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Yao Y, Yang B, Shi J. Crystalline Copper Hydroxide Nanosheets with KatG-like Dual Activities for Synergized Nanocatalytic Tumor Therapy. NANO LETTERS 2025; 25:8369-8378. [PMID: 40336174 DOI: 10.1021/acs.nanolett.5c01657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2025]
Abstract
The enzyme-mimicking catalytic activities of inorganic nanomaterials have attracted broad attention recently. Catalase-peroxidase (KatG) is a bifunctional enzyme with both catalase and peroxidase activities that converts hydrogen peroxide (H2O2) into both oxygen (O2) and a radical, respectively. Herein, crystalline Cu(OH)2 nanosheets have been synthesized and demonstrated as inorganic nanocatalysts with KatG-like activity for nanocatalytic tumor therapy. The distinct crystalline structure of the Cu(OH)2 nanosheets features abundant bis(μ-hydroxo)CuIICuII dinuclear catalytically active sites, enabling efficient redox cycling to favor one two-electron transfer for O2 generation (catalatic catalysis) and two consecutive single-electron transfers for hydroxyl radical (•OH) generation (peroxidatic catalysis), successively. During tumor therapy, the O2 generation by the nanomaterial mitigates intratumoral hypoxia and sensitizes cancer cells to oxidative attack, resulting in significantly enhanced anticancer efficacy. This work bridges dual-active nanocatalysis with bifunctional enzymatic catalysis, presenting a crystalline inorganic nanomaterial with KatG-like activity and its synergy for nanocatalytic tumor therapy.
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Affiliation(s)
- Yufan Yao
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences; Research Unit of Nanocatalytic Medicine in Specific Therapy for Serious Disease, Chinese Academy of Medical Sciences (2021RU012), Shanghai, 200050, P. R. China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Bowen Yang
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences; Research Unit of Nanocatalytic Medicine in Specific Therapy for Serious Disease, Chinese Academy of Medical Sciences (2021RU012), Shanghai, 200050, P. R. China
| | - Jianlin Shi
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences; Research Unit of Nanocatalytic Medicine in Specific Therapy for Serious Disease, Chinese Academy of Medical Sciences (2021RU012), Shanghai, 200050, P. R. China
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2
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Graciano A, Liu A. Protein-derived cofactors: chemical innovations expanding enzyme catalysis. Chem Soc Rev 2025; 54:4502-4530. [PMID: 40151987 PMCID: PMC11951088 DOI: 10.1039/d4cs00981a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2025] [Indexed: 03/29/2025]
Abstract
Protein-derived cofactors, formed through posttranslational modification of a single amino acid or covalent crosslinking of amino acid side chains, represent a rapidly expanding class of catalytic moieties that redefine enzyme functionality. Once considered rare, these cofactors are recognized across all domains of life, with their repertoire growing from 17 to 38 types in two decades in our survey. Their biosynthesis proceeds via diverse pathways, including oxidation, metal-assisted rearrangements, and enzymatic modifications, yielding intricate motifs that underpin distinctive catalytic strategies. These cofactors span paramagnetic and non-radical states, including both mono-radical and crosslinked radical forms, sometimes accompanied by additional modifications. While their discovery has accelerated, mechanistic understanding lags, as conventional mutagenesis disrupts cofactor assembly. Emerging approaches, such as site-specific incorporation of non-canonical amino acids, now enable precise interrogation of cofactor biogenesis and function, offering a viable and increasingly rigorous means to gain mechanistic insights. Beyond redox chemistry and electron transfer, these cofactors confer enzymes with expanded functionalities. Recent studies have unveiled new paradigms, such as long-range remote catalysis and redox-regulated crosslinks as molecular switches. Advances in structural biology, mass spectrometry, and biophysical spectroscopy continue to elucidate their mechanisms. Moreover, synthetic biology and biomimetic chemistry are increasingly leveraging these natural designs to engineer enzyme-inspired catalysts. This review integrates recent advances in cofactor biogenesis, reactivity, metabolic regulation, and synthetic applications, highlighting the expanding chemical landscape and growing diversity of protein-derived cofactors and their far-reaching implications for enzymology, biocatalysis, and biotechnology.
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Affiliation(s)
- Angelica Graciano
- Department of Chemistry, The University of Texas at San Antonio, Texas 78249, USA.
| | - Aimin Liu
- Department of Chemistry, The University of Texas at San Antonio, Texas 78249, USA.
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3
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Li J, Duan R, Traore ES, Nguyen RC, Davis I, Griffth WP, Goodwin DC, Jarzecki AA, Liu A. Indole N-Linked Hydroperoxyl Adduct of Protein-Derived Cofactor Modulating Catalase-Peroxidase Functions. Angew Chem Int Ed Engl 2024; 63:e202407018. [PMID: 39300819 DOI: 10.1002/anie.202407018] [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: 04/15/2024] [Revised: 09/02/2024] [Accepted: 09/19/2024] [Indexed: 09/22/2024]
Abstract
Bifunctional catalase-peroxidase (KatG) features a posttranslational methionine-tyrosine-tryptophan (MYW) crosslinked cofactor crucial for its catalase function, enabling pathogens to neutralize hydrogen peroxide during infection. We discovered the presence of indole nitrogen-linked hydroperoxyl adduct (MYW-OOH) in Mycobacterium tuberculosis KatG in the solution state under ambient conditions, suggesting its natural occurrence. By isolating predominantly MYW-OOH-containing KatG protein, we investigated the chemical stability and functional impact of MYW-OOH. We discovered that MYW-OOH inhibits catalase activity, presenting a unique temporary lock. Exposure to peroxide or increased temperature removes the hydroperoxyl adduct from the protein cofactor, converting MYW-OOH to MYW and restoring the detoxifying ability of the enzyme against hydrogen peroxide. Thus, the N-linked hydroperoxyl group is releasable. KatG with MYW-OOH represents a catalase dormant, but primed, state of the enzyme. These findings provide insight into chemical strategies targeting the bifunctional enzyme KatG in pathogens, highlighting the role of N-linked hydroperoxyl modifications in enzymatic function.
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Affiliation(s)
- Jiasong Li
- Department of Chemistry, The University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX 78249, USA
| | - Ran Duan
- Department of Chemistry, The University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX 78249, USA
| | - Ephrahime S Traore
- Department of Chemistry, The University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX 78249, USA
| | - Romie C Nguyen
- Department of Chemistry, The University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX 78249, USA
| | - Ian Davis
- Department of Chemistry, The University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX 78249, USA
| | - Wendell P Griffth
- Department of Chemistry, The University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX 78249, USA
| | - Douglas C Goodwin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA
| | - Andrzej A Jarzecki
- Department of Chemistry and Biochemistry, Brooklyn College, New York, NY 11210, USA
| | - Aimin Liu
- Department of Chemistry, The University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX 78249, USA
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4
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Liu A. Catalase-peroxidase (KatG): a potential frontier in tuberculosis drug development. Crit Rev Biochem Mol Biol 2024; 59:434-446. [PMID: 40013498 PMCID: PMC11935562 DOI: 10.1080/10409238.2025.2470630] [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: 11/30/2024] [Revised: 02/17/2025] [Accepted: 02/19/2025] [Indexed: 02/28/2025]
Abstract
Mycobacterium tuberculosis (Mtb) depends on the bifunctional enzyme catalase-peroxidase (KatG) for survival within the host. KatG exhibits both catalase and peroxidase activities, serving distinct yet critical roles. While its peroxidase activity is essential for activating the frontline tuberculosis drug isoniazid, its catalase activity protects Mtb from oxidative stress. This bifunctional enzyme is equipped with a unique, protein-derived cofactor, methionine-tyrosine-tryptophan (MYW), which enables catalase activity to efficiently disproportionate hydrogen peroxide in phagocytes. Recent studies reveal that the MYW cofactor naturally exists in a hydroperoxylated form (MYW-OOH) when cell cultures are grown under ambient conditions. New findings highlight a dynamic regulation of KatG activity, wherein the modification of the protein cofactor is removable-from MYW-OOH to MYW-at body temperature or in the presence of micromolar concentrations of hydrogen peroxide. This reversible modification modulates KatG's dual activities: MYW-OOH inhibits catalase activity while enhancing peroxidase activity, demonstrating the chemical accessibility of the cofactor. Such duality positions KatG as a unique target for tuberculosis drug development. Therapeutic strategies that exploit cofactor modification could hold promise, particularly against drug-resistant strains with impaired peroxidase activity. By selectively inhibiting catalase activity, these approaches would render Mtb more vulnerable to oxidative stress while enhancing isoniazid activation-a double-edged strategy for combating tuberculosis.
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Affiliation(s)
- Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78256, USA
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5
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Zhu Y, Ding W, Chen Y, Shan Y, Liu C, Fan X, Lin S, Chen PR. Genetically encoded bioorthogonal tryptophan decaging in living cells. Nat Chem 2024; 16:533-542. [PMID: 38418535 DOI: 10.1038/s41557-024-01463-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/29/2024] [Indexed: 03/01/2024]
Abstract
Tryptophan (Trp) plays a critical role in the regulation of protein structure, interactions and functions through its π system and indole N-H group. A generalizable method for blocking and rescuing Trp interactions would enable the gain-of-function manipulation of various Trp-containing proteins in vivo, but generating such a platform remains challenging. Here we develop a genetically encoded N1-vinyl-caged Trp capable of rapid and bioorthogonal decaging through an optimized inverse electron-demand Diels-Alder reaction, allowing site-specific activation of Trp on a protein of interest in living cells. This chemical activation of a genetically encoded caged-tryptophan (Trp-CAGE) strategy enables precise activation of the Trp of interest underlying diverse important molecular interactions. We demonstrate the utility of Trp-CAGE across various protein families, such as catalase-peroxidases and kinases, as translation initiators and posttranslational modification readers, allowing the modulation of epigenetic signalling in a temporally controlled manner. Coupled with computer-aided prediction, our strategy paves the way for bioorthogonal Trp activation on more than 28,000 candidate proteins within their native cellular settings.
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Affiliation(s)
- Yuchao Zhu
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Wenlong Ding
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Yulin Chen
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Ye Shan
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Chao Liu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Xinyuan Fan
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
| | - Shixian Lin
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China.
- Department of Medical Oncology, State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Peng R Chen
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
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Batabyal M, Upadhyay A, Kadu R, Birudukota NC, Chopra D, Kumar S. Tetravalent Spiroselenurane Catalysts: Intramolecular Se···N Chalcogen Bond-Driven Catalytic Disproportionation of H 2O 2 to H 2O and O 2 and Activation of I 2 and NBS. Inorg Chem 2022; 61:8729-8745. [PMID: 35638247 DOI: 10.1021/acs.inorgchem.2c00651] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chalcogen-bonding interactions have recently gained considerable attention in the field of synthetic chemistry, structure, and bonding. Here, three organo-spiroselenuranes, having a Se(IV) center with a strong intramolecular Se···N chalcogen-bonded interaction, have been isolated by the oxidation of the respective bis(2-benzamide) selenides derived from an 8-aminoquinoline ligand. Further, the synthesized spiroselenuranes, when assayed for their antioxidant activity, show disproportionation of hydrogen peroxide into H2O and O2 with first-order kinetics with respect to H2O2 for the first time by any organoselenium molecules as monitored by 1H NMR spectroscopy. Electron-donating 5-methylthio-benzamide ring-substituted spiroselenurane disproportionates hydrogen peroxide at a high rate of 15.6 ± 0.4 × 103 μM min-1 with a rate constant of 8.57 ± 0.50 × 10-3 s-1, whereas 5-methoxy and unsubstituted-benzamide spiroselenuranes catalyzed the disproportionation of H2O2 at rates of 7.9 ± 0.3 × 103 and 2.9 ± 0.3 × 103 μM min-1 with rate constants of 1.16 ± 0.02 × 10-3 and 0.325 ± 0.025 × 10-3 s-1, respectively. The evolved oxygen gas from the spiroselenurane-catalyzed disproportion of H2O2 has also been confirmed by a gas chromatograph-thermal conductivity detector (GCTCD) and a portable digital polarographic dissolved O2 probe. Additionally, the synthesized spiroselenuranes exhibit thiol peroxidase antioxidant activities for the reduction of H2O2 by a benzenethiol co-reductant monitored by UV-visible spectroscopy. Next, the Se···N bonded spiroselenuranes have been explored as catalysts in synthetic oxidation iodolactonization and bromination of arenes. The synthesized spiroselenurane has activated I2 toward the iodolactonization of alkenoic acids under base-free conditions. Similarly, efficient chemo- and regioselective monobromination of various arenes with NBS catalyzed by chalcogen-bonded synthesized spiroselenuranes has been achieved. Mechanistic insight into the spiroselenuranes in oxidation reactions has been gained by 77Se NMR, mass spectrometry, UV-visible spectroscopy, single-crystal X-ray structure, and theoretical (DFT, NBO, and AIM) studies. It seems that the highly electrophilic nature of the selenium center is attributed to the presence of an intramolecular Se···N interaction and a vacant coordination site in spiroselenuranes is crucial for the activation of H2O2, I2, and NBS. The reaction of H2O2, I2, and NBS with tetravalent spiroselenurane would lead to an octahedral-Se(VI) intermediate, which is reduced back to Se(IV) due to thermodynamic instability of selenium in its highest oxidation state and the presence of a strong intramolecular N-donor atom.
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Affiliation(s)
- Monojit Batabyal
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri Bhopal 462 066, Madhya Pradesh, India
| | - Aditya Upadhyay
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri Bhopal 462 066, Madhya Pradesh, India
| | - Rahul Kadu
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri Bhopal 462 066, Madhya Pradesh, India.,MIT School of Engineering, MIT Art, Design and Technology University Pune, Loni Kalbhor, Maharashtra 412201, India
| | - Nihal Chaitanya Birudukota
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri Bhopal 462 066, Madhya Pradesh, India
| | - Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri Bhopal 462 066, Madhya Pradesh, India
| | - Sangit Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri Bhopal 462 066, Madhya Pradesh, India
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7
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Liu CX, Zhao X, Wang L, Yang ZC. Quinoline derivatives as potential anti-tubercular agents: Synthesis, molecular docking and mechanism of action. Microb Pathog 2022; 165:105507. [DOI: 10.1016/j.micpath.2022.105507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 02/27/2022] [Accepted: 03/26/2022] [Indexed: 10/18/2022]
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8
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Sahrmann PG, Donnan PH, Merz KM, Mansoorabadi SO, Goodwin DC. MRP.py: A Parametrizer of Post-Translationally Modified Residues. J Chem Inf Model 2020; 60:4424-4428. [PMID: 32672967 DOI: 10.1021/acs.jcim.0c00472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
MRP.py is a Python-based parametrization program for covalently modified amino acid residues for molecular dynamics simulations. Charge derivation is performed via an RESP charge fit, and force constants are obtained through rewriting of either protein or GAFF database parameters. This allows for the description of interfacial interactions between the modifed residue and protein. MRP.py is capable of working with a variety of protein databases. MRP.py's highly general and systematic method of obtaining parameters allows the user to circumvent the process of parametrizing the modified residue-protein interface. Two examples, a covalently bound inhibitor and covalent adduct consisting of modified residues, are provided in the Supporting Information.
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Affiliation(s)
- Patrick G Sahrmann
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama36849-5312, United States
| | - Patrick H Donnan
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama36849-5312, United States
| | - Kenneth M Merz
- Department of Chemistry and the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1312, United States
| | - Steven O Mansoorabadi
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama36849-5312, United States
| | - Douglas C Goodwin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama36849-5312, United States
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9
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Li X, Zhu W, Liu Y. Mechanistic Insights into the Oxidative Rearrangement Catalyzed by the Unprecedented Dioxygenase ChaP Involved in Chartreusin Biosynthesis. Inorg Chem 2020; 59:13988-13999. [PMID: 32951427 DOI: 10.1021/acs.inorgchem.0c01706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
ChaP is a non-heme iron-dependent dioxygenase belonging to the vicinal oxygen chelate (VOC) enzyme superfamily that catalyzes the final α-pyrone ring formation in the biosynthesis of chartreusin. In contrast to other common dioxygenases, for example, 2,3-catechol dioxygenase which uses the dioxygen molecule as the oxidant, ChaP requires the flavin-activated oxygen (O22-) as the equivalent. Previous experiments showed that the ChaP-catalyzed ring rearrangement contains two successive C-C bond cleavages and one lactonization; however, the detailed reaction mechanism is unknown. In this work, on the basis of the recently obtained crystal structure of ChaP, the computational model was constructed and the catalytic mechanism of ChaP was explored by performing quantum mechanical/molecular mechanical (QM/MM) calculations. Our calculation results reveal that ChaP uses the proximal oxygen in iron-coordinated HOO- to attack the carbonyl carbon of the substrate, whereas the previous proposal that Asp49 acts as a base to deprotonate the iron-coordinated HOO- to generate O22- is unlikely. In the first stage reaction, owing to the coordination of the substrate with iron, the substrate is activated by accepting an electron from iron and the resulting oxy-radical intermediate formed by O-O cleavage can easily trigger the ring rearrangement. In the final decarboxylation, the phenolic anion of the substrate cooperatively accepts the proton of iron-coordinated HOO- to facilitate the attack of the distal oxygen, and the proton-coupled electron transfer (PCET) from the substrate to the FeIV═O plays a key role for the decarboxylation. These findings may provide useful information for understanding the ChaP-catalyzed oxidative rearrangement and other flavin-dependent non-heme dioxygenases.
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Affiliation(s)
- Xinyi Li
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Wenyou Zhu
- College of Chemistry and Chemical Engineering, Xuzhou Institute of Technology, Xuzhou, Jiangsu 221111, China
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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10
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Li H, Liu Y. Mechanistic Investigation of Isonitrile Formation Catalyzed by the Nonheme Iron/α-KG-Dependent Decarboxylase (ScoE). ACS Catal 2020. [DOI: 10.1021/acscatal.9b05411] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Hong Li
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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11
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Boubeta FM, Soler-Illia GJAA, Tagliazucchi M. Electrostatically Driven Protein Adsorption: Charge Patches versus Charge Regulation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15727-15738. [PMID: 30451508 DOI: 10.1021/acs.langmuir.8b03411] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The mechanisms of electrostatically driven adsorption of proteins on charged surfaces are studied with a new theoretical framework. The acid-base behavior, charge distribution, and electrostatic contributions to the thermodynamic properties of the proteins are modeled in the presence of a charged surface. The method is validated against experimental titration curves and apparent p Kas. The theory predicts that electrostatic interactions favor the adsorption of proteins at their isoelectric points on charged surfaces despite the fact that the protein has no net charge in solution. Two known mechanisms explain adsorption under these conditions: (i) charge regulation (the charge of the protein changes due to the presence of the surface) and (ii) charge patches (the protein orients to place charged amino acids near opposite surface charges). This work shows that both mechanisms contribute to adsorption at low ionic strengths, whereas only the charge-patch mechanism operates at high ionic strength. Interestingly, the contribution of charge regulation is insensitive to protein orientation under all conditions, which validates the use of constant-charge simulations to determine the most stable orientation of adsorbed proteins. The present study also shows that the charged surface can induce large shifts in the apparent p Kas of individual amino acids in adsorbed proteins. Our conclusions are valid for all proteins studied in this work (lysozyme, α-amylase, ribonuclease A, and β-lactoglobulin), as well as for proteins that are not isoelectric but have instead a net charge in solution of the same sign as the surface charge, i.e. the problem of protein adsorption on the "wrong side" of the isoelectric point.
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Affiliation(s)
| | - G J A A Soler-Illia
- Instituto de Nanosistemas , Universidad Nacional de General San Martín , Avenida 25 de Mayo y Francia , 1650 San Martín , Argentina
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12
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Wang B, Fita I, Rovira C. Theory Uncovers the Role of the Methionine-Tyrosine-Tryptophan Radical Adduct in the Catalase Reaction of KatGs: O2
Release Mediated by Proton-Coupled Electron Transfer. Chemistry 2018; 24:5388-5395. [DOI: 10.1002/chem.201706076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Binju Wang
- Departament de Química Inorgànica i Orgànica, (secció de Química Orgànica) &, Institut de Química Teòrica i Computacional (IQTCUB); Universitat de Barcelona; Martí i Franquès 1 08028 Barcelona Spain
| | - Ignacio Fita
- Instituto de Biología Molecular (IBMB-CSIC) and; Maria de Maeztu Unit of Excellence. Barcelona Science Park; Baldiri i Reixac 10. 08028 Barcelona Spain
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica, (secció de Química Orgànica) &, Institut de Química Teòrica i Computacional (IQTCUB); Universitat de Barcelona; Martí i Franquès 1 08028 Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA); Passeig Lluís Companys 23 08010 Barcelona Spain
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13
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Laborde J, Deraeve C, de Mesquita Vieira FG, Sournia-Saquet A, Rechignat L, Villela AD, Abbadi BL, Macchi FS, Pissinate K, Bizarro CV, Machado P, Basso LA, Pratviel G, de França Lopes LG, Sousa EHS, Bernardes-Génisson V. Synthesis and mechanistic investigation of iron(II) complexes of isoniazid and derivatives as a redox-mediated activation strategy for anti-tuberculosis therapy. J Inorg Biochem 2018; 179:71-81. [DOI: 10.1016/j.jinorgbio.2017.11.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 11/14/2017] [Accepted: 11/17/2017] [Indexed: 12/27/2022]
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14
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Laborde J, Deraeve C, Bernardes-Génisson V. Update of Antitubercular Prodrugs from a Molecular Perspective: Mechanisms of Action, Bioactivation Pathways, and Associated Resistance. ChemMedChem 2017; 12:1657-1676. [DOI: 10.1002/cmdc.201700424] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/12/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Julie Laborde
- CNRS; LCC (Laboratoire de Chimie de Coordination); 205, route de Narbonne, BP 44099 31077 Toulouse, Cedex 4 France
- Université de Toulouse; UPS, INPT; 31077 Toulouse, Cedex 4 France
| | - Céline Deraeve
- CNRS; LCC (Laboratoire de Chimie de Coordination); 205, route de Narbonne, BP 44099 31077 Toulouse, Cedex 4 France
- Université de Toulouse; UPS, INPT; 31077 Toulouse, Cedex 4 France
| | - Vania Bernardes-Génisson
- CNRS; LCC (Laboratoire de Chimie de Coordination); 205, route de Narbonne, BP 44099 31077 Toulouse, Cedex 4 France
- Université de Toulouse; UPS, INPT; 31077 Toulouse, Cedex 4 France
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15
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Njuma OJ, Davis I, Ndontsa EN, Krewall JR, Liu A, Goodwin DC. Mutual synergy between catalase and peroxidase activities of the bifunctional enzyme KatG is facilitated by electron hole-hopping within the enzyme. J Biol Chem 2017; 292:18408-18421. [PMID: 28972181 DOI: 10.1074/jbc.m117.791202] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 09/22/2017] [Indexed: 11/06/2022] Open
Abstract
KatG is a bifunctional, heme-dependent enzyme in the front-line defense of numerous bacterial and fungal pathogens against H2O2-induced oxidative damage from host immune responses. Contrary to the expectation that catalase and peroxidase activities should be mutually antagonistic, peroxidatic electron donors (PxEDs) enhance KatG catalase activity. Here, we establish the mechanism of synergistic cooperation between these activities. We show that at low pH values KatG can fully convert H2O2 to O2 and H2O only if a PxED is present in the reaction mixture. Stopped-flow spectroscopy results indicated rapid initial rates of H2O2 disproportionation slowing concomitantly with the accumulation of ferryl-like heme states. These states very slowly returned to resting (i.e. ferric) enzyme, indicating that they represented catalase-inactive intermediates. We also show that an active-site tryptophan, Trp-321, participates in off-pathway electron transfer. A W321F variant in which the proximal tryptophan was replaced with a non-oxidizable phenylalanine exhibited higher catalase activity and less accumulation of off-pathway heme intermediates. Finally, rapid freeze-quench EPR experiments indicated that both WT and W321F KatG produce the same methionine-tyrosine-tryptophan (MYW) cofactor radical intermediate at the earliest reaction time points and that Trp-321 is the preferred site of off-catalase protein oxidation in the native enzyme. Of note, PxEDs did not affect the formation of the MYW cofactor radical but could reduce non-productive protein-based radical species that accumulate during reaction with H2O2 Our results suggest that catalase-inactive intermediates accumulate because of off-mechanism oxidation, primarily of Trp-321, and PxEDs stimulate KatG catalase activity by preventing the accumulation of inactive intermediates.
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Affiliation(s)
- Olive J Njuma
- From the Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312
| | - Ian Davis
- the Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249-0698, and.,the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Elizabeth N Ndontsa
- From the Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312
| | - Jessica R Krewall
- From the Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312
| | - Aimin Liu
- the Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249-0698, and
| | - Douglas C Goodwin
- From the Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312,
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16
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Machuqueiro M, Victor B, Switala J, Villanueva J, Rovira C, Fita I, Loewen PC. The Catalase Activity of Catalase-Peroxidases Is Modulated by Changes in the pKa of the Distal Histidine. Biochemistry 2017; 56:2271-2281. [DOI: 10.1021/acs.biochem.6b01276] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Miguel Machuqueiro
- Centro de Química
e Bioquímica, Departamento de Química e Bioquímica,
Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Bruno Victor
- Centro de Química
e Bioquímica, Departamento de Química e Bioquímica,
Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Jacek Switala
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T
2N2, Canada
| | - Jacylyn Villanueva
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T
2N2, Canada
| | - Carme Rovira
- Departament de Química
Organica and Institut de Química Teòrica i Computacional
(IQTCUB), Universtat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Ignacio Fita
- Institut de Biología
Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Baldiri
i Reixac 10-12, 08028 Barcelona, Spain
| | - Peter C. Loewen
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T
2N2, Canada
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17
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Wang B, Shaik S. The Nickel-Pincer Complex in Lactate Racemase Is an Electron Relay and Sink that acts through Proton-Coupled Electron Transfer. Angew Chem Int Ed Engl 2017; 56:10098-10102. [DOI: 10.1002/anie.201612065] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Binju Wang
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry; The Hebrew University of Jerusalem; 91904 Jerusalem Israel
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry; The Hebrew University of Jerusalem; 91904 Jerusalem Israel
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18
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Wang B, Shaik S. The Nickel-Pincer Complex in Lactate Racemase Is an Electron Relay and Sink that acts through Proton-Coupled Electron Transfer. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612065] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Binju Wang
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry; The Hebrew University of Jerusalem; 91904 Jerusalem Israel
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry; The Hebrew University of Jerusalem; 91904 Jerusalem Israel
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19
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Gasselhuber B, Graf MMH, Jakopitsch C, Zamocky M, Nicolussi A, Furtmüller PG, Oostenbrink C, Carpena X, Obinger C. Interaction with the Redox Cofactor MYW and Functional Role of a Mobile Arginine in Eukaryotic Catalase-Peroxidase. Biochemistry 2016; 55:3528-41. [PMID: 27293030 PMCID: PMC4928148 DOI: 10.1021/acs.biochem.6b00436] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Catalase-peroxidases
(KatGs) are unique bifunctional heme peroxidases
with an additional posttranslationally formed redox-active Met-Tyr-Trp
cofactor that is essential for catalase activity. On the basis of
studies of bacterial KatGs, controversial mechanisms of hydrogen peroxide
oxidation were proposed. The recent discovery of eukaryotic KatGs
with differing pH optima of catalase activity now allows us to scrutinize
those postulated reaction mechanisms. In our study, secreted KatG
from the fungus Magnaporthe grisea (MagKatG2) was used to analyze the role of a remote KatG-typical mobile
arginine that was shown to interact with the Met-Tyr-Trp adduct in
a pH-dependent manner in bacterial KatGs. Here we present crystal
structures of MagKatG2 at pH 3.0, 5.5, and 7.0 and
investigate the mobility of Arg461 by molecular dynamics simulation.
Data suggest that at pH ≥4.5 Arg461 mostly interacts with the
deprotonated adduct Tyr. Elimination of Arg461 by mutation to Ala
slightly increases the thermal stability but does not alter the active
site architecture or the kinetics of cyanide binding. However, the
variant Arg461Ala lost the wild-type-typical optimum of catalase activity
at pH 5.25 (kcat = 6450 s–1) but exhibits a broad plateau between pH 4.5 and 7.5 (kcat = 270 s–1 at pH 5.5). Moreover,
significant differences in the kinetics of interconversion of redox
intermediates of wild-type and mutant protein mixed with either peroxyacetic
acid or hydrogen peroxide are observed. These findings together with
published data from bacterial KatGs allow us to propose a role of
Arg461 in the H2O2 oxidation reaction of KatG.
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Affiliation(s)
- Bernhard Gasselhuber
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
| | - Michael M H Graf
- Department of Material Sciences and Process Engineering, Institute for Molecular Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
| | - Christa Jakopitsch
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
| | - Marcel Zamocky
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria.,Institute of Molecular Biology, Slovak Academy of Sciences , Dubravska cesta 21, SK-84551 Bratislava, Slovakia
| | - Andrea Nicolussi
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
| | - Paul G Furtmüller
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, Institute for Molecular Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
| | - Xavi Carpena
- Institut de Biologia Molecular (IBMB-CSIC) , Parc Cientific de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Christian Obinger
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
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20
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Wang B, Cao Z, Sharon DA, Shaik S. Computations Reveal a Rich Mechanistic Variation of Demethylation of N-Methylated DNA/RNA Nucleotides by FTO. ACS Catal 2015. [DOI: 10.1021/acscatal.5b01867] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Binju Wang
- Institute
of Chemistry and The Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Zexing Cao
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, People’s Republic of China
| | - Dina A. Sharon
- Institute
of Chemistry and The Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Sason Shaik
- Institute
of Chemistry and The Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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21
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Sgrignani J, Iannuzzi M, Magistrato A. Role of Water in the Puzzling Mechanism of the Final Aromatization Step Promoted by the Human Aromatase Enzyme. Insights from QM/MM MD Simulations. J Chem Inf Model 2015; 55:2218-26. [DOI: 10.1021/acs.jcim.5b00249] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jacopo Sgrignani
- CNR-IOM-Democritos
National Simulation Center c/o International School for Advanced Studies
(SISSA/ISAS), via Bonomea 265, Trieste, Trieste, Italy
| | - Marcella Iannuzzi
- Physical
Chemistry Institute, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Zurich, Switzerland
| | - Alessandra Magistrato
- CNR-IOM-Democritos
National Simulation Center c/o International School for Advanced Studies
(SISSA/ISAS), via Bonomea 265, Trieste, Trieste, Italy
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22
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Gasselhuber B, Carpena X, Graf MMH, Pirker KF, Nicolussi A, Sündermann A, Hofbauer S, Zamocky M, Furtmüller PG, Jakopitsch C, Oostenbrink C, Fita I, Obinger C. Eukaryotic Catalase-Peroxidase: The Role of the Trp-Tyr-Met Adduct in Protein Stability, Substrate Accessibility, and Catalysis of Hydrogen Peroxide Dismutation. Biochemistry 2015; 54:5425-38. [DOI: 10.1021/acs.biochem.5b00831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bernhard Gasselhuber
- Department
of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Xavi Carpena
- Institut de Biologia Molecular (IBMB-CSIC), Parc Cientific de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Michael M. H. Graf
- Department
of Material Sciences and Process Engineering, Institute for Molecular
Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Katharina F. Pirker
- Department
of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Andrea Nicolussi
- Department
of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Axel Sündermann
- Department
of Material Sciences and Process Engineering, Institute for Molecular
Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Stefan Hofbauer
- Department
for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Biocenter 5, A-1030 Vienna, Austria
| | - Marcel Zamocky
- Department
of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
- Institute
of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta
21, SK-84551 Bratislava, Slovakia
| | - Paul G. Furtmüller
- Department
of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Christa Jakopitsch
- Department
of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Chris Oostenbrink
- Department
of Material Sciences and Process Engineering, Institute for Molecular
Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Ignacio Fita
- Institut de Biologia Molecular (IBMB-CSIC), Parc Cientific de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Christian Obinger
- Department
of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
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23
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Campomanes P, Rothlisberger U, Alfonso-Prieto M, Rovira C. The Molecular Mechanism of the Catalase-like Activity in Horseradish Peroxidase. J Am Chem Soc 2015; 137:11170-8. [DOI: 10.1021/jacs.5b06796] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Pablo Campomanes
- Laboratory
of Computational Chemistry and Biochemistry, Institute of Chemical
Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry, Institute of Chemical
Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Mercedes Alfonso-Prieto
- Departament de Química Orgànica & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08208 Barcelona, Spain
| | - Carme Rovira
- Departament de Química Orgànica & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08208 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
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24
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Kruft BI, Magliozzo RS, Jarzęcki AA. Density Functional Theory Insights into the Role of the Methionine–Tyrosine–Tryptophan Adduct Radical in the KatG Catalase Reaction: O2 Release from the Oxyheme Intermediate. J Phys Chem A 2015; 119:6850-66. [DOI: 10.1021/jp511358p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Bonnie I. Kruft
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, United States
- The Graduate Center, City University of New York, Brooklyn, New York 10016, United States
| | - Richard S. Magliozzo
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, United States
- The Graduate Center, City University of New York, Brooklyn, New York 10016, United States
| | - Andrzej A. Jarzęcki
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, United States
- The Graduate Center, City University of New York, Brooklyn, New York 10016, United States
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25
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Kudalkar SN, Njuma OJ, Li Y, Muldowney M, Fuanta NR, Goodwin DC. A role for catalase-peroxidase large loop 2 revealed by deletion mutagenesis: control of active site water and ferric enzyme reactivity. Biochemistry 2015; 54:1648-62. [PMID: 25674665 DOI: 10.1021/bi501221a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Catalase-peroxidases (KatGs), the only catalase-active members of their superfamily, all possess a 35-residue interhelical loop called large loop 2 (LL2). It is essential for catalase activity, but little is known about its contribution to KatG function. LL2 shows weak sequence conservation; however, its length is nearly identical across KatGs, and its apex invariably makes contact with the KatG-unique C-terminal domain. We used site-directed and deletion mutagenesis to interrogate the role of LL2 and its interaction with the C-terminal domain in KatG structure and catalysis. Single and double substitutions of the LL2 apex had little impact on the active site heme [by magnetic circular dichroism or electron paramagnetic resonance (EPR)] and activity (catalase or peroxidase). Conversely, deletion of a single amino acid from the LL2 apex reduced catalase activity by 80%. Deletion of two or more apex amino acids or all of LL2 diminished catalase activity by 300-fold. Peroxide-dependent but not electron donor-dependent kcat/KM values for deletion variant peroxidase activity were reduced 20-200-fold, and kon for cyanide binding diminished by 3 orders of magnitude. EPR spectra for deletion variants were all consistent with an increase in the level of pentacoordinate high-spin heme at the expense of hexacoordinate high-spin states. Together, these data suggest a shift in the distribution of active site waters, altering the reactivity of the ferric state, toward, among other things, compound I formation. These results identify the importance of LL2 length conservation for maintaining an intersubunit interaction that is essential for an active site water distribution that facilitates KatG catalytic activity.
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Affiliation(s)
- Shalley N Kudalkar
- Department of Chemistry and Biochemistry, Auburn University , Auburn, Alabama 36849-5312, United States
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26
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Teixeira VH, Ventura C, Leitão R, Ràfols C, Bosch E, Martins F, Machuqueiro M. Molecular Details of INH-C10 Binding to wt KatG and Its S315T Mutant. Mol Pharm 2015; 12:898-909. [DOI: 10.1021/mp500736n] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Vitor H. Teixeira
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Cristina Ventura
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Instituto Superior de Educação e Ciências, Alameda das Linhas de Torres 179, 1750 Lisboa, Portugal
| | - Ruben Leitão
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Área
Departamental de Engenharia Química, Instituto Superior de
Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro
Emídio Navarro, 1, 1959-007 Lisboa, Portugal
| | - Clara Ràfols
- Departament
de Química Analítica and Institut de Biomedicina (IBUB), Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Elisabeth Bosch
- Departament
de Química Analítica and Institut de Biomedicina (IBUB), Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Filomena Martins
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Miguel Machuqueiro
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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