | - César Díaz-Pérez
- Facultad de Agrobiologia, Campus Celaya-Salvatierra, Universiad de Guanajuato, Guanajuato, Gto., Mexico
| | - Roxana Yughadi Gaona-García
- Lab. de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. U-3, Ciudad Universitaria, 58030, Morelia, Mich., Mexico
| | - Alejandra Hernández-Santoyo
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Pedro E Lázaro-Mixteco
- Facultad de Ingeniería Química, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich., Mexico
| | - Homero Reyes-De La Cruz
- Lab. de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. U-3, Ciudad Universitaria, 58030, Morelia, Mich., Mexico
| | - Jesús Campos-García
- Lab. de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. U-3, Ciudad Universitaria, 58030, Morelia, Mich., Mexico.
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2
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Romero ML, Garcia Seisdedos H, Ibarra‐Molero B. Active site center redesign increases protein stability preserving catalysis in thioredoxin. Protein Sci 2022; 31:e4417. [PMID: 39287965 PMCID: PMC9601870 DOI: 10.1002/pro.4417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/15/2022] [Accepted: 07/31/2022] [Indexed: 11/08/2022]
Abstract
The stabilization of natural proteins is a long-standing desired goal in protein engineering. Optimizing the hydrophobicity of the protein core often results in extensive stability enhancements. However, the presence of totally or partially buried catalytic charged residues, essential for protein function, has limited the applicability of this strategy. Here, focusing on the thioredoxin, we aimed to augment protein stability by removing buried charged residues in the active site without loss of catalytic activity. To this end, we performed a charged-to-hydrophobic substitution of a buried and functional group, resulting in a significant stability increase yet abolishing catalytic activity. Then, to simulate the catalytic role of the buried ionizable group, we designed a combinatorial library of variants targeting a set of seven surface residues adjacent to the active site. Notably, more than 50% of the library variants restored, to some extent, the catalytic activity. The combination of experimental study of 2% of the library with the prediction of the whole mutational space by partial least squares regression revealed that a single point mutation at the protein surface is sufficient to fully restore the catalytic activity without thermostability cost. As a result, we engineered one of the highest thermal stabilities reported for a protein with a natural occurring fold (137°C). Further, our hyperstable variant preserves the catalytic activity both in vitro and in vivo.
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Affiliation(s)
- Maria Luisa Romero
- Departamento de Química FísicaUniversidad de GranadaGranada
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
| | - Hector Garcia Seisdedos
- Departamento de Química FísicaUniversidad de GranadaGranada
- Department of Structural BiologyWeizmann Institute of ScienceRehovotIsrael
- Department of Structural BiologyInstituto de Biologia Molecular de Barcelona (IBMB‐CSIC)BarcelonaSpain
| | - Beatriz Ibarra‐Molero
- Departamento de Química FísicaUniversidad de GranadaGranada
- Department of Structural BiologyInstituto de Biologia Molecular de Barcelona (IBMB‐CSIC)BarcelonaSpain
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3
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Chan YH, Zeldovich KB, Matthews CR. An allosteric pathway explains beneficial fitness in yeast for long-range mutations in an essential TIM barrel enzyme. Protein Sci 2020; 29:1911-1923. [PMID: 32643222 PMCID: PMC7454521 DOI: 10.1002/pro.3911] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 11/06/2022]
Abstract
Protein evolution proceeds by a complex response of organismal fitness to mutations that can simultaneously affect protein stability, structure, and enzymatic activity. To probe the relationship between genotype and phenotype, we chose a fundamental paradigm for protein evolution, folding, and design, the (βα)8 TIM barrel fold. Here, we demonstrate the role of long-range allosteric interactions in the adaptation of an essential hyperthermophilic TIM barrel enzyme to mesophilic conditions in a yeast host. Beneficial fitness effects observed with single and double mutations of the canonical βα-hairpin clamps and the α-helical shell distal to the active site revealed an underlying energy network between opposite faces of the cylindrical β-barrel. We experimentally determined the fitness of multiple mutants in the energetic phase plane, contrasting the energy barrier of the chemical reaction and the folding free energy of the protein. For the system studied, the reaction energy barrier was the primary determinant of organism fitness. Our observations of long-range epistatic interactions uncovered an allosteric pathway in an ancient and ubiquitous enzyme that may provide a novel way of designing proteins with a desired activity and stability profile.
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Affiliation(s)
- Yvonne H Chan
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Sanofi Pasteur, Cambridge, Massachusetts, USA
| | - Konstantin B Zeldovich
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Sanofi Pasteur, Cambridge, Massachusetts, USA
| | - Charles R Matthews
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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4
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Tiwari SP, Reuter N. Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes. PLoS Comput Biol 2016; 12:e1004834. [PMID: 27015412 PMCID: PMC4807811 DOI: 10.1371/journal.pcbi.1004834] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 02/25/2016] [Indexed: 11/19/2022] Open
Abstract
The conservation of the intrinsic dynamics of proteins emerges as we attempt to understand the relationship between sequence, structure and functional conservation. We characterise the conservation of such dynamics in a case where the structure is conserved but function differs greatly. The triosephosphate isomerase barrel fold (TBF), renowned for its 8 β-strand-α-helix repeats that close to form a barrel, is one of the most diverse and abundant folds found in known protein structures. Proteins with this fold have diverse enzymatic functions spanning five of six Enzyme Commission classes, and we have picked five different superfamily candidates for our analysis using elastic network models. We find that the overall shape is a large determinant in the similarity of the intrinsic dynamics, regardless of function. In particular, the β-barrel core is highly rigid, while the α-helices that flank the β-strands have greater relative mobility, allowing for the many possibilities for placement of catalytic residues. We find that these elements correlate with each other via the loops that link them, as opposed to being directly correlated. We are also able to analyse the types of motions encoded by the normal mode vectors of the α-helices. We suggest that the global conservation of the intrinsic dynamics in the TBF contributes greatly to its success as an enzymatic scaffold both through evolution and enzyme design.
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Affiliation(s)
- Sandhya P. Tiwari
- Department of Molecular Biology, University of Bergen, Pb. 7803, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Pb. 7803, Bergen, Norway
| | - Nathalie Reuter
- Department of Molecular Biology, University of Bergen, Pb. 7803, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Pb. 7803, Bergen, Norway
- * E-mail:
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5
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Huang PS, Feldmeier K, Parmeggiani F, Velasco DAF, Höcker B, Baker D. De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy. Nat Chem Biol 2015; 12:29-34. [PMID: 26595462 PMCID: PMC4684731 DOI: 10.1038/nchembio.1966] [Citation(s) in RCA: 172] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 10/07/2015] [Indexed: 12/26/2022]
Abstract
Despite efforts for over 25 years, de novo protein design has not succeeded in achieving the TIM-barrel fold. Here we describe the computational design of four-fold symmetrical (β/α)8 barrels guided by geometrical and chemical principles. Experimental characterization of 33 designs revealed the importance of side chain-backbone hydrogen bonds for defining the strand register between repeat units. The X-ray crystal structure of a designed thermostable 184-residue protein is nearly identical to that of the designed TIM-barrel model. PSI-BLAST searches do not identify sequence similarities to known TIM-barrel proteins, and sensitive profile-profile searches indicate that the design sequence is distant from other naturally occurring TIM-barrel superfamilies, suggesting that Nature has sampled only a subset of the sequence space available to the TIM-barrel fold. The ability to design TIM barrels de novo opens new possibilities for custom-made enzymes.
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Affiliation(s)
- Po-Ssu Huang
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Kaspar Feldmeier
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Fabio Parmeggiani
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | | | - Birte Höcker
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
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6
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Dong YN, Chen HQ, Sun YH, Zhang H, Chen W. A differentially conserved residue (Ile42) of GH42 β-galactosidase from Geobacillus stearothermophilus BgaB is involved in both catalysis and thermostability. J Dairy Sci 2015; 98:2268-76. [DOI: 10.3168/jds.2014-9117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 12/19/2014] [Indexed: 12/31/2022]
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7
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 256] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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8
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Bordeaux M, Galarneau A, Drone J. Catalytic, Mild, and Selective Oxyfunctionalization of Linear Alkanes: Current Challenges. Angew Chem Int Ed Engl 2012; 51:10712-23. [DOI: 10.1002/anie.201203280] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Indexed: 02/02/2023]
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9
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Bordeaux M, Galarneau A, Drone J. Katalytische, milde und selektive Oxyfunktionalisierung von linearen Alkanen: aktuelle Herausforderungen. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201203280] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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10
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List F, Sterner R, Wilmanns M. Related (βα)8-barrel proteins in histidine and tryptophan biosynthesis: a paradigm to study enzyme evolution. Chembiochem 2011; 12:1487-94. [PMID: 21656890 DOI: 10.1002/cbic.201100082] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Indexed: 12/12/2022]
Affiliation(s)
- Felix List
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
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11
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Pei XQ, Yi ZL, Tang CG, Wu ZL. Three amino acid changes contribute markedly to the thermostability of β-glucosidase BglC from Thermobifida fusca. BIORESOURCE TECHNOLOGY 2011; 102:3337-42. [PMID: 21129951 DOI: 10.1016/j.biortech.2010.11.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 11/06/2010] [Indexed: 05/07/2023]
Abstract
Thermostability of β-glucosidase was enhanced by family shuffling, site saturation mutagenesis, and site-directed mutagenesis. Family shuffling was carried out based on β-glucosidase BglC from Thermobifida fusca and β-glucosidase BglB from Paebibacillus polymxyxa with the help of synthetic primers. High-throughput screening revealed mutants with higher thermostability than both parental enzymes. The most thermostable mutant VM2 containing three key amino acid changes in L444Y/G447S/A433V had a 144-fold increase in half-life of inactivation as compared to the parental enzyme BglC. The mutant VM2 showed 28% and 94% increase in k(cat) towards p-nitrophenyl-β-D-glucopyranoside (pNPG) and cellobiose, respectively. The mutant with enhanced stability would facilitate the recycle of β-glucosidase in the bioconversion of cellulosic biomass.
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Affiliation(s)
- Xiao-Qiong Pei
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
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12
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de Kraker JW, Gershenzon J. From amino acid to glucosinolate biosynthesis: protein sequence changes in the evolution of methylthioalkylmalate synthase in Arabidopsis. THE PLANT CELL 2011; 23:38-53. [PMID: 21205930 PMCID: PMC3051243 DOI: 10.1105/tpc.110.079269] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 12/02/2010] [Accepted: 12/16/2010] [Indexed: 05/18/2023]
Abstract
Methylthioalkylmalate synthase (MAM) catalyzes the committed step in the side chain elongation of Met, yielding important precursors for glucosinolate biosynthesis in Arabidopsis thaliana and other Brassicaceae species. MAM is believed to have evolved from isopropylmalate synthase (IPMS), an enzyme involved in Leu biosynthesis, based on phylogenetic analyses and an overlap of catalytic abilities. Here, we investigated the changes in protein structure that have occurred during the recruitment of IPMS from amino acid to glucosinolate metabolism. The major sequence difference between IPMS and MAM is the absence of 120 amino acids at the C-terminal end of MAM that constitute a regulatory domain for Leu-mediated feedback inhibition. Truncation of this domain in Arabidopsis IPMS2 results in loss of Leu feedback inhibition and quaternary structure, two features common to MAM enzymes, plus an 8.4-fold increase in the k(cat)/K(m) for a MAM substrate. Additional exchange of two amino acids in the active site resulted in a MAM-like enzyme that had little residual IPMS activity. Hence, combination of the loss of the regulatory domain and a few additional amino acid exchanges can explain the evolution of MAM from IPMS during its recruitment from primary to secondary metabolism.
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13
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Wierenga RK, Kapetaniou EG, Venkatesan R. Triosephosphate isomerase: a highly evolved biocatalyst. Cell Mol Life Sci 2010; 67:3961-82. [PMID: 20694739 PMCID: PMC11115733 DOI: 10.1007/s00018-010-0473-9] [Citation(s) in RCA: 160] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 07/15/2010] [Accepted: 07/16/2010] [Indexed: 02/04/2023]
Abstract
Triosephosphate isomerase (TIM) is a perfectly evolved enzyme which very fast interconverts dihydroxyacetone phosphate and D: -glyceraldehyde-3-phosphate. Its catalytic site is at the dimer interface, but the four catalytic residues, Asn11, Lys13, His95 and Glu167, are from the same subunit. Glu167 is the catalytic base. An important feature of the TIM active site is the concerted closure of loop-6 and loop-7 on ligand binding, shielding the catalytic site from bulk solvent. The buried active site stabilises the enediolate intermediate. The catalytic residue Glu167 is at the beginning of loop-6. On closure of loop-6, the Glu167 carboxylate moiety moves approximately 2 Å to the substrate. The dynamic properties of the Glu167 side chain in the enzyme substrate complex are a key feature of the proton shuttling mechanism. Two proton shuttling mechanisms, the classical and the criss-cross mechanism, are responsible for the interconversion of the substrates of this enolising enzyme.
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Affiliation(s)
- R K Wierenga
- Biocenter Oulu and Department of Biochemistry, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland.
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14
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Shen H, Xu F, Hu H, Wang F, Wu Q, Huang Q, Wang H. Coevolving residues of (β/α)8-barrel proteins play roles in stabilizing active site architecture and coordinating protein dynamics. J Struct Biol 2008; 164:281-92. [DOI: 10.1016/j.jsb.2008.09.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Revised: 08/31/2008] [Accepted: 09/04/2008] [Indexed: 11/16/2022]
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15
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Sasaki M, Uno M, Akanuma S, Yamagishi A. Random mutagenesis improves the low-temperature activity of the tetrameric 3-isopropylmalate dehydrogenase from the hyperthermophile Sulfolobus tokodaii. Protein Eng Des Sel 2008; 21:721-7. [DOI: 10.1093/protein/gzn054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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16
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Hild E, Brumbley SM, O'Shea MG, Nevalainen H, Bergquist PL. A Paenibacillus sp. dextranase mutant pool with improved thermostability and activity. Appl Microbiol Biotechnol 2007; 75:1071-8. [PMID: 17426967 DOI: 10.1007/s00253-007-0936-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Revised: 03/06/2007] [Accepted: 03/07/2007] [Indexed: 10/23/2022]
Abstract
Random mutagenesis was used to create a library of chimeric dextranase (dex1) genes. A plate-screening protocol was developed with improved thermostability as a selection criterion. The mutant library was screened for active dextranase variants by observing clearing zones on dextran-blue agar plates at 50 degrees C after exposure to 68 degrees C for 2 h, a temperature regime at which wild-type activity was abolished. A number of potentially improved variants were identified by this strategy, five of which were further characterised. DNA sequencing revealed ten nucleotide substitutions, ranging from one to four per variant. Thermal inactivation studies showed reduced (2.9-fold) thermostability for one variant and similar thermostability for a second variant, but confirmed improved thermostability for three mutants with 2.3- (28.9 min) to 6.9-fold (86.6 min) increases in half-lives at 62 degrees C compared to that of the wild-type enzyme (12.6 min). Using a 10-min assay, apparent temperature optima of the variants were similar to that of the wild type (T (opt) 60 degrees C). However, one of these variants had increased enzyme activity. Therefore, the first-generation dextranase mutant pool obtained in this study has sufficient molecular diversity for further improvements in both thermostability and activity through recombination (gene shuffling).
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Affiliation(s)
- Erika Hild
- Department of Chemistry & Biomolecular Sciences, Macquarie University, Sydney, New South Wales, 2109, Australia
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17
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Sterner R, Höcker B. Catalytic Versatility, Stability, and Evolution of the (βα)8-Barrel Enzyme Fold. Chem Rev 2005; 105:4038-55. [PMID: 16277370 DOI: 10.1021/cr030191z] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Reinhard Sterner
- Institut für Biophysik und physikalische Biochemie, Universität Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany.
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18
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Directed enzyme evolution: Bridging the gap between natural enzymes and commercial applications. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.bioeng.2005.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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