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Kim Y, Lee SH, Gade P, Nattermann M, Maltseva N, Endres M, Chen J, Wichmann P, Hu Y, Marchal DG, Yoshikuni Y, Erb TJ, Gonzalez R, Michalska K, Joachimiak A. Revealing reaction intermediates in one-carbon elongation by thiamine diphosphate/CoA-dependent enzyme family. Commun Chem 2024; 7:160. [PMID: 39034323 PMCID: PMC11271303 DOI: 10.1038/s42004-024-01242-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 07/10/2024] [Indexed: 07/23/2024] Open
Abstract
2-Hydroxyacyl-CoA lyase/synthase (HACL/S) is a thiamine diphosphate (ThDP)-dependent versatile enzyme originally discovered in the mammalian α-oxidation pathway. HACL/S natively cleaves 2-hydroxyacyl-CoAs and, in its reverse direction, condenses formyl-CoA with aldehydes or ketones. The one-carbon elongation biochemistry based on HACL/S has enabled the use of molecules derived from greenhouse gases as biomanufacturing feedstocks. We investigated several HACL/S family members with high activity in the condensation of formyl-CoA and aldehydes, and distinct chain-length specificities and kinetic parameters. Our analysis revealed the structures of enzymes in complex with acyl-CoA substrates and products, several covalent intermediates, bound ThDP and ADP, as well as the C-terminal active site region. One of these observed states corresponds to the intermediary α-carbanion with hydroxymethyl-CoA covalently attached to ThDP. This research distinguishes HACL/S from related sub-families and identifies key residues involved in substrate binding and catalysis. These findings expand our knowledge of acyloin-condensation biochemistry and offer attractive prospects for biocatalysis using carbon elongation.
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Affiliation(s)
- Youngchang Kim
- eBERlight and Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
| | - Seung Hwan Lee
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Priyanka Gade
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
| | - Maren Nattermann
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Natalia Maltseva
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
| | - Michael Endres
- eBERlight and Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Jing Chen
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Philipp Wichmann
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Yang Hu
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Daniel G Marchal
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Yasuo Yoshikuni
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Ramon Gonzalez
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA.
| | - Karolina Michalska
- eBERlight and Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA.
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA.
| | - Andrzej Joachimiak
- eBERlight and Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA.
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA.
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
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Youssef HIA. Detection of oxalyl-CoA decarboxylase (oxc) and formyl-CoA transferase (frc) genes in novel probiotic isolates capable of oxalate degradation in vitro. Folia Microbiol (Praha) 2024; 69:423-432. [PMID: 38217756 PMCID: PMC11003902 DOI: 10.1007/s12223-024-01128-5] [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: 07/11/2023] [Accepted: 12/28/2023] [Indexed: 01/15/2024]
Abstract
Oxalate degradation is one of lactic acid bacteria's desirable activities. It is achieved by two enzymes, formyl coenzyme A transferase (frc) and oxalyl coenzyme A decarboxylase (oxc). The current study aimed to screen 15 locally isolated lactic acid bacteria to select those with the highest oxalate degradation ability. It also aimed to amplify the genes involved in degradation. MRS broth supplemented with 20 mM sodium oxalate was used to culture the tested isolates for 72 h. This was followed by an enzymatic assay to detect remaining oxalate. All isolates showed oxalate degradation activity to variable degrees. Five isolates demonstrated high oxalate degradation, 78 to 88%. To investigate the oxalate-degradation potential of the selected isolates, they have been further tested for the presence of genes that encode for enzymes involved in oxalate catabolism, formyl coenzyme A transferase (frc) and oxalyl coenzyme A decarboxylase (oxc). Three strains showed bands with the specific OXC and FRC forward and reverse primers designated as (SA-5, 9 and 37). Species-level identification revealed Loigolactobacillus bifermentans, Lacticaseibacillus paracasei, and Lactiplantibacillus plantarum. Preliminary results revealed that the tested probiotic strains harbored both oxc and frc whose products are putatively involved in oxalate catabolism. The probiotic potential of the selected strains was evaluated, and they showed high survival rates to both simulated gastric and intestinal fluids and variable degrees of antagonism against the tested Gram-positive and negative pathogens and were sensitive to clarithromycin but resistant to both metronidazole and ceftazidime. Finally, these strains could be exploited as an innovative approach to establish oxalate homeostasis in humans and prevent kidney stone formation.
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Cheng N, Paris V, Rao X, Wang X, Nakata PA. A conserved oxalyl-coenzyme A decarboxylase in oxalate catabolism. PLANT SIGNALING & BEHAVIOR 2022; 17:2062555. [PMID: 35510715 PMCID: PMC9090294 DOI: 10.1080/15592324.2022.2062555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
The ability to biosynthesize oxalic acid can provide beneficial functions to plants; however, uncontrolled or prolonged exposure to this strong organic acid results in multiple physiological problems. Such problems include a disruption of membrane integrity, mitochondrial function, metal chelation, and free radical formation. Recent work suggests that a CoA-dependent pathway of oxalate catabolism plays a critical role in regulating tissue oxalate concentrations in plants. Although this CoA-dependent pathway of oxalate catabolism is important, large gaps in our knowledge of the enzymes catalyzing each step remain. Evidence that an oxalyl-CoA decarboxylase (OXC) catalyzes the second step in this pathway, accelerating the conversion of oxalyl-CoA to formyl-CoA, has been reported. Induction studies revealed that OXC gene expression was upregulated in response to an exogenous oxalate supply. Phylogenetic analysis indicates that OXCs are conserved across plant species. Evolutionarily the plant OXCs can be separated into dicot and monocot classes. Multiple sequence alignments and molecular modeling suggest that OXCs have similar functionality with three conserved domains, the N-terminal PYR domain, the middle R domain, and the C-terminal PP domain. Further study of this CoA-dependent pathway of oxalate degradation would benefit efforts to develop new strategies to improve the nutrition quality of crops.
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Affiliation(s)
- Ninghui Cheng
- USDA-ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Texas, United States
| | - Vincent Paris
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Texas, United States
| | - Xiaolan Rao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, P. R. China
| | - Xiaoqiang Wang
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Texas, United States
| | - Paul A. Nakata
- USDA-ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Texas, United States
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4
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Zahn M, König G, Cuong Pham HV, Seroka B, Lazny R, Yang G, Ouerfelli O, Lotowski Z, Rohwerder T. Mechanistic details of the actinobacterial lyase-catalyzed degradation reaction of 2-hydroxyisobutyryl-CoA. J Biol Chem 2021; 298:101522. [PMID: 34952003 PMCID: PMC8760513 DOI: 10.1016/j.jbc.2021.101522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/16/2021] [Accepted: 12/19/2021] [Indexed: 11/28/2022] Open
Abstract
Actinobacterial 2-hydroxyacyl-CoA lyase reversibly catalyzes the thiamine diphosphate-dependent cleavage of 2-hydroxyisobutyryl-CoA to formyl-CoA and acetone. This enzyme has great potential for use in synthetic one-carbon assimilation pathways for sustainable production of chemicals, but lacks details of substrate binding and reaction mechanism for biochemical reengineering. We determined crystal structures of the tetrameric enzyme in the closed conformation with bound substrate, covalent postcleavage intermediate, and products, shedding light on active site architecture and substrate interactions. Together with molecular dynamics simulations of the covalent precleavage complex, the complete catalytic cycle is structurally portrayed, revealing a proton transfer from the substrate acyl Cβ hydroxyl to residue E493 that returns it subsequently to the postcleavage Cα-carbanion intermediate. Kinetic parameters obtained for mutants E493A, E493Q, and E493K confirm the catalytic role of E493 in the WT enzyme. However, the 10- and 50-fold reduction in lyase activity in the E493A and E493Q mutants, respectively, compared with WT suggests that water molecules may contribute to proton transfer. The putative catalytic glutamate is located on a short α-helix close to the active site. This structural feature appears to be conserved in related lyases, such as human 2-hydroxyacyl-CoA lyase 2. Interestingly, a unique feature of the actinobacterial 2-hydroxyacyl-CoA lyase is a large C-terminal lid domain that, together with active site residues L127 and I492, restricts substrate size to ≤C5 2-hydroxyacyl residues. These details about the catalytic mechanism and determinants of substrate specificity pave the ground for designing tailored catalysts for acyloin condensations for one-carbon and short-chain substrates in biotechnological applications.
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Affiliation(s)
- Michael Zahn
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom.
| | - Gerhard König
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom
| | - Huy Viet Cuong Pham
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Barbara Seroka
- Faculty of Chemistry, University of Bialystok, K. Ciolkowskiego 1K, 15-245 Bialystok, Poland
| | - Ryszard Lazny
- Faculty of Chemistry, University of Bialystok, K. Ciolkowskiego 1K, 15-245 Bialystok, Poland
| | - Guangli Yang
- Organic Synthesis Core Facility, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY 10065, USA
| | - Ouathek Ouerfelli
- Organic Synthesis Core Facility, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY 10065, USA
| | - Zenon Lotowski
- Faculty of Chemistry, University of Bialystok, K. Ciolkowskiego 1K, 15-245 Bialystok, Poland
| | - Thore Rohwerder
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
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Bitard-Feildel T. Navigating the amino acid sequence space between functional proteins using a deep learning framework. PeerJ Comput Sci 2021; 7:e684. [PMID: 34616884 PMCID: PMC8459775 DOI: 10.7717/peerj-cs.684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
MOTIVATION Shedding light on the relationships between protein sequences and functions is a challenging task with many implications in protein evolution, diseases understanding, and protein design. The protein sequence space mapping to specific functions is however hard to comprehend due to its complexity. Generative models help to decipher complex systems thanks to their abilities to learn and recreate data specificity. Applied to proteins, they can capture the sequence patterns associated with functions and point out important relationships between sequence positions. By learning these dependencies between sequences and functions, they can ultimately be used to generate new sequences and navigate through uncharted area of molecular evolution. RESULTS This study presents an Adversarial Auto-Encoder (AAE) approached, an unsupervised generative model, to generate new protein sequences. AAEs are tested on three protein families known for their multiple functions the sulfatase, the HUP and the TPP families. Clustering results on the encoded sequences from the latent space computed by AAEs display high level of homogeneity regarding the protein sequence functions. The study also reports and analyzes for the first time two sampling strategies based on latent space interpolation and latent space arithmetic to generate intermediate protein sequences sharing sequential properties of original sequences linked to known functional properties issued from different families and functions. Generated sequences by interpolation between latent space data points demonstrate the ability of the AAE to generalize and produce meaningful biological sequences from an evolutionary uncharted area of the biological sequence space. Finally, 3D structure models computed by comparative modelling using generated sequences and templates of different sub-families point out to the ability of the latent space arithmetic to successfully transfer protein sequence properties linked to function between different sub-families. All in all this study confirms the ability of deep learning frameworks to model biological complexity and bring new tools to explore amino acid sequence and functional spaces.
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Affiliation(s)
- Tristan Bitard-Feildel
- IBPS, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, Sorbonne Université, Paris, France
- Institut des Sciences du Calcul et de des Données (ISCD), Sorbonne Université, Paris, France
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The Effect of Oxalobacter formigenes Colonization in Patients with Calcium Oxalate Renal Stones in Comparison with Healthy People in Qom: A Case-Control Study. Nephrourol Mon 2021. [DOI: 10.5812/numonthly.115769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Urinary stones are a major problem world, and their incidence has increased significantly in recent years. Objectives: This study aimed to develop a simple and rapid molecular method based on PCR and qPCR assays to detect Oxalobacter formigenes (which causes oxalate degradation in intestines) in fecal samples of healthy volunteers and patients with calcium oxalate nephrolithiasis, and determine the amount of urinary oxalate in the two groups. Methods: This study was performed on urine and fecal samples of 73 patients with kidney stones and 52 healthy individuals. After DNA extraction, PCR and qPCR assays were performed on two gene regions of O. formigenes, OXC, and FRC. Also, urine oxalate was measured in the study population using biochemical methods. Results: We found that the presence of O. formigenes could reduce the risk of kidney stones and calcium oxalate stones. In fact, both FRC and OXC genes were involved in the diagnosis of O. formigenes; however, the results based on the FRC gene showed higher efficiency. In addition, the presence or absence of stones did not affect the amount of urinary excretion of oxalate, rather it is affected by diet. Conclusions: Molecular identification of O. formigenes by PCR and qPCR assays allows rapid, specific, and reproducible detection in fecal samples, which also allows immediate processing of these samples in clinical conditions.
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7
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Nattermann M, Burgener S, Pfister P, Chou A, Schulz L, Lee SH, Paczia N, Zarzycki J, Gonzalez R, Erb TJ. Engineering a Highly Efficient Carboligase for Synthetic One-Carbon Metabolism. ACS Catal 2021; 11:5396-5404. [PMID: 34484855 PMCID: PMC8411744 DOI: 10.1021/acscatal.1c01237] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/06/2021] [Indexed: 12/15/2022]
Abstract
![]()
One of the biggest
challenges to realize a circular carbon economy
is the synthesis of complex carbon compounds from one-carbon (C1)
building blocks. Since the natural solution space of C1–C1
condensations is limited to highly complex enzymes, the development
of more simple and robust biocatalysts may facilitate the engineering
of C1 assimilation routes. Thiamine diphosphate-dependent enzymes
harbor great potential for this task, due to their ability to create
C–C bonds. Here, we employed structure-guided iterative saturation
mutagenesis to convert oxalyl-CoA decarboxylase (OXC) from Methylobacterium extorquens into a glycolyl-CoA synthase
(GCS) that allows for the direct condensation of the two C1 units
formyl-CoA and formaldehyde. A quadruple variant MeOXC4 showed a 100 000-fold
switch between OXC and GCS activities, a 200-fold increase in the
GCS activity compared to the wild type, and formaldehyde affinity
that is comparable to natural formaldehyde-converting enzymes. Notably,
MeOCX4 outcompetes all other natural and engineered enzymes for C1–C1
condensations by more than 40-fold in catalytic efficiency and is
highly soluble in Escherichia coli.
In addition to the increased GCS activity, MeOXC4 showed up to 300-fold
higher activity than the wild type toward a broad range of carbonyl
acceptor substrates. When applied in vivo, MeOXC4 enables the production
of glycolate from formaldehyde, overcoming the current bottleneck
of C1–C1 condensation in whole-cell bioconversions and paving
the way toward synthetic C1 assimilation routes in vivo.
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Affiliation(s)
- Maren Nattermann
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Simon Burgener
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Pascal Pfister
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Alexander Chou
- Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, Florida 33620, United States
| | - Luca Schulz
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Seung Hwan Lee
- Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, Florida 33620, United States
| | - Nicole Paczia
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Jan Zarzycki
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Ramon Gonzalez
- Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, Florida 33620, United States
| | - Tobias J. Erb
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
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Jiang T, Chen W, Cao L, He Y, Zhou H, Mao H. Abundance, Functional, and Evolutionary Analysis of Oxalyl-Coenzyme A Decarboxylase in Human Microbiota. Front Microbiol 2020; 11:672. [PMID: 32390974 PMCID: PMC7190790 DOI: 10.3389/fmicb.2020.00672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 03/24/2020] [Indexed: 11/13/2022] Open
Abstract
Oxalic acid and its oxalate salts have been linked to kidney stones and other health problems and about 80% kidney stones are made up of calcium oxalate. Oxalyl coenzyme A decarboxylase (OXC) is a key enzyme in the catabolism of oxalate. In this study, we performed bioinformatic and biochemical analysis of OXC. First, we mined the OXC sequences from a public protein database and collected 1396 putative OXC sequences. These sequences were widely spread and mainly distributed in Actinobacteria, Alphaproteobacteria, Gammaproteobacteria, and Betaproteobacteria and classified into seven clusters. The phylogenetic relationship and evolutionary rate of the 7 clusters showed that OXC are highly conserved. Second, the abundance of the different clusters of OXC was explored in 380 human microbiome datasets, which showed that OXCs in Cluster 1 were relatively high in the gut while OXCs in Clusters 2-4 were relatively enriched in the vagina. Third, we measured the activity of one OXC from Mycobacterium mageritense (OXCmm) in Cluster 3, in which there was no experimentally characterized enzymes. Mutation analysis showed that OXCmm shared the same active sites with the OXC from Oxalobacter formigenes. Taken together, this analysis provides a better insight into the distribution and catalysis of OXC and further potential alternative application of OXC active bacteria as probiotics in the management of kidney stone disease.
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Affiliation(s)
- Tao Jiang
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Wenwei Chen
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Linsheng Cao
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yanfeng He
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Huiliang Zhou
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Houping Mao
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
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Oxalyl‐CoA Decarboxylase katalysiert die nukleophile ein‐Kohlenstoff‐Verlängerung von Aldehyden zu chiralen α‐Hydroxysäuren. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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10
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Burgener S, Cortina NS, Erb TJ. Oxalyl-CoA Decarboxylase Enables Nucleophilic One-Carbon Extension of Aldehydes to Chiral α-Hydroxy Acids. Angew Chem Int Ed Engl 2020; 59:5526-5530. [PMID: 31894608 PMCID: PMC7154664 DOI: 10.1002/anie.201915155] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Indexed: 11/11/2022]
Abstract
The synthesis of complex molecules from simple, renewable carbon units is the goal of a sustainable economy. Here we explored the biocatalytic potential of the thiamine-diphosphate-dependent (ThDP) oxalyl-CoA decarboxylase (OXC)/2-hydroxyacyl-CoA lyase (HACL) superfamily that naturally catalyzes the shortening of acyl-CoA thioester substrates through the release of the C1 -unit formyl-CoA. We show that the OXC/HACL superfamily contains promiscuous members that can be reversed to perform nucleophilic C1 -extensions of various aldehydes to yield the corresponding 2-hydroxyacyl-CoA thioesters. We improved the catalytic properties of Methylorubrum extorquens OXC by rational enzyme engineering and combined it with two newly described enzymes-a specific oxalyl-CoA synthetase and a 2-hydroxyacyl-CoA thioesterase. This enzymatic cascade enabled continuous conversion of oxalate and aromatic aldehydes into valuable (S)-α-hydroxy acids with enantiomeric excess up to 99 %.
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Affiliation(s)
- Simon Burgener
- Department of Biochemistry & Synthetic MetabolismMax-Planck-Institute for terrestrial MicrobiologyKarl-von-Frisch-Str. 1035043MarburgGermany
| | - Niña Socorro Cortina
- Department of Biochemistry & Synthetic MetabolismMax-Planck-Institute for terrestrial MicrobiologyKarl-von-Frisch-Str. 1035043MarburgGermany
| | - Tobias J. Erb
- Department of Biochemistry & Synthetic MetabolismMax-Planck-Institute for terrestrial MicrobiologyKarl-von-Frisch-Str. 1035043MarburgGermany
- LOEWE-Center for Synthetic MicrobiologyPhilipps-University MarburgKarl-von-Frisch-Str. 835043MarburgGermany
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11
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Walsh CT. Biologically generated carbon dioxide: nature's versatile chemical strategies for carboxy lyases. Nat Prod Rep 2019; 37:100-135. [PMID: 31074473 DOI: 10.1039/c9np00015a] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Covering: up to 2019Metabolic production of CO2 is natural product chemistry on a mammoth scale. Just counting humans, among all other respiring organisms, the seven billion people on the planet exhale about 3 billion tons of CO2 per year. Essentially all of the biogenic CO2 arises by action of discrete families of decarboxylases. The mechanistic routes to CO2 release from carboxylic acid metabolites vary with the electronic demands and structures of specific substrates and illustrate the breadth of chemistry employed for C-COO (C-C bond) disconnections. Most commonly decarboxylated are α-keto acid and β-keto acid substrates, the former requiring thiamin-PP as cofactor, the latter typically cofactor-free. The extensive decarboxylation of amino acids, e.g. to neurotransmitter amines, is synonymous with the coenzyme form of vitamin B6, pyridoxal-phosphate, although covalent N-terminal pyruvamide residues serve in some amino acid decarboxylases. All told, five B vitamins (B1, B2, B3, B6, B7), ATP, S-adenosylmethionine, manganese and zinc ions are pressed into service for specific decarboxylase catalyses. There are additional cofactor-independent decarboxylases that operate by distinct chemical routes. Finally, while most decarboxylases use heterolytic ionic mechanisms, a small number of decarboxylases carry out radical pathways.
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12
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Abarghooi -Kahaki F, Basiri A, Bandehpour M, Kazemi B. Designing a diagnostic kit for Oxalyl CoA Decarboxylase enzyme by ELISA method. Immunol Lett 2019; 205:78-83. [DOI: 10.1016/j.imlet.2018.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/09/2018] [Indexed: 11/28/2022]
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13
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Hampel S, Steitz JP, Baierl A, Lehwald P, Wiesli L, Richter M, Fries A, Pohl M, Schneider G, Dobritzsch D, Müller M. Structural and Mutagenesis Studies of the Thiamine-Dependent, Ketone-Accepting YerE from Pseudomonas protegens. Chembiochem 2018; 19:2283-2292. [DOI: 10.1002/cbic.201800325] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Sabrina Hampel
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | - Jan-Patrick Steitz
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | - Anna Baierl
- IBG-1: Biotechnology; Forschungszentrum Jülich GmbH; Wilhelm-Johnen Str. 52425 Jülich Germany
| | - Patrizia Lehwald
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | - Luzia Wiesli
- Empa - Swiss Federal Laboratories for Materials Science and Technology; Laboratory for Biointerfaces; Lerchenfeldstrasse 5 9014 St. Gallen Switzerland
| | - Michael Richter
- Empa - Swiss Federal Laboratories for Materials Science and Technology; Laboratory for Biointerfaces; Lerchenfeldstrasse 5 9014 St. Gallen Switzerland
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB; Branch BioCat; Schulgasse 11a 94315 Straubing Germany
| | - Alexander Fries
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | - Martina Pohl
- IBG-1: Biotechnology; Forschungszentrum Jülich GmbH; Wilhelm-Johnen Str. 52425 Jülich Germany
| | - Gunter Schneider
- Department of Medical Biochemistry and Biophysics; Karolinska Institutet; Tomtebodavägen 6 17177 Stockholm Sweden
| | - Doreen Dobritzsch
- Vising address: Department of Chemistry-BMC; Uppsala Universitet; Husargatan 3 75237 Uppsala Sweden
| | - Michael Müller
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
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14
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Pierce E, Mansoorabadi SO, Can M, Reed GH, Ragsdale SW. Properties of Intermediates in the Catalytic Cycle of Oxalate Oxidoreductase and Its Suicide Inactivation by Pyruvate. Biochemistry 2017; 56:2824-2835. [PMID: 28514140 PMCID: PMC5463272 DOI: 10.1021/acs.biochem.7b00222] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Oxalate:ferredoxin oxidoreductase (OOR) is an unusual member of the thiamine pyrophosphate (TPP)-dependent 2-oxoacid:ferredoxin oxidoreductase (OFOR) family in that it catalyzes the coenzyme A (CoA)-independent conversion of oxalate into 2 equivalents of carbon dioxide. This reaction is surprising because binding of CoA to the acyl-TPP intermediate of other OFORs results in formation of a CoA ester, and in the case of pyruvate:ferredoxin oxidoreductase (PFOR), CoA binding generates the central metabolic intermediate acetyl-CoA and promotes a 105-fold acceleration of the rate of electron transfer. Here we describe kinetic, spectroscopic, and computational results to show that CoA has no effect on catalysis by OOR and describe the chemical rationale for why this cofactor is unnecessary in this enzymatic transformation. Our results demonstrate that, like PFOR, OOR binds pyruvate and catalyzes decarboxylation to form the same hydroxyethylidine-TPP (HE-TPP) intermediate and one-electron transfer to generate the HE-TPP radical. However, in OOR, this intermediate remains stranded at the active site as a covalent inhibitor. These and other results indicate that, like other OFOR family members, OOR generates an oxalate-derived adduct with TPP (oxalyl-TPP) that undergoes decarboxylation and one-electron transfer to form a radical intermediate remaining bound to TPP (dihydroxymethylidene-TPP). However, unlike in PFOR, where CoA binding drives formation of the product, in OOR, proton transfer and a conformational change in the "switch loop" alter the redox potential of the radical intermediate sufficiently to promote the transfer of an electron into the iron-sulfur cluster network, leading directly to a second decarboxylation and completing the catalytic cycle.
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Affiliation(s)
- Elizabeth Pierce
- Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109-0606, United States
| | - Steven O Mansoorabadi
- Department of Chemistry and Biochemistry, Auburn University , 179 Chemistry Building, Auburn, Alabama 36849, United States
| | - Mehmet Can
- Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109-0606, United States
| | - George H Reed
- Department of Biochemistry, University of Wisconsin-Madison , 440 Henry Mall, Madison, Wisconsin 53726, United States
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109-0606, United States
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15
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Peng C, Liang X, Liu EE, Zhang JJ, Peng XX. The oxalyl-CoA synthetase-regulated oxalate and its distinct effects on resistance to bacterial blight and aluminium toxicity in rice. PLANT BIOLOGY (STUTTGART, GERMANY) 2017; 19:345-353. [PMID: 28039904 DOI: 10.1111/plb.12542] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 12/29/2016] [Indexed: 05/25/2023]
Abstract
Oxalic acid is widely distributed in biological systems and known to play functional roles in plants. The gene AAE3 was recently identified to encode an oxalyl-CoA synthetase (OCS) in Arabidopsis that catalyses the conversion of oxalate and CoA into oxalyl-CoA. It will be particularly important to characterise the homologous gene in rice since rice is not only a monocotyledonous model plant, but also a staple food crop. Various enzymatic and biological methods have been used to characterise the homologous gene. We first defined that AAE3 in the rice genome (OsAAE3) also encodes an OCS enzyme. Its Km for oxalate is 1.73 ± 0.12 mm, and Vm is 6824.9 ± 410.29 U·min-1 ·mg protein-1 . Chemical modification and site-directed mutagenesis analyses identified thiols as the active site residues for rice OCS catalysis, suggesting that the enzyme might be regulated by redox state. Subcellular localisation assay showed that the enzyme is located in the cytosol and predominantly distributed in leaf epidermal cells. As expected, oxalate levels increased when OCS was suppressed in RNAi transgenic plants. More interestingly, OCS-suppressed plants were more susceptible to bacterial blight but more resistant to Al toxicity. The results demonstrate that the OsAAE3-encoded protein also acts as an OCS in rice, and may play different roles in coping with stresses. These molecular, enzymatic and functional data provide first-hand information to further clarify the function and mechanism of OCS in rice plants.
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Affiliation(s)
- C Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - X Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - E-E Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - J-J Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - X-X Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
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16
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Comprehensive understanding of acetohydroxyacid synthase inhibition by different herbicide families. Proc Natl Acad Sci U S A 2017; 114:E1091-E1100. [PMID: 28137884 PMCID: PMC5321015 DOI: 10.1073/pnas.1616142114] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Five commercial herbicide families inhibit acetohydroxyacid synthase (AHAS, E.C. 2.2.1.6), which is the first enzyme in the branched-chain amino acid biosynthesis pathway. The popularity of these herbicides is due to their low application rates, high crop vs. weed selectivity, and low toxicity in animals. Here, we have determined the crystal structures of Arabidopsis thaliana AHAS in complex with two members of the pyrimidinyl-benzoate (PYB) and two members of the sulfonylamino-carbonyl-triazolinone (SCT) herbicide families, revealing the structural basis for their inhibitory activity. Bispyribac, a member of the PYBs, possesses three aromatic rings and these adopt a twisted "S"-shaped conformation when bound to A. thaliana AHAS (AtAHAS) with the pyrimidinyl group inserted deepest into the herbicide binding site. The SCTs bind such that the triazolinone ring is inserted deepest into the herbicide binding site. Both compound classes fill the channel that leads to the active site, thus preventing substrate binding. The crystal structures and mass spectrometry also show that when these herbicides bind, thiamine diphosphate (ThDP) is modified. When the PYBs bind, the thiazolium ring is cleaved, but when the SCTs bind, ThDP is modified to thiamine 2-thiazolone diphosphate. Kinetic studies show that these compounds not only trigger reversible accumulative inhibition of AHAS, but also can induce inhibition linked with ThDP degradation. Here, we describe the features that contribute to the extraordinarily powerful herbicidal activity exhibited by four classes of AHAS inhibitors.
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17
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Brylinski M. Local Alignment of Ligand Binding Sites in Proteins for Polypharmacology and Drug Repositioning. Methods Mol Biol 2017; 1611:109-122. [PMID: 28451975 PMCID: PMC5513668 DOI: 10.1007/978-1-4939-7015-5_9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The administration of drugs is a key strategy in pharmacotherapy to treat diseases. Drugs are typically developed to modulate the function of specific proteins, which are directly associated with particular disease states. Nonetheless, recent studies suggest that protein-drug interactions are rather promiscuous and the majority of pharmaceuticals exhibit activity against multiple, often unrelated proteins. Certainly, the lack of selectivity often leads to drug side effects; on the other hand, these polypharmacological attributes can be used to develop drugs acting on multiple targets within a unique disease pathway, as well as to identify new targets for existing drugs, which is known as drug repositioning. To support drug development and repurposing, we developed eMatchSite, a new approach to detect those binding sites having the capability to bind similar compounds. eMatchSite is available as a standalone software and a webserver at http://www.brylinski.org/ematchsite .
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Affiliation(s)
- Michal Brylinski
- Department of Biological Sciences, Louisiana State University, 407 Choppin Hall, Baton Rouge, LA, 70803, USA.
- Center for Computation and Technology, Louisiana State University, 2054 Digital Media Center, Baton Rouge, LA, 70803, USA.
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18
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Mechanistic and Structural Insight to an Evolved Benzoylformate Decarboxylase with Enhanced Pyruvate Decarboxylase Activity. Catalysts 2016. [DOI: 10.3390/catal6120190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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19
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Liu Y, Li Y, Wang X. Acetohydroxyacid synthases: evolution, structure, and function. Appl Microbiol Biotechnol 2016; 100:8633-49. [DOI: 10.1007/s00253-016-7809-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/28/2016] [Accepted: 08/12/2016] [Indexed: 10/21/2022]
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20
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Sheng X, Liu Y, Zhang R. A theoretical study of the catalytic mechanism of oxalyl-CoA decarboxylase, an enzyme for treating urolithiasis. RSC Adv 2014. [DOI: 10.1039/c4ra03611e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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21
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Andrews FH, Rogers MP, Paul LN, McLeish MJ. Perturbation of the monomer-monomer interfaces of the benzoylformate decarboxylase tetramer. Biochemistry 2014; 53:4358-67. [PMID: 24956165 PMCID: PMC4215898 DOI: 10.1021/bi500081r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The X-ray structure of benzoylformate
decarboxylase (BFDC) from Pseudomonas putida ATCC
12633 shows it to be a tetramer.
This was believed to be typical of all thiamin diphosphate-dependent
decarboxylases until recently when the structure of KdcA, a branched-chain
2-keto acid decarboxylase from Lactococcus lactis, showed it to be a homodimer. This lent credence to earlier unfolding
experiments on pyruvate decarboxylase from Saccharomyces cerevisiae that indicated that it might be active as a dimer. To investigate
this possibility in BFDC, we sought to shift the equilibrium toward
dimer formation. Point mutations were made in the noncatalytic monomer–monomer
interfaces, but these had a minimal effect on both tetramer formation
and catalytic activity. Subsequently, the R141E/Y288A/A306F variant
was shown by analytical ultracentrifugation to be partially dimeric.
It was also found to be catalytically inactive. Further experiments
revealed that just two mutations, R141E and A306F, were sufficient
to markedly alter the dimer–tetramer equilibrium and to provide
an ∼450-fold decrease in kcat.
Equilibrium denaturation studies suggested that the residual activity
was possibly due to the presence of residual tetramer. The structures
of the R141E and A306F variants, determined to <1.5 Å resolution,
hinted that disruption of the monomer interfaces will be accompanied
by movement of a loop containing Leu109 and Leu110. As these residues
contribute to the hydrophobicity of the active site and the correct
positioning of the substrate, it seems that tetramer formation may
well be critical to the catalytic activity of BFDC.
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Affiliation(s)
- Forest H Andrews
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis , Indianapolis, Indiana 46202, United States
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22
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The modular structure of ThDP-dependent enzymes. Proteins 2014; 82:2523-37. [DOI: 10.1002/prot.24615] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 05/06/2014] [Accepted: 05/20/2014] [Indexed: 01/12/2023]
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23
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24
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Andrews FH, Tom AR, Gunderman PR, Novak WRP, McLeish MJ. A Bulky Hydrophobic Residue Is Not Required To Maintain the V-Conformation of Enzyme-Bound Thiamin Diphosphate. Biochemistry 2013; 52:3028-30. [DOI: 10.1021/bi400368j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Forest H. Andrews
- Department of Chemistry and
Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Alan R. Tom
- Department of Chemistry, Wabash College, Crawfordsville, Indiana 47933, United
States
| | - Peter R. Gunderman
- Department of Chemistry, Wabash College, Crawfordsville, Indiana 47933, United
States
| | - Walter R. P. Novak
- Department of Chemistry, Wabash College, Crawfordsville, Indiana 47933, United
States
| | - Michael J. McLeish
- Department of Chemistry and
Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
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25
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YfdW and YfdU are required for oxalate-induced acid tolerance in Escherichia coli K-12. J Bacteriol 2013; 195:1446-55. [PMID: 23335415 DOI: 10.1128/jb.01936-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli has several mechanisms for surviving low-pH stress. We report that oxalic acid, a small-chain organic acid (SCOA), induces a moderate acid tolerance response (ATR) in two ways. Adaptation of E. coli K-12 at pH 5.5 with 50 mM oxalate and inclusion of 25 mM oxalate in pH 3.0 minimal challenge medium separately conferred protection, with 67% ± 7% and 87% ± 17% survival after 2 h, respectively. The combination of oxalate adaptation and oxalate supplementation in the challenge medium resulted in increased survival over adaptation or oxalate in the challenge medium alone. The enzymes YfdW, a formyl coenzyme A (CoA) transferase, and YfdU, an oxalyl-CoA decarboxylase, are required for the adaptation effect but not during challenge. Unlike other SCOAs, this oxalate ATR is not a part of the RpoS regulon but appears to be linked to the signal protein GadE. We theorize that this oxalate ATR could enhance the pathogenesis of virulent E. coli consumed with oxalate-containing foods like spinach.
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26
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Lee JJ, Park KW, Kwak YS, Ahn JY, Jung YH, Lee BH, Jeong JC, Lee HS, Kwak SS. Comparative proteomic study between tuberous roots of light orange- and purple-fleshed sweetpotato cultivars. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 193-194:120-129. [PMID: 22794925 DOI: 10.1016/j.plantsci.2012.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 06/05/2012] [Accepted: 06/06/2012] [Indexed: 05/15/2023]
Abstract
This study compares the differences in proteomes expressed in tuberous roots of a light orange-fleshed sweetpotato (Ipomoea batatas (L.) Lam. cultivar Yulmi) and a purple-fleshed sweetpotato cultivar (Shinjami). More than 370 protein spots were reproducibly detected by two-dimensional gel electrophoresis, in which 35 spots were up-regulated (Yulmi vs. Shinjami) or uniquely expressed (only Yulmi or Shinjami) in either of the two cultivars. Of these 35 protein spots, 23 were expressed in Yulmi and 12 were expressed in Shinjami. These protein spots were analyzed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry and electrospray ionization tandem mass spectrometry. Fifteen proteins in Yulmi and eight proteins in Shinjami were identified from the up-regulated (Yulmi vs. Shinjami) or uniquely expressed (only Yulmi or Shinjami) proteins, respectively. In Yulmi, α-amylase and isomerase precursor-like protein were uniquely expressed or up-regulated and activities of α-amylase, monodehydroascorbate reductase, and dehydroascorbate reductase were higher than in Shinjami. In Shinjami, peroxidase precursor and aldo-keto reductase were uniquely expressed or up-regulated and peroxidase and aldo-keto reductase activities were higher than in Yulmi. PSG-RGH7 uniquely expressed only in Shinjami and the cultivar was evaluated more resistant than Yulmi against the root-knot nematode, Meloidogyne incognita (Kofold and White, 1919) Chitwood 1949 on the basis of shoot and root growth. Egg mass formation was 14.9-fold less in Shinjami than in Yulmi. These results provide important clues that can provide a foundation for sweetpotato proteomics and lead to the characterization of the physiological function of differentially expressed proteins.
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Affiliation(s)
- Jeung Joo Lee
- Department of Applied Biology, IALS, Gyeongsang National University, Jinju 660-751, Republic of Korea
| | - Kee Woong Park
- Department of Crop Science, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Youn-Sig Kwak
- Department of Applied Biology, IALS, Gyeongsang National University, Jinju 660-751, Republic of Korea
| | - Jae Young Ahn
- Department of Applied Biology, IALS, Gyeongsang National University, Jinju 660-751, Republic of Korea
| | - Young Hak Jung
- Division of Applied Life Science (BK21 Program), IALS, PMBBRC, Gyeongsang National University, Jinju 660-751, Republic of Korea
| | - Byung-Hyun Lee
- Division of Applied Life Science (BK21 Program), IALS, PMBBRC, Gyeongsang National University, Jinju 660-751, Republic of Korea
| | - Jae Cheol Jeong
- Environmental Biotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Haeng-Soon Lee
- Environmental Biotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Sang-Soo Kwak
- Environmental Biotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea.
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27
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Steinbach A, Fraas S, Harder J, Warkentin E, Kroneck PMH, Ermler U. Crystal structure of a ring-cleaving cyclohexane-1,2-dione hydrolase, a novel member of the thiamine diphosphate enzyme family. FEBS J 2012; 279:1209-19. [DOI: 10.1111/j.1742-4658.2012.08513.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Substrate specificity in thiamin diphosphate-dependent decarboxylases. Bioorg Chem 2011; 43:26-36. [PMID: 22245019 DOI: 10.1016/j.bioorg.2011.12.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 12/19/2011] [Accepted: 12/20/2011] [Indexed: 11/20/2022]
Abstract
Thiamin diphosphate (ThDP) is the biologically active form of vitamin B(1), and ThDP-dependent enzymes are found in all forms of life. The catalytic mechanism of this family requires the formation of a common intermediate, the 2α-carbanion-enamine, regardless of whether the enzyme is involved in C-C bond formation or breakdown, or even formation of C-N, C-O and C-S bonds. This demands that the enzymes must screen substrates prior to, and/or after, formation of the common intermediate. This review is focused on the group for which the second step is the protonation of the 2α-carbanion, i.e., the ThDP-dependent decarboxylases. Based on kinetic data, sequence/structure alignments and mutagenesis studies the factors involved in substrate specificity have been identified.
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29
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Werther T, Zimmer A, Wille G, Golbik R, Weiss MS, König S. New insights into structure-function relationships of oxalyl CoA decarboxylase from Escherichia coli. FEBS J 2010. [DOI: 10.1111/j.1742-4658.2010.07673.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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30
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Nahum LA, Goswami S, Serres MH. Protein families reflect the metabolic diversity of organisms and provide support for functional prediction. Physiol Genomics 2009; 38:250-60. [PMID: 19491149 DOI: 10.1152/physiolgenomics.90244.2008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Comparative genomics has shown that protein families vary significantly within and across organisms in both number and functional composition. In the present work, we tested how the diversity at the family level reflects biological differences among organisms and contributes to their unique characteristics. For this purpose, we collected sequence-similar proteins of three selected families from model bacteria: Escherichia coli, Bacillus subtilis, and Pseudomonas aeruginosa. Protein relationships were identified using a phylogenomic approach to connect the functional diversity of enzymes to the metabolic capabilities of these organisms. All protein families studied have distinct functional compositions across the selected bacteria as supported by our Bayesian analysis. Some conserved functional features among family members included a shared reaction mechanism, cofactor usage, and/or ligand specificity. Many observations of the presence/absence of protein functions matched current knowledge of the physiology and biochemistry of the bacteria. In some cases, new functional predictions were made to family members previously uncharacterized. We believe that genome comparisons at the protein family level would also be useful in predicting metabolic diversity for organisms that are relatively unknown or currently uncultured in the laboratory.
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Affiliation(s)
- Laila A Nahum
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts
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31
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Makarchikov AF. Vitamin B1: Metabolism and functions. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2009. [DOI: 10.1134/s1990750809020024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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32
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Kluger R, Tittmann K. Thiamin diphosphate catalysis: enzymic and nonenzymic covalent intermediates. Chem Rev 2008; 108:1797-833. [PMID: 18491870 DOI: 10.1021/cr068444m] [Citation(s) in RCA: 195] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ronald Kluger
- Davenport Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada.
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33
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Kim SY, Shin SJ, Song CH, Jo EK, Kim HJ, Park JK. Identification of novel metronidazole-inducible genes in Mycobacterium smegmatis using a customized amplification library. FEMS Microbiol Lett 2008; 282:282-9. [DOI: 10.1111/j.1574-6968.2008.01143.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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34
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Toyota CG, Berthold CL, Gruez A, Jónsson S, Lindqvist Y, Cambillau C, Richards NGJ. Differential substrate specificity and kinetic behavior of Escherichia coli YfdW and Oxalobacter formigenes formyl coenzyme A transferase. J Bacteriol 2008; 190:2556-64. [PMID: 18245280 PMCID: PMC2293189 DOI: 10.1128/jb.01823-07] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Accepted: 01/25/2008] [Indexed: 01/29/2023] Open
Abstract
The yfdXWUVE operon appears to encode proteins that enhance the ability of Escherichia coli MG1655 to survive under acidic conditions. Although the molecular mechanisms underlying this phenotypic behavior remain to be elucidated, findings from structural genomic studies have shown that the structure of YfdW, the protein encoded by the yfdW gene, is homologous to that of the enzyme that mediates oxalate catabolism in the obligate anaerobe Oxalobacter formigenes, O. formigenes formyl coenzyme A transferase (FRC). We now report the first detailed examination of the steady-state kinetic behavior and substrate specificity of recombinant, wild-type YfdW. Our studies confirm that YfdW is a formyl coenzyme A (formyl-CoA) transferase, and YfdW appears to be more stringent than the corresponding enzyme (FRC) in Oxalobacter in employing formyl-CoA and oxalate as substrates. We also report the effects of replacing Trp-48 in the FRC active site with the glutamine residue that occupies an equivalent position in the E. coli protein. The results of these experiments show that Trp-48 precludes oxalate binding to a site that mediates substrate inhibition for YfdW. In addition, the replacement of Trp-48 by Gln-48 yields an FRC variant for which oxalate-dependent substrate inhibition is modified to resemble that seen for YfdW. Our findings illustrate the utility of structural homology in assigning enzyme function and raise the question of whether oxalate catabolism takes place in E. coli upon the up-regulation of the yfdXWUVE operon under acidic conditions.
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Affiliation(s)
- Cory G Toyota
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
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35
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Berthold CL, Toyota CG, Richards NGJ, Lindqvist Y. Reinvestigation of the catalytic mechanism of formyl-CoA transferase, a class III CoA-transferase. J Biol Chem 2007; 283:6519-29. [PMID: 18162462 DOI: 10.1074/jbc.m709353200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Formyl-coenzyme A transferase from Oxalobacter formigenes belongs to the Class III coenzyme A transferase family and catalyzes the reversible transfer of a CoA carrier between formyl-CoA and oxalate, forming oxalyl-CoA and formate. Formyl-CoA transferase has a unique three-dimensional fold composed of two interlaced subunits locked together like rings of a chain. We here present an intermediate in the reaction, formyl-CoA transferase containing the covalent beta-aspartyl-CoA thioester, adopting different conformations in the two active sites of the dimer, which was identified through crystallographic freeze-trapping experiments with formyl-CoA and oxalyl-CoA in the absence of acceptor carboxylic acid. The formation of the enzyme-CoA thioester was also confirmed by mass spectrometric data. Further structural data include a trapped aspartyl-formyl anhydride protected by a glycine loop closing down over the active site. In a crystal structure of the beta-aspartyl-CoA thioester of an inactive mutant variant, oxalate was found bound to the open conformation of the glycine loop. Together with hydroxylamine trapping experiments and kinetic as well as mutagenesis data, the structures of these formyl-CoA transferase complexes provide new information on the Class III CoA-transferase family and prompt redefinition of the catalytic steps and the modified reaction mechanism of formyl-CoA transferase proposed here.
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Affiliation(s)
- Catrine L Berthold
- Department of Medical Biochemistry and Biophysics, Molecular Structural Biology, Karolinska Institutet, Stockholm, Sweden
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Versées W, Spaepen S, Wood MDH, Leeper FJ, Vanderleyden J, Steyaert J. Molecular Mechanism of Allosteric Substrate Activation in a Thiamine Diphosphate-dependent Decarboxylase. J Biol Chem 2007; 282:35269-78. [PMID: 17905741 DOI: 10.1074/jbc.m706048200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Thiamine diphosphate-dependent enzymes are involved in a wide variety of metabolic pathways. The molecular mechanism behind active site communication and substrate activation, observed in some of these enzymes, has since long been an area of debate. Here, we report the crystal structures of a phenylpyruvate decarboxylase in complex with its substrates and a covalent reaction intermediate analogue. These structures reveal the regulatory site and unveil the mechanism of allosteric substrate activation. This signal transduction relies on quaternary structure reorganizations, domain rotations, and a pathway of local conformational changes that are relayed from the regulatory site to the active site. The current findings thus uncover the molecular mechanism by which the binding of a substrate in the regulatory site is linked to the mounting of the catalytic machinery in the active site in this thiamine diphosphate-dependent enzyme.
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Affiliation(s)
- Wim Versées
- Department of Ultrastructure, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
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Juan ECM, Hoque MM, Hossain MT, Yamamoto T, Imamura S, Suzuki K, Sekiguchi T, Takénaka A. The structures of pyruvate oxidase from Aerococcus viridans with cofactors and with a reaction intermediate reveal the flexibility of the active-site tunnel for catalysis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:900-7. [PMID: 18007037 PMCID: PMC2339753 DOI: 10.1107/s1744309107041012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Accepted: 08/20/2007] [Indexed: 11/10/2022]
Abstract
The crystal structures of pyruvate oxidase from Aerococcus viridans (AvPOX) complexed with flavin adenine dinucleotide (FAD), with FAD and thiamine diphosphate (ThDP) and with FAD and the 2-acetyl-ThDP intermediate (AcThDP) have been determined at 1.6, 1.8 and 1.9 A resolution, respectively. Each subunit of the homotetrameric AvPOX enzyme consists of three domains, as observed in other ThDP-dependent enzymes. FAD is bound within one subunit in the elongated conformation and with the flavin moiety being planar in the oxidized form, while ThDP is bound in a conserved V-conformation at the subunit-subunit interface. The structures reveal flexible regions in the active-site tunnel which may undergo conformational changes to allow the entrance of the substrates and the exit of the reaction products. Of particular interest is the role of Lys478, the side chain of which may be bent or extended depending on the stage of catalysis. The structures also provide insight into the routes for electron transfer to FAD and the involvement of active-site residues in the catalysis of pyruvate to its products.
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Affiliation(s)
- Ella Czarina Magat Juan
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Md Mominul Hoque
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Md Tofazzal Hossain
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | | | | | - Kaoru Suzuki
- College of Science and Engineering, Iwaki Meisei University, Iwaki 970-8551, Japan
| | - Takeshi Sekiguchi
- College of Science and Engineering, Iwaki Meisei University, Iwaki 970-8551, Japan
| | - Akio Takénaka
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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Berthold CL, Toyota CG, Moussatche P, Wood MD, Leeper F, Richards NGJ, Lindqvist Y. Crystallographic snapshots of oxalyl-CoA decarboxylase give insights into catalysis by nonoxidative ThDP-dependent decarboxylases. Structure 2007; 15:853-61. [PMID: 17637344 DOI: 10.1016/j.str.2007.06.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Revised: 06/01/2007] [Accepted: 06/01/2007] [Indexed: 10/23/2022]
Abstract
Despite more than five decades of extensive studies of thiamin diphosphate (ThDP) enzymes, there remain many uncertainties as to how these enzymes achieve their rate enhancements. Here, we present a clear picture of catalysis for the simple nonoxidative decarboxylase, oxalyl-coenzyme A (CoA) decarboxylase, based on crystallographic snapshots along the catalytic cycle and kinetic data on active site mutants. First, we provide crystallographic evidence that, upon binding of oxalyl-CoA, the C-terminal 13 residues fold over the substrate, aligning the substrate alpha-carbon for attack by the ThDP-C2 atom. The second structure presented shows a covalent reaction intermediate after decarboxylation, interpreted as being nonplanar. Finally, the structure of a product complex is presented. In accordance with mutagenesis data, no side chains of the enzyme are implied to directly participate in proton transfer except the glutamic acid (Glu-56), which promotes formation of the 1',4'-iminopyrimidine tautomer of ThDP needed for activation.
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Affiliation(s)
- Catrine L Berthold
- Department of Medical Biochemistry and Biophysics, Molecular Structural Biology, Karolinska Institutet, S-17177 Stockholm, Sweden
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Bendazzoli C, Turroni S, Gotti R, Olmo S, Brigidi P, Cavrini V. Determination of oxalyl-coenzyme A decarboxylase activity in Oxalobacter formigenes and Lactobacillus acidophilus by capillary electrophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 854:350-6. [PMID: 17499563 DOI: 10.1016/j.jchromb.2007.04.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Revised: 04/17/2007] [Accepted: 04/20/2007] [Indexed: 11/19/2022]
Abstract
Oxalyl-coenzyme A decarboxylase (OXC) is a key enzyme in the catabolism of the highly toxic oxalate, catalysing the decarboxylation of oxalyl-coenzyme A (Ox-CoA) to formyl-coenzyme A (For-CoA). In the present study, a capillary electrophoretic (CE) method was proposed for the assessment of the activity of recombinant OXC from two bacteria, namely Oxalobacter formigenes DSM 4420 and Lactobacillus acidophilus LA 14. In particular, the degradation of the substrate Ox-CoA occurring in the enzymatic reaction could be monitored by the off-line CE method. A capillary permanently coated with polyethylenimine (PEI) was used and in the presence of a neutral background electrolyte (50 mM phosphate buffer at pH 7.0), a reversal of the electroosmotic flow was obtained. Under these conditions, the anodic migration of Ox-CoA (substrate) and For-CoA (reaction product) occurred and their separation was accomplished in less than 12 min. The CE method was validated for selectivity, linearity (range of Ox-CoA within 0.005-0.650 mM), sensitivity (LOD of 1.5 microM at the detection wavelength of 254 nm), precision and accuracy. Steady state kinetic constants (V(max), K(m) or k') of OXC were finally estimated for both the bacteria showing that although L. acidophilus LA 14 provided a lower oxalate breakdown than O. formigenes DSM 4420, it could be a potentially useful probiotic in the prevention of diseases related to oxalate.
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Affiliation(s)
- Claudia Bendazzoli
- Department of Pharmaceutical Sciences, University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
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Turroni S, Vitali B, Bendazzoli C, Candela M, Gotti R, Federici F, Pirovano F, Brigidi P. Oxalate consumption by lactobacilli: evaluation of oxalyl-CoA decarboxylase and formyl-CoA transferase activity in Lactobacillus acidophilus. J Appl Microbiol 2007; 103:1600-9. [DOI: 10.1111/j.1365-2672.2007.03388.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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41
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Versées W, Spaepen S, Vanderleyden J, Steyaert J. The crystal structure of phenylpyruvate decarboxylase from Azospirillum brasilense at 1.5 Å resolution. FEBS J 2007; 274:2363-75. [PMID: 17403037 DOI: 10.1111/j.1742-4658.2007.05771.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phenylpyruvate decarboxylase (PPDC) of Azospirillum brasilense, involved in the biosynthesis of the plant hormone indole-3-acetic acid and the antimicrobial compound phenylacetic acid, is a thiamine diphosphate-dependent enzyme that catalyses the nonoxidative decarboxylation of indole- and phenylpyruvate. Analogous to yeast pyruvate decarboxylases, PPDC is subject to allosteric substrate activation, showing sigmoidal v versus [S] plots. The present paper reports the crystal structure of this enzyme determined at 1.5 A resolution. The subunit architecture of PPDC is characteristic for other members of the pyruvate oxidase family, with each subunit consisting of three domains with an open alpha/beta topology. An active site loop, bearing the catalytic residues His112 and His113, could not be modelled due to flexibility. The biological tetramer is best described as an asymmetric dimer of dimers. A cysteine residue that has been suggested as the site for regulatory substrate binding in yeast pyruvate decarboxylase is not conserved, requiring a different mechanism for allosteric substrate activation in PPDC. Only minor changes occur in the interactions with the cofactors, thiamine diphosphate and Mg2+, compared to pyruvate decarboxylase. A greater diversity is observed in the substrate binding pocket accounting for the difference in substrate specificity. Moreover, a catalytically important glutamate residue conserved in nearly all decarboxylases is replaced by a leucine in PPDC. The consequences of these differences in terms of the catalytic and regulatory mechanism of PPDC are discussed.
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Affiliation(s)
- Wim Versées
- Department of Ultrastructure, Vrije Universiteit Brussel, Brussels, Belgium.
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Abstract
Three-dimensional structures have been determined for 13 different enzymes that use thiamine diphosphate (ThDP) as a cofactor. These enzymes fall into five families, where members within a family have similar structures. In different families, there are similarities between some domains that clearly point to a common ancestor for all of these enzymes. Where the enzyme structures differ, evolutionary relationships between families can be discerned. Here, I present an analysis of these families and propose an evolutionary pathway to explain the diversity of structures that are now known.
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Affiliation(s)
- Ronald G Duggleby
- School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia.
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McCourt JA, Duggleby RG. Acetohydroxyacid synthase and its role in the biosynthetic pathway for branched-chain amino acids. Amino Acids 2006; 31:173-210. [PMID: 16699828 DOI: 10.1007/s00726-005-0297-3] [Citation(s) in RCA: 171] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2005] [Accepted: 12/09/2005] [Indexed: 11/25/2022]
Abstract
The branched-chain amino acids are synthesized by plants, fungi and microorganisms, but not by animals. Therefore, the enzymes of this pathway are potential target sites for the development of antifungal agents, antimicrobials and herbicides. Most research has focused upon the first enzyme in this biosynthetic pathway, acetohydroxyacid synthase (AHAS) largely because it is the target site for many commercial herbicides. In this review we provide a brief overview of the important properties of each enzyme within the pathway and a detailed summary of the most recent AHAS research, against the perspective of work that has been carried out over the past 50 years.
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Affiliation(s)
- J A McCourt
- School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Australia
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