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Buhrman G, Enríquez P, Dillard L, Baer H, Truong V, Grunden AM, Rose RB. Structure, Function, and Thermal Adaptation of the Biotin Carboxylase Domain Dimer from Hydrogenobacter thermophilus 2-Oxoglutarate Carboxylase. Biochemistry 2021; 60:324-345. [PMID: 33464881 DOI: 10.1021/acs.biochem.0c00815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
2-Oxoglutarate carboxylase (OGC), a unique member of the biotin-dependent carboxylase family from the order Aquificales, captures dissolved CO2 via the reductive tricarboxylic acid (rTCA) cycle. Structure and function studies of OGC may facilitate adaptation of the rTCA cycle to increase the level of carbon fixation for biofuel production. Here we compare the biotin carboxylase (BC) domain of Hydrogenobacter thermophilus OGC with the well-studied mesophilic homologues to identify features that may contribute to thermal stability and activity. We report three OGC BC X-ray structures, each bound to bicarbonate, ADP, or ADP-Mg2+, and propose that substrate binding at high temperatures is facilitated by interactions that stabilize the flexible subdomain B in a partially closed conformation. Kinetic measurements with varying ATP and biotin concentrations distinguish two temperature-dependent steps, consistent with biotin's rate-limiting role in organizing the active site. Transition state thermodynamic values derived from the Eyring equation indicate a larger positive ΔH⧧ and a less negative ΔS⧧ compared to those of a previously reported mesophilic homologue. These thermodynamic values are explained by partially rate limiting product release. Phylogenetic analysis of BC domains suggests that OGC diverged prior to Aquificales evolution. The phylogenetic tree identifies mis-annotations of the Aquificales BC sequences, including the Aquifex aeolicus pyruvate carboxylase structure. Notably, our structural data reveal that the OGC BC dimer comprises a "wet" dimerization interface that is dominated by hydrophilic interactions and structural water molecules common to all BC domains and likely facilitates the conformational changes associated with the catalytic cycle. Mutations in the dimerization domain demonstrate that dimerization contributes to thermal stability.
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Affiliation(s)
- Greg Buhrman
- Department of Molecular & Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7622, United States
| | - Paul Enríquez
- Department of Molecular & Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7622, United States
| | - Lucas Dillard
- Department of Molecular & Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7622, United States
| | - Hayden Baer
- Department of Molecular & Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7622, United States
| | - Vivian Truong
- Department of Molecular & Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7622, United States
| | - Amy M Grunden
- Department of Plant & Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695-7612, United States
| | - Robert B Rose
- Department of Molecular & Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7622, United States
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Nittinger E, Flachsenberg F, Bietz S, Lange G, Klein R, Rarey M. Placement of Water Molecules in Protein Structures: From Large-Scale Evaluations to Single-Case Examples. J Chem Inf Model 2018; 58:1625-1637. [DOI: 10.1021/acs.jcim.8b00271] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Eva Nittinger
- Universität Hamburg, ZBH − Center for Bioinformatics, Bundesstraße 43, 20146 Hamburg, Germany
| | - Florian Flachsenberg
- Universität Hamburg, ZBH − Center for Bioinformatics, Bundesstraße 43, 20146 Hamburg, Germany
| | - Stefan Bietz
- Universität Hamburg, ZBH − Center for Bioinformatics, Bundesstraße 43, 20146 Hamburg, Germany
| | - Gudrun Lange
- Bayer CropScience AG, Industriepark Hoechst G836, 65926 Frankfurt am Main, Germany
| | - Robert Klein
- Bayer CropScience AG, Industriepark Hoechst G836, 65926 Frankfurt am Main, Germany
| | - Matthias Rarey
- Universität Hamburg, ZBH − Center for Bioinformatics, Bundesstraße 43, 20146 Hamburg, Germany
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Thompson MP, Turner NJ. Two-Enzyme Hydrogen-Borrowing Amination of Alcohols Enabled by a Cofactor-Switched Alcohol Dehydrogenase. ChemCatChem 2017. [DOI: 10.1002/cctc.201701092] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Matthew P. Thompson
- School of Chemistry, Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Nicholas J. Turner
- School of Chemistry, Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
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Moschetti T, Sharpe T, Fischer G, Marsh ME, Ng HK, Morgan M, Scott DE, Blundell TL, R. Venkitaraman A, Skidmore J, Abell C, Hyvönen M. Engineering Archeal Surrogate Systems for the Development of Protein-Protein Interaction Inhibitors against Human RAD51. J Mol Biol 2016; 428:4589-4607. [PMID: 27725183 PMCID: PMC5117717 DOI: 10.1016/j.jmb.2016.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 10/02/2016] [Accepted: 10/04/2016] [Indexed: 02/02/2023]
Abstract
Protein-protein interactions (PPIs) are increasingly important targets for drug discovery. Efficient fragment-based drug discovery approaches to tackle PPIs are often stymied by difficulties in the production of stable, unliganded target proteins. Here, we report an approach that exploits protein engineering to "humanise" thermophilic archeal surrogate proteins as targets for small-molecule inhibitor discovery and to exemplify this approach in the development of inhibitors against the PPI between the recombinase RAD51 and tumour suppressor BRCA2. As human RAD51 has proved impossible to produce in a form that is compatible with the requirements of fragment-based drug discovery, we have developed a surrogate protein system using RadA from Pyrococcus furiosus. Using a monomerised RadA as our starting point, we have adopted two parallel and mutually instructive approaches to mimic the human enzyme: firstly by mutating RadA to increase sequence identity with RAD51 in the BRC repeat binding sites, and secondly by generating a chimeric archaeal human protein. Both approaches generate proteins that interact with a fourth BRC repeat with affinity and stoichiometry comparable to human RAD51. Stepwise humanisation has also allowed us to elucidate the determinants of RAD51 binding to BRC repeats and the contributions of key interacting residues to this interaction. These surrogate proteins have enabled the development of biochemical and biophysical assays in our ongoing fragment-based small-molecule inhibitor programme and they have allowed us to determine hundreds of liganded structures in support of our structure-guided design process, demonstrating the feasibility and advantages of using archeal surrogates to overcome difficulties in handling human proteins.
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Affiliation(s)
- Tommaso Moschetti
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Timothy Sharpe
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Gerhard Fischer
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - May E. Marsh
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Hong Kin Ng
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Matthew Morgan
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Duncan E. Scott
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Ashok R. Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
| | - John Skidmore
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK,Corresponding author.
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Redesigning alcohol dehydrogenases/reductases for more efficient biosynthesis of enantiopure isomers. Biotechnol Adv 2015; 33:1671-84. [DOI: 10.1016/j.biotechadv.2015.08.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 08/11/2015] [Accepted: 08/12/2015] [Indexed: 11/20/2022]
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Guo J, Loveridge EJ, Luk LYP, Allemann RK. Effect of Dimerization on Dihydrofolate Reductase Catalysis. Biochemistry 2013; 52:3881-7. [DOI: 10.1021/bi4005073] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Jiannan Guo
- School of Chemistry and
Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff
CF10 3AT, United Kingdom
| | - E. Joel Loveridge
- School of Chemistry and
Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff
CF10 3AT, United Kingdom
| | - Louis Y. P. Luk
- School of Chemistry and
Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff
CF10 3AT, United Kingdom
| | - Rudolf K. Allemann
- School of Chemistry and
Cardiff Catalysis Institute, Cardiff University, Main Building, Park Place, Cardiff
CF10 3AT, United Kingdom
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Collas F, Kuit W, Clément B, Marchal R, López-Contreras AM, Monot F. Simultaneous production of isopropanol, butanol, ethanol and 2,3-butanediol by Clostridium acetobutylicum ATCC 824 engineered strains. AMB Express 2012; 2:45. [PMID: 22909015 PMCID: PMC3583297 DOI: 10.1186/2191-0855-2-45] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 07/06/2012] [Indexed: 01/19/2023] Open
Abstract
Isopropanol represents a widely-used commercial alcohol which is currently produced from petroleum. In nature, isopropanol is excreted by some strains of Clostridium beijerinckii, simultaneously with butanol and ethanol during the isopropanol butanol ethanol (IBE) fermentation. In order to increase isopropanol production, the gene encoding the secondary-alcohol dehydrogenase enzyme from C. beijerinckii NRRL B593 (adh) which catalyzes the reduction of acetone to isopropanol, was cloned into the acetone, butanol and ethanol (ABE)-producing strain C. acetobutylicum ATCC 824. The transformants showed high capacity for conversion of acetone into isopropanol (> 95%). To increase isopropanol production levels in ATCC 824, polycistronic transcription units containing, in addition to the adh gene, homologous genes of the acetoacetate decarboxylase (adc), and/or the acetoacetyl-CoA:acetate/butyrate:CoA transferase subunits A and B (ctfA and ctfB) were constructed and introduced into the wild-type strain. Combined overexpression of the ctfA and ctfB genes resulted in enhanced solvent production. In non-pH-controlled batch cultures, the total solvents excreted by the transformant overexpressing the adh, ctfA, ctfB and adc genes were 24.4 g/L IBE (including 8.8 g/L isopropanol), while the control strain harbouring an empty plasmid produced only 20.2 g/L ABE (including 7.6 g/L acetone). The overexpression of the adc gene had limited effect on IBE production. Interestingly, all transformants with the adh gene converted acetoin (a minor fermentation product) into 2,3-butanediol, highlighting the wide metabolic versatility of solvent-producing Clostridia.
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Loveridge EJ, Allemann RK. The temperature dependence of the kinetic isotope effects of dihydrofolate reductase from Thermotoga maritima is influenced by intersubunit interactions. Biochemistry 2010; 49:5390-6. [PMID: 20515024 DOI: 10.1021/bi100761x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Dihydrofolate reductase from the hyperthermophile Thermotoga maritima (TmDHFR) is unique among structurally characterized chromosomal DHFRs in that it forms a stable homodimer. Dimerization is believed to play a key role in the high thermal stability of TmDHFR, which is reflected in a melting temperature in excess of 85 degrees C. The dimer interface of TmDHFR is composed of a hydrophobic core with charged residues around the periphery. In particular, Lys129 of each subunit forms three-membered salt bridges with Glu136 and Glu138 of the other subunit. To probe the role of these salt bridges in the dimerization and thermal stability of TmDHFR, we generated a series of variants (TmDHFR-K129E, TmDHFR-E136K, TmDHFR-E138K, and TmDHFR-E136K/E138K) in which these residues were exchanged for residues whose side chains bear the opposite charge. Our results indicate that these salt bridges are key for the high thermal stability of TmDHFR but are not a requirement for dimerization. Although the rate of dihydrofolate reduction by TmDHFR is not significantly affected by the loss of the K129-E136-E138 salt bridges, changes to the temperature dependence of the kinetic isotope effect on hydride transfer are observed. These changes are in agreement with the proposal that DHFR catalysis may be affected by changes to the conformational ensemble of the enzyme rather than only to the coupling of protein motions to the reaction coordinate.
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Affiliation(s)
- E Joel Loveridge
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
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