1
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Campbell J, Wang Y. Observing extradiol dioxygenases in action through a crystalline lens. Methods Enzymol 2024; 704:3-25. [PMID: 39300653 DOI: 10.1016/bs.mie.2024.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Extradiol dioxygenases are a class of non-heme iron-dependent enzymes found in eukaryotes and prokaryotes that play a vital role in the aerobic catabolism of aromatic compounds. They are generally divided into three evolutionarily independent superfamilies with different protein folds. Our recent studies have shed light on the catalytic mechanisms and structure-function relationships of two specific extradiol dioxygenases: 3-hydroxyanthranilate-3,4-dioxygenase, a Type III enzyme essential in mammals for producing a precursor for nicotinamide adenine dinucleotide, and L-3,4-dihydroxyphenylalanine dioxygenase, an uncommon form of Type I enzymes involved in natural product biosynthesis. This work details the expression and isolation methods for these extradiol dioxygenases and introduces approaches to achieve homogeneity and high occupancy of the enzyme metal centers. Techniques such as ultraviolet-visible and electron paramagnetic resonance spectroscopies, as well as oxygen electrode measurements, are discussed for probing the interaction of the non-heme iron center with ligands and characterizing enzymatic activities. Moreover, protein crystallization has been demonstrated as a powerful tool to study these enzymes. We highlight in crystallo reactions and single-crystal spectroscopic methods to further elucidate enzymatic functions and protein dynamics.
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Affiliation(s)
- Jackson Campbell
- Department of Chemistry, University of Georgia, Athens, GA, United States
| | - Yifan Wang
- Department of Chemistry, University of Georgia, Athens, GA, United States.
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2
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Newton A, McCann L, Huo L, Liu A. Kynurenine Pathway Regulation at Its Critical Junctions with Fluctuation of Tryptophan. Metabolites 2023; 13:metabo13040500. [PMID: 37110158 PMCID: PMC10143591 DOI: 10.3390/metabo13040500] [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: 02/22/2023] [Revised: 03/14/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
The kynurenine pathway (KP) is the primary route for the catabolism of the essential amino acid tryptophan. The central KP metabolites are neurologically active molecules or biosynthetic precursors to critical molecules, such as NAD+. Within this pathway are three enzymes of interest, HAO, ACMSD, and AMSDH, whose substrates and/or products can spontaneously cyclize to form side products such as quinolinic acid (QA or QUIN) and picolinic acid. Due to their unstable nature for spontaneous autocyclization, it might be expected that the levels of these side products would be dependent on tryptophan intake; however, this is not the case in healthy individuals. On top of that, the regulatory mechanisms of the KP remain unknown, even after a deeper understanding of the structure and mechanism of the enzymes that handle these unstable KP metabolic intermediates. Thus, the question arises, how do these enzymes compete with the autocyclization of their substrates, especially amidst increased tryptophan levels? Here, we propose the formation of a transient enzyme complex as a regulatory mechanism for metabolite distribution between enzymatic and non-enzymatic routes during periods of increased metabolic intake. Amid high levels of tryptophan, HAO, ACMSD, and AMSDH may bind together, forming a tunnel to shuttle the metabolites through each enzyme, consequently regulating the autocyclization of their products. Though further research is required to establish the formation of transient complexation as a solution to the regulatory mysteries of the KP, our docking model studies support this new hypothesis.
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Affiliation(s)
- Ashley Newton
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Luree McCann
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Lu Huo
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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3
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Wu L, An J, Jing X, Chen CC, Dai L, Xu Y, Liu W, Guo RT, Nie Y. Molecular Insights into the Regioselectivity of the Fe(II)/2-Ketoglutarate-Dependent Dioxygenase-Catalyzed C–H Hydroxylation of Amino Acids. ACS Catal 2022. [DOI: 10.1021/acscatal.2c03106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lunjie Wu
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jianhong An
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu 214122, China
- School of Ophthalmology and Optometry, and Eye Hospital, Wenzhou Medical University, State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou, Zhejiang 325000, China
| | - Xiaoran Jing
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Longhai Dai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Weidong Liu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Yao Nie
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu 214122, China
- Suqian Industrial Technology Research Institute of Jiangnan University, Suqian, Jiangsu 223814, China
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4
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Abstract
Here, the choice of the first coordination shell of the metal center is analyzed from the perspective of charge maintenance in a binary enzyme-substrate complex and an O2-bound ternary complex in the nonheme iron oxygenases. Comparing homogentisate 1,2-dioxygenase and gentisate dioxygenase highlights the significance of charge maintenance after substrate binding as an important factor that drives the reaction coordinate. We then extend the charge analysis to several common types of nonheme iron oxygenases containing either a 2-His-1-carboxylate facial triad or a 3-His or 4-His ligand motif, including extradiol and intradiol ring-cleavage dioxygenases, thiol dioxygenases, α-ketoglutarate-dependent oxygenases, and carotenoid cleavage oxygenases. After forming the productive enzyme-substrate complex, the overall charge of the iron complex at the 0, +1, or +2 state is maintained in the remaining catalytic steps. Hence, maintaining a constant charge is crucial to promote the reaction of the iron center beginning from the formation of the Michaelis or ternary complex. The charge compensation to the iron ion is tuned not only by protein-derived carboxylate ligands but also by substrates. Overall, these analyses indicate that charge maintenance at the iron center is significant when all the necessary components form a productive complex. This charge maintenance concept may apply to most oxygen-activating metalloenzymes systems that do not draw electrons and protons step-by-step from a separate reactant, such as NADH, via a reductase. The charge maintenance perception may also be useful in proposing catalytic pathways or designing prototypical reactions using artificial or engineered enzymes for biotechnological applications.
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Affiliation(s)
- Ephrahime S. Traore
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Aimin Liu
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
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5
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Szot JO, Slavotinek A, Chong K, Brandau O, Nezarati M, Cueto-González AM, Patel MS, Devine WP, Rego S, Acyinena AP, Shannon P, Myles-Reid D, Blaser S, Mieghem TV, Yavuz-Kienle H, Skladny H, Miller K, Riera MDT, Martínez SA, Tizzano EF, Dupuis L, James Stavropoulos D, McNiven V, Mendoza-Londono R, Elliott AM, Phillips RS, Chapman G, Dunwoodie SL. New cases that expand the genotypic and phenotypic spectrum of Congenital NAD Deficiency Disorder. Hum Mutat 2021; 42:862-876. [PMID: 33942433 DOI: 10.1002/humu.24211] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/31/2021] [Accepted: 04/19/2021] [Indexed: 12/19/2022]
Abstract
Nicotinamide adenine dinucleotide (NAD) is an essential coenzyme involved in over 400 cellular reactions. During embryogenesis, mammals synthesize NAD de novo from dietary l -tryptophan via the kynurenine pathway. Biallelic, inactivating variants in three genes encoding enzymes of this biosynthesis pathway (KYNU, HAAO, and NADSYN1) disrupt NAD synthesis and have been identified in patients with multiple malformations of the heart, kidney, vertebrae, and limbs; these patients have Congenital NAD Deficiency Disorder HAAO and four families with biallelic variants in KYNU. These patients present similarly with multiple malformations of the heart, kidney, vertebrae, and limbs, of variable severity. We show that each variant identified in these patients results in loss-of-function, revealed by a significant reduction in NAD levels via yeast genetic complementation assays. For the first time, missense mutations are identified as a cause of malformation and shown to disrupt enzyme function. These missense and frameshift variants cause moderate to severe NAD deficiency in yeast, analogous to insufficient synthesized NAD in patients. We hereby expand the genotypic and corresponding phenotypic spectrum of Congenital NAD Deficiency Disorder.
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Affiliation(s)
- Justin O Szot
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Anne Slavotinek
- Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Karen Chong
- Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - Marjan Nezarati
- Genetics Program, North York General Hospital, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Anna M Cueto-González
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Millan S Patel
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Walter P Devine
- Department of Anatomic Pathology, University of California, San Francisco, California, USA
| | - Shannon Rego
- Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Alicia P Acyinena
- Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Patrick Shannon
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Diane Myles-Reid
- Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Susan Blaser
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tim V Mieghem
- Fetal Medicine Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | | | - Kristen Miller
- Genetics Program, North York General Hospital, Toronto, Ontario, Canada
| | - Miereia D T Riera
- Metabolic Unit and Pediatric Neurology Department, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Silvia A Martínez
- Fetal Medicine Unit and Obstetrics Department, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Eduardo F Tizzano
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Medicine Genetics Group, Vall d'Hebron Research Institute, Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona, Barcelona, Spain
| | - Lucie Dupuis
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Dimitri James Stavropoulos
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Vanda McNiven
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Roberto Mendoza-Londono
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Alison M Elliott
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert S Phillips
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - Gavin Chapman
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
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6
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Heinemann PM, Armbruster D, Hauer B. Active-site loop variations adjust activity and selectivity of the cumene dioxygenase. Nat Commun 2021; 12:1095. [PMID: 33597523 PMCID: PMC7889853 DOI: 10.1038/s41467-021-21328-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/11/2021] [Indexed: 01/31/2023] Open
Abstract
Active-site loops play essential roles in various catalytically important enzyme properties like activity, selectivity, and substrate scope. However, their high flexibility and diversity makes them challenging to incorporate into rational enzyme engineering strategies. Here, we report the engineering of hot-spots in loops of the cumene dioxygenase from Pseudomonas fluorescens IP01 with high impact on activity, regio- and enantioselectivity. Libraries based on alanine scan, sequence alignments, and deletions along with a novel insertion approach result in up to 16-fold increases in activity and the formation of novel products and enantiomers. CAVER analysis suggests possible increases in the active pocket volume and formation of new active-site tunnels, suggesting additional degrees of freedom of the substrate in the pocket. The combination of identified hot-spots with the Linker In Loop Insertion approach proves to be a valuable addition to future loop engineering approaches for enhanced biocatalysts.
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Affiliation(s)
- Peter M Heinemann
- Institute of Biochemistry and Technical Biochemistry, Department of Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Daniel Armbruster
- Institute of Biochemistry and Technical Biochemistry, Department of Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Bernhard Hauer
- Institute of Biochemistry and Technical Biochemistry, Department of Technical Biochemistry, University of Stuttgart, Stuttgart, Germany.
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7
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Yang Y, Borel T, de Azambuja F, Johnson D, Sorrentino JP, Udokwu C, Davis I, Liu A, Altman RA. Diflunisal Derivatives as Modulators of ACMS Decarboxylase Targeting the Tryptophan-Kynurenine Pathway. J Med Chem 2020; 64:797-811. [PMID: 33369426 DOI: 10.1021/acs.jmedchem.0c01762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In the kynurenine pathway for tryptophan degradation, an unstable metabolic intermediate, α-amino-β-carboxymuconate-ε-semialdehyde (ACMS), can nonenzymatically cyclize to form quinolinic acid, the precursor for de novo biosynthesis of nicotinamide adenine dinucleotide (NAD+). In a competing reaction, ACMS is decarboxylated by ACMS decarboxylase (ACMSD) for further metabolism and energy production. Therefore, the inhibition of ACMSD increases NAD+ levels. In this study, an Food and Drug Administration (FDA)-approved drug, diflunisal, was found to competitively inhibit ACMSD. The complex structure of ACMSD with diflunisal revealed a previously unknown ligand-binding mode and was consistent with the results of inhibition assays, as well as a structure-activity relationship (SAR) study. Moreover, two synthesized diflunisal derivatives showed half-maximal inhibitory concentration (IC50) values 1 order of magnitude better than diflunisal at 1.32 ± 0.07 μM (22) and 3.10 ± 0.11 μM (20), respectively. The results suggest that diflunisal derivatives have the potential to modulate NAD+ levels. The ligand-binding mode revealed here provides a new direction for developing inhibitors of ACMSD.
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Affiliation(s)
- Yu Yang
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Timothy Borel
- Department of Medicinal Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
| | | | - David Johnson
- Computational Chemical Biology Core and Molecular Graphics and Modeling Laboratory, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Jacob P Sorrentino
- Department of Medicinal Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Chinedum Udokwu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Ian Davis
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Ryan A Altman
- Department of Medicinal Chemistry and Molecular Pharmacology and Department of Chemistry, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
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8
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Wang Y, Liu KF, Yang Y, Davis I, Liu A. Observing 3-hydroxyanthranilate-3,4-dioxygenase in action through a crystalline lens. Proc Natl Acad Sci U S A 2020; 117:19720-19730. [PMID: 32732435 PMCID: PMC7443976 DOI: 10.1073/pnas.2005327117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The synthesis of quinolinic acid from tryptophan is a critical step in the de novo biosynthesis of nicotinamide adenine dinucleotide (NAD+) in mammals. Herein, the nonheme iron-based 3-hydroxyanthranilate-3,4-dioxygenase responsible for quinolinic acid production was studied by performing time-resolved in crystallo reactions monitored by UV-vis microspectroscopy, electron paramagnetic resonance (EPR) spectroscopy, and X-ray crystallography. Seven catalytic intermediates were kinetically and structurally resolved in the crystalline state, and each accompanies protein conformational changes at the active site. Among them, a monooxygenated, seven-membered lactone intermediate as a monodentate ligand of the iron center at 1.59-Å resolution was captured, which presumably corresponds to a substrate-based radical species observed by EPR using a slurry of small-sized single crystals. Other structural snapshots determined at around 2.0-Å resolution include monodentate and subsequently bidentate coordinated substrate, superoxo, alkylperoxo, and two metal-bound enol tautomers of the unstable dioxygenase product. These results reveal a detailed stepwise O-atom transfer dioxygenase mechanism along with potential isomerization activity that fine-tunes product profiling and affects the production of quinolinic acid at a junction of the metabolic pathway.
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Yu Yang
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Ian Davis
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Aimin Liu
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249;
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9
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Yang Y, Davis I, Matsui T, Rubalcava I, Liu A. Quaternary structure of α-amino-β-carboxymuconate-ϵ-semialdehyde decarboxylase (ACMSD) controls its activity. J Biol Chem 2019; 294:11609-11621. [PMID: 31189654 PMCID: PMC6663868 DOI: 10.1074/jbc.ra119.009035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/10/2019] [Indexed: 01/07/2023] Open
Abstract
α-Amino-β-carboxymuconate-ϵ-semialdehyde decarboxylase (ACMSD) plays an important role in l-tryptophan degradation via the kynurenine pathway. ACMSD forms a homodimer and is functionally inactive as a monomer because its catalytic assembly requires an arginine residue from a neighboring subunit. However, how the oligomeric state and self-association of ACMSD are controlled in solution remains unexplored. Here, we demonstrate that ACMSD from Pseudomonas fluorescens can self-assemble into homodimer, tetramer, and higher-order structures. Using size-exclusion chromatography coupled with small-angle X-ray scattering (SEC-SAXS) analysis, we investigated the ACMSD tetramer structure, and fitting the SAXS data with X-ray crystal structures of the monomeric component, we could generate a pseudo-atomic structure of the tetramer. This analysis revealed a tetramer model of ACMSD as a head-on dimer of dimers. We observed that the tetramer is catalytically more active than the dimer and is in equilibrium with the monomer and dimer. Substituting a critical residue of the dimer-dimer interface, His-110, altered the tetramer dissociation profile by increasing the higher-order oligomer portion in solution without changing the X-ray crystal structure. ACMSD self-association was affected by pH, ionic strength, and other electrostatic interactions. Alignment of ACMSD sequences revealed that His-110 is highly conserved in a few bacteria that utilize nitrobenzoic acid as a sole source of carbon and energy, suggesting a dedicated functional role of ACMSD's self-assembly into the tetrameric and higher-order structures. These results indicate that the dynamic oligomerization status potentially regulates ACMSD activity and that SEC-SAXS coupled with X-ray crystallography is a powerful tool for studying protein self-association.
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Affiliation(s)
- Yu Yang
- Department of Chemistry, University of Texas, San Antonio, Texas 78249
| | - Ian Davis
- Department of Chemistry, University of Texas, San Antonio, Texas 78249
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025
| | - Ivan Rubalcava
- Department of Chemistry, University of Texas, San Antonio, Texas 78249
| | - Aimin Liu
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, To whom correspondence should be addressed. Tel.:
210-458-7062; E-mail:
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10
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Wang Y, Shin I, Fu Y, Colabroy KL, Liu A. Crystal Structures of L-DOPA Dioxygenase from Streptomyces sclerotialus. Biochemistry 2019; 58:5339-5350. [PMID: 31180203 DOI: 10.1021/acs.biochem.9b00396] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Extradiol dioxygenases are essential biocatalysts for breaking down catechols. The vicinal oxygen chelate (VOC) superfamily contains a large number of extradiol dioxygenases, most of which are found as part of catabolic pathways degrading a variety of natural and human-made aromatic rings. The l-3,4-dihydroxyphenylalanine (L-DOPA) extradiol dioxygenases compose a multitude of pathways that produce various antibacterial or antitumor natural products. The structural features of these dioxygenases are anticipated to be distinct from those of other VOC extradiol dioxygenases. Herein, we identified a new L-DOPA dioxygenase from the thermophilic bacterium Streptomyces sclerotialus (SsDDO) through a sequence and genome context analysis. The activity of SsDDO was kinetically characterized with L-DOPA using an ultraviolet-visible spectrophotometer and an oxygen electrode. The optimal temperature of the assay was 55 °C, at which the Km and kcat of SsDDO were 110 ± 10 μM and 2.0 ± 0.1 s-1, respectively. We determined the de novo crystal structures of SsDDO in the ligand-free form and as a substrate-bound complex, refined to 1.99 and 2.31 Å resolution, respectively. These structures reveal that SsDDO possesses a form IV arrangement of βαβββ modules, the first characterization of this assembly from among the VOC/type I extradiol dioxygenase protein family. Electron paramagnetic resonance spectra of Fe-NO adducts for the resting and substrate-bound enzyme were obtained. This work contributes to our understanding of a growing class of topologically distinct VOC dioxygenases, and the obtained structural features will improve our understanding of the extradiol cleavage reaction within the VOC superfamily.
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Affiliation(s)
- Yifan Wang
- Department of Chemistry , University of Texas at San Antonio , San Antonio , Texas 78249 , United States
| | - Inchul Shin
- Department of Chemistry , University of Texas at San Antonio , San Antonio , Texas 78249 , United States
| | - Yizhi Fu
- Department of Chemistry , Muhlenberg College , Allentown , Pennsylvania 18104 , United States
| | - Keri L Colabroy
- Department of Chemistry , Muhlenberg College , Allentown , Pennsylvania 18104 , United States
| | - Aimin Liu
- Department of Chemistry , University of Texas at San Antonio , San Antonio , Texas 78249 , United States
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