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Rashid MH, Yellarthi SPK, Yellarthi PK, Didugu BGL, Mamillapalli A. Combined assessment of lysine and N-acetyl cadaverine levels assist as a potential biomarker of the smoker periodontitis. Amino Acids 2024; 56:41. [PMID: 38851640 PMCID: PMC11162398 DOI: 10.1007/s00726-024-03396-4] [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] [Received: 01/25/2024] [Accepted: 04/16/2024] [Indexed: 06/10/2024]
Abstract
Periodontitis is an inflammatory condition of supporting structures of teeth leading to attachment and bone loss. Cigarette smoking is the single most important and modifiable risk factor with 5 to 20-fold susceptibility for periodontal diseases. Reverse smoking is a peculiar habit of smoking where the lit end is kept inside the mouth, which is predominant in the northern coastal districts of Andhra Pradesh. Polyamines are biologically active amines involved in tissue regeneration and modulation of inflammation. The study aimed to evaluate polyamines and check their utility as a marker in detection of periodontitis among different groups. Total polyamine levels showed significant increase in reverse smokers with periodontitis when compared to the other groups. Qualitative analysis by thin layer chromatography showed three polyamine bands with varying intensity among the different groups. Mass spectrometric and NMR analyses of the three bands identified them as N1, N8-diacetyl spermidine, N-acetyl cadaverine and lysine. Most significantly elevated levels of lysine was observed in the smoker and reverse smoker periodontitis groups when compared to healthy and non-smoker periodontitis groups. The significantly elevated levels of N-acetyl cadaverine could be responsible for the more destruction of periodontium in the reverse smoker group. Antioxidant potential decreased significantly in different smoker periodontitis groups. The present study suggests that the quantitative analysis of salivary polyamines, lysine and N-acetyl cadaverine can aid as an easy noninvasive diagnostic method for assessing the periodontal status, especially in smokers.
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Affiliation(s)
- Md Haroon Rashid
- Department of Biotechnology, School of Science, GITAM (Deemed to be University), Visakhapatnam, Andhra Pradesh, 530 045, India
| | - Sandhya Pavan Kumar Yellarthi
- Department of Periodontics and Oral Implantology, GITAM Dental College and Hospital, Visakhapatnam, Andhra Pradesh, 530 045, India
| | - Pavan Kumar Yellarthi
- Department of Oral Medicine and Radiology, GITAM Dental College and Hospital, Visakhapatnam, Andhra Pradesh, 530 045, India
| | - Brinda Goda Lakshmi Didugu
- Department of Biotechnology, School of Science, GITAM (Deemed to be University), Visakhapatnam, Andhra Pradesh, 530 045, India
| | - Anitha Mamillapalli
- Department of Biotechnology, School of Science, GITAM (Deemed to be University), Visakhapatnam, Andhra Pradesh, 530 045, India.
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2
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Quaye JA, Wood KE, Snelgrove C, Ouedraogo D, Gadda G. An active site mutation induces oxygen reactivity in D-arginine dehydrogenase: A case of superoxide diverting protons. J Biol Chem 2024; 300:107381. [PMID: 38762175 PMCID: PMC11193025 DOI: 10.1016/j.jbc.2024.107381] [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] [Received: 04/12/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024] Open
Abstract
Enzymes are potent catalysts that increase biochemical reaction rates by several orders of magnitude. Flavoproteins are a class of enzymes whose classification relies on their ability to react with molecular oxygen (O2) during catalysis using ionizable active site residues. Pseudomonas aeruginosa D-arginine dehydrogenase (PaDADH) is a flavoprotein that oxidizes D-arginine for P. aeruginosa survival and biofilm formation. The crystal structure of PaDADH reveals the interaction of the glutamate 246 (E246) side chain with the substrate and at least three other active site residues, establishing a hydrogen bond network in the active site. Additionally, E246 likely ionizes to facilitate substrate binding during PaDADH catalysis. This study aimed to investigate how replacing the E246 residue with leucine affects PaDADH catalysis and its ability to react with O2 using steady-state kinetics coupled with pH profile studies. The data reveal a gain of O2 reactivity in the E246L variant, resulting in a reduced flavin semiquinone species and superoxide (O2•-) during substrate oxidation. The O2•- reacts with active site protons, resulting in an observed nonstoichiometric slope of 1.5 in the enzyme's log (kcat/Km) pH profile with D-arginine. Adding superoxide dismutase results in an observed correction of the slope to 1.0. This study demonstrates how O2•- can alter the slopes of limbs in the pH profiles of flavin-dependent enzymes and serves as a model for correcting nonstoichiometric slopes in elucidating reaction mechanisms of flavoproteins.
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Affiliation(s)
- Joanna A Quaye
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Kendall E Wood
- Biology Department, Morehouse College, Atlanta, Georgia, USA
| | - Claire Snelgrove
- The Gwinnett School of Mathematics, Science, and Technology, Lawrenceville, Georgia, USA
| | - Daniel Ouedraogo
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA; Department of Biology, Georgia State University, Atlanta, Georgia, USA; Department of the Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA.
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3
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Fang D, Zhang Z, Zhai J, Guo B, Li P, Liu X, Song J, Xie S, Wu R, Zhao Y, Wang C. Enzymatic-related network of catalysis, polyamine, and tumors for acetylpolyamine oxidase: from calculation to experiment. Chem Sci 2024; 15:2867-2882. [PMID: 38404376 PMCID: PMC10882482 DOI: 10.1039/d3sc06037c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 12/22/2023] [Indexed: 02/27/2024] Open
Abstract
The regulation of enzymes and development of polyamine analogs capable of controlling the dynamics of endogenous polyamines to achieve anti-tumor effects is one of the biggest challenges in polyamine research. However, the root of the problem remains unsolved. This study represents a significant milestone as it unveils, for the first time, the comprehensive catalytic map of acetylpolyamine oxidase that includes chemical transformation and product release kinetics, by utilizing multiscale simulations with over six million dynamical snapshots. The transportation of acetylspermine is strongly exothermic, and high binding affinity of enzyme and reactant is observed. The transfer of hydride from polyamine to FAD is the rate-limiting step, via an H-shift coupled electron transfer mechanism. The two products are released in a detour stepwise mechanism, which also impacts the enzymatic efficiency. Inspired by these mechanistic insights into enzymatic catalysis, we propose a novel strategy that regulates the polyamine level and catalytic progress through the action of His64. Directly suppressing APAO by mutating His64 further inhibited growth and migration of tumor cells and tumor tissue in vitro and in vivo. Therefore, the network connecting microcosmic and macroscopic scales opens up new avenues for designing polyamine compounds and conducting anti-tumor research in the future.
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Affiliation(s)
- Dong Fang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University Kaifeng 475000 P. R. China
- School of Pharmacy, Henan University Kaifeng 475000 P. R. China
| | - Zhiyang Zhang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University Kaifeng 475000 P. R. China
| | - Jihang Zhai
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University Kaifeng 475000 P. R. China
| | - Baolin Guo
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University Kaifeng 475000 P. R. China
| | - Pengfei Li
- Department of Chemistry and Biochemistry, Loyola University Chicago Chicago Illinois 60660 USA
| | - Xiaoyuan Liu
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University Kaifeng 475000 P. R. China
| | - Jinshuai Song
- Green Catalysis Center, College of Chemistry, Zhengzhou University Zhengzhou 450001 P. R. China
| | - Songqiang Xie
- School of Pharmacy, Henan University Kaifeng 475000 P. R. China
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University Guangzhou 510006 P. R. China
| | - Yuan Zhao
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University Kaifeng 475000 P. R. China
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University Kaifeng 475000 P. R. China
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4
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Xuan M, Gu X, Li J, Huang D, Xue C, He Y. Polyamines: their significance for maintaining health and contributing to diseases. Cell Commun Signal 2023; 21:348. [PMID: 38049863 PMCID: PMC10694995 DOI: 10.1186/s12964-023-01373-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 10/29/2023] [Indexed: 12/06/2023] Open
Abstract
Polyamines are essential for the growth and proliferation of mammalian cells and are intimately involved in biological mechanisms such as DNA replication, RNA transcription, protein synthesis, and post-translational modification. These mechanisms regulate cellular proliferation, differentiation, programmed cell death, and the formation of tumors. Several studies have confirmed the positive effect of polyamines on the maintenance of health, while others have demonstrated that their activity may promote the occurrence and progression of diseases. This review examines a variety of topics, such as polyamine source and metabolism, including metabolism, transport, and the potential impact of polyamines on health and disease. In addition, a brief summary of the effects of oncogenes and signaling pathways on tumor polyamine metabolism is provided. Video Abstract.
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Affiliation(s)
- Mengjuan Xuan
- Department of Infectious Disease, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Xinyu Gu
- Department of Oncology, College of Clinical Medicine, The First Affiliated Hospital, Henan University of Science and Technology, Luoyang, 471000, Henan, China
| | - Juan Li
- Department of Infectious Disease, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Di Huang
- Department of Child Health Care, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Chen Xue
- Department of Infectious Disease, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China.
| | - Yuting He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
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5
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Lima A, Didugu BGL, Chunduri AR, Rajan R, Jha A, Mamillapalli A. Thermal tolerance role of novel polyamine, caldopentamine, identified in fifth instar Bombyx mori. Amino Acids 2023; 55:287-298. [PMID: 36562834 DOI: 10.1007/s00726-022-03226-5] [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] [Received: 06/23/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
Silkworms have limited ability to regulate their body temperature; therefore, environmental changes, such as global warming, can adversely affect their viability. Polyamines have shown protection to various organisms against heat stress. This study evaluated the qualitative and quantitative changes in heat-stressed Bombyx mori larvae polyamines. Fifth instar Bombyx mori larvae were divided into two groups; control group, reared at room temperature, i.e., 28 ± 2 °C, and the heat shock group, exposed to 40 °C. Dansylation of the whole worm polyamines and subsequent thin-layer chromatography revealed the presence of components with the same Rf value as dansyl-putrescine, spermidine, and spermine. The dansyl-putrescine, spermidine, and spermine polyamines were identified by mass spectrometric analyses. After heat shock, the thin-layer chromatography of the whole-larvae tissue extracts showed qualitative and quantitative changes in dansylated polyamines. A new polyamine, caldopentamine, was identified, which showed elevated levels in heat-stressed larvae. This polyamine could play a role in helping the larvae tolerate various stress, including thermal stress. No significant changes in silk fiber's economic and mechanical properties were observed in our study. This study indicated that PA, caldopentamine, supplementation could improve heat-stress tolerance in Bombyx mori.
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Affiliation(s)
- Anugata Lima
- Department of Biotechnology, School of Science, GITAM (Deemed to Be University), Visakhapatnam, Andhra Pradesh, 530045, India
| | - Brinda Goda Lakshmi Didugu
- Department of Biotechnology, School of Science, GITAM (Deemed to Be University), Visakhapatnam, Andhra Pradesh, 530045, India
| | - Alekhya Rani Chunduri
- Department of Biotechnology, School of Science, GITAM (Deemed to Be University), Visakhapatnam, Andhra Pradesh, 530045, India
| | - Resma Rajan
- Department of Biotechnology, School of Science, GITAM (Deemed to Be University), Visakhapatnam, Andhra Pradesh, 530045, India
| | - Anjali Jha
- Department of Chemistry, School of Science, GITAM (Deemed to Be University), Visakhapatnam, Andhra Pradesh, 530045, India
| | - Anitha Mamillapalli
- Department of Biotechnology, School of Science, GITAM (Deemed to Be University), Visakhapatnam, Andhra Pradesh, 530045, India.
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6
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Chen Y, León-Letelier RA, Abdel Sater AH, Vykoukal J, Dennison JB, Hanash S, Fahrmann JF. c-MYC-Driven Polyamine Metabolism in Ovarian Cancer: From Pathogenesis to Early Detection and Therapy. Cancers (Basel) 2023; 15:623. [PMID: 36765581 PMCID: PMC9913358 DOI: 10.3390/cancers15030623] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/14/2023] [Indexed: 01/20/2023] Open
Abstract
c-MYC and its paralogues MYCN and MYCL are among the most frequently amplified and/or overexpressed oncoproteins in ovarian cancer. c-MYC plays a key role in promoting ovarian cancer initiation and progression. The polyamine pathway is a bona fide target of c-MYC signaling, and polyamine metabolism is strongly intertwined with ovarian malignancy. Targeting of the polyamine pathway via small molecule inhibitors has garnered considerable attention as a therapeutic strategy for ovarian cancer. Herein, we discuss the involvement of c-MYC signaling and that of its paralogues in promoting ovarian cancer tumorigenesis. We highlight the potential of targeting c-MYC-driven polyamine metabolism for the treatment of ovarian cancers and the utility of polyamine signatures in biofluids for early detection applications.
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Affiliation(s)
| | | | | | | | | | | | - Johannes F. Fahrmann
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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7
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Che S, Liang Y, Chen Y, Wu W, Liu R, Zhang Q, Bartlam M. Structure of Pseudomonas aeruginosa spermidine dehydrogenase: a polyamine oxidase with a novel heme-binding fold. FEBS J 2022; 289:1911-1928. [PMID: 34741591 DOI: 10.1111/febs.16264] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 10/31/2021] [Accepted: 11/04/2021] [Indexed: 11/29/2022]
Abstract
The opportunistic pathogen Pseudomonas aeruginosa can utilize polyamines (including putrescine, cadaverine, 4-aminobutyrate, spermidine, and spermine) as its sole source of carbon and nitrogen. Spermidine dehydrogenase (SpdH) is a component of one of the two polyamine utilization pathways identified in P. aeruginosa, but little is known about its structure and function. Here, we report the first crystal structure of SpdH from P. aeruginosa to 1.85 Å resolution. The resulting core structure confirms that SpdH belongs to the polyamine oxidase (PAO) family with flavin-binding and substrate-binding domains. A unique N-terminal extension wraps around the flavin-binding domain of SpdH and is required for heme binding, placing a heme cofactor in close proximity to the FAD cofactor. Structural and mutational analysis reveals that residues in the putative active site at the re side of the FAD isoalloxazine ring form part of the catalytic machinery. PaSpdH features an unusual active site and lacks the conserved lysine that forms part of a lysine-water-flavin N5 atom interaction in other PAO enzymes characterized to date. Mutational analysis further confirms that heme is required for catalytic activity. This work provides an important starting point for understanding the role of SpdH, which occurs universally in P. aeruginosa strains, in polyamine metabolism.
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Affiliation(s)
- Shiyou Che
- State Key Laboratory of Medicinal Chemical Biology, Nankai International Advanced Research Institute (Shenzhen Futian), College of Life Sciences, Nankai University, Tianjin, China
| | - Yakun Liang
- State Key Laboratory of Medicinal Chemical Biology, Nankai International Advanced Research Institute (Shenzhen Futian), College of Life Sciences, Nankai University, Tianjin, China
| | - Yujing Chen
- State Key Laboratory of Medicinal Chemical Biology, Nankai International Advanced Research Institute (Shenzhen Futian), College of Life Sciences, Nankai University, Tianjin, China
| | - Wenyue Wu
- State Key Laboratory of Medicinal Chemical Biology, Nankai International Advanced Research Institute (Shenzhen Futian), College of Life Sciences, Nankai University, Tianjin, China
| | - Ruihua Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai International Advanced Research Institute (Shenzhen Futian), College of Life Sciences, Nankai University, Tianjin, China
| | - Qionglin Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai International Advanced Research Institute (Shenzhen Futian), College of Life Sciences, Nankai University, Tianjin, China
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, Nankai International Advanced Research Institute (Shenzhen Futian), College of Life Sciences, Nankai University, Tianjin, China
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8
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Di Paolo ML, Cervelli M, Mariottini P, Leonetti A, Polticelli F, Rosini M, Milelli A, Basagni F, Venerando R, Agostinelli E, Minarini A. Exploring the activity of polyamine analogues on polyamine and spermine oxidase: methoctramine, a potent and selective inhibitor of polyamine oxidase. J Enzyme Inhib Med Chem 2019; 34:740-752. [PMID: 30829081 PMCID: PMC6407594 DOI: 10.1080/14756366.2019.1584620] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/06/2019] [Accepted: 02/14/2019] [Indexed: 01/16/2023] Open
Abstract
Fourteen polyamine analogues, asymmetric or symmetric substituted spermine (1-9) or methoctramine (10-14) analogues, were evaluated as potential inhibitors or substrates of two enzymes of the polyamine catabolic pathway, spermine oxidase (SMOX) and acetylpolyamine oxidase (PAOX). Compound 2 turned out to be the best substrate for PAOX, having the highest affinity and catalytic efficiency with respect to its physiological substrates. Methoctramine (10), a well-known muscarinic M2 receptor antagonist, emerged as the most potent competitive PAOX inhibitor known so far (Ki = 10 nM), endowed with very good selectivity compared with SMOX (Ki=1.2 μM vs SMOX). The efficacy of methoctramine in inhibiting PAOX activity was confirmed in the HT22 cell line. Methoctramine is a very promising tool in the design of drugs targeting the polyamine catabolism pathway, both to understand the physio-pathological role of PAOX vs SMOX and for pharmacological applications, being the polyamine pathway involved in various pathologies.
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Affiliation(s)
| | | | | | | | - Fabio Polticelli
- Department of Sciences, University of Roma Tre, Roma, Italy
- Roma Tre Section, National Institute of Nuclear Physics, Roma, Italy
| | - Michela Rosini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Andrea Milelli
- Department for Life Quality Studies, Alma Mater Studiorum-University of Bologna, Rimini, Italy
| | - Filippo Basagni
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Rina Venerando
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Enzo Agostinelli
- Department of Biochemical Science "A. Rossi Fanelli", University of Rome "La Sapienza", Rome, Italy
- International Polyamines Foundation – ONLUS –Via del Forte Tiburtino 98, Rome, Italy
| | - Anna Minarini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, Italy
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9
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On the use of noncompetitive kinetic isotope effects to investigate flavoenzyme mechanism. Methods Enzymol 2019; 620:115-143. [PMID: 31072484 DOI: 10.1016/bs.mie.2019.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
This account describes the application of kinetic isotope effects (KIEs) to investigate the mechanistic properties of flavin dependent enzymes. Assays can be conducted during steady-state catalytic turnover of the flavoenzyme with its substrate or by using rapid-kinetic techniques to measure either the reductive or oxidative half-reactions of the enzyme. Great care should be taken to ensure that the observed effects are due to isotopic substitution and not other factors such as pH effects or changes in the solvent viscosity of the reaction mixture. Different types of KIEs are described along with a physical description of their origins and the unique information each can provide about the mechanism of an enzyme. Detailed experimental techniques are outlined with special emphasis on the proper controls and data analysis that must be carried out to avoid erroneous conclusions. Examples are provided for each type of KIE measurement from references in the literature. It is our hope that this article will clarify any confusion concerning the utility of KIEs in the study of flavoprotein mechanism and encourage their use by the community.
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10
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Keinänen TA, Grigorenko N, Khomutov AR, Huang Q, Uimari A, Alhonen L, Hyvönen MT, Vepsäläinen J. Controlling the regioselectivity and stereospecificity of FAD-dependent polyamine oxidases with the use of amine-attached guide molecules as conformational modulators. Biosci Rep 2018; 38:BSR20180527. [PMID: 30006473 PMCID: PMC6131205 DOI: 10.1042/bsr20180527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 07/03/2018] [Accepted: 07/05/2018] [Indexed: 01/03/2023] Open
Abstract
Enzymes generally display strict stereospecificity and regioselectivity for their substrates. Here by using FAD-dependent human acetylpolyamine oxidase (APAO), human spermine (Spm) oxidase (SMOX) and yeast polyamine oxidase (Fms1), we demonstrate that these fundamental properties of the enzymes may be regulated using simple guide molecules, being either covalently attached to polyamines or used as a supplement to the substrate mixtures. APAO, which naturally metabolizes achiral N1-acetylated polyamines, displays aldehyde-controllable stereospecificity with chiral 1-methylated polyamines, like (R)- and (S)-1-methylspermidine (1,8-diamino-5-azanonane) (1-MeSpd). Among the novel N1-acyl derivatives of MeSpd, isonicotinic acid (P4) or benzoic acid (Bz) with (R)-MeSpd had Km of 3.6 ± 0.6/1.2 ± 0.7 µM and kcat of 5.2 ± 0.6/4.6 ± 0.7 s-1 respectively, while N1 -AcSpd had Km 8.2 ± 0.4 µM and kcat 2.7 ± 0.0 s-1 On the contrary, corresponding (S)-MeSpd amides were practically inactive (kcat < 0.03 s-1) but they retained micromole level Km for APAO. SMOX did not metabolize any of the tested compounds (kcat < 0.05 s-1) that acted as non-competitive inhibitors having Ki ≥ 155 µM for SMOX. In addition, we tested (R,R)-1,12-bis-methylspermine (2,13-diamino-5,10-diazatetradecane) (R,R)-(Me2Spm) and (S,S)-Me2Spm as substrates for Fms1. Fms1 preferred (S,S)- to (R,R)-diastereoisomer, but with notably lower kcat in comparison with spermine. Interestingly, Fms1 was prone to aldehyde supplementation in its regioselectivity, i.e. the cleavage site of spermidine. Thus, aldehyde supplementation to generate aldimines or N-terminal substituents in polyamines, i.e. attachment of guide molecule, generates novel ligands with altered charge distribution changing the binding and catalytic properties with polyamine oxidases. This provides means for exploiting hidden capabilities of polyamine oxidases for controlling their regioselectivity and stereospecificity.
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Affiliation(s)
- Tuomo A Keinänen
- School of Pharmacy, Biocenter Kuopio, University of Eastern Finland, Kuopio Campus, P.O. Box 1627, Kuopio FI-70211, Finland
| | - Nikolay Grigorenko
- BASF Schweiz AG, Dispersions and Pigments Division, Klybeckstrasse 141, P.O. Box CH 4002, Basel, Switzerland
| | - Alex R Khomutov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov St 32, Moscow 119991, Russia
| | - Qingqiu Huang
- MacCHESS at the Cornell High Energy Synchrotron Source, Cornell University Ithaca, NY 14853-8001, U.S.A
| | - Anne Uimari
- Natural Resources Institute Finland, Natural Resources Division, Neulaniementie 5, Kuopio FI-70210, Finland
| | - Leena Alhonen
- School of Pharmacy, Biocenter Kuopio, University of Eastern Finland, Kuopio Campus, P.O. Box 1627, Kuopio FI-70211, Finland
| | - Mervi T Hyvönen
- School of Pharmacy, Biocenter Kuopio, University of Eastern Finland, Kuopio Campus, P.O. Box 1627, Kuopio FI-70211, Finland
| | - Jouko Vepsäläinen
- School of Pharmacy, Biocenter Kuopio, University of Eastern Finland, Kuopio Campus, P.O. Box 1627, Kuopio FI-70211, Finland
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11
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Fitzpatrick PF, Chadegani F, Zhang S, Dougherty V. Mechanism of Flavoprotein l-6-Hydroxynicotine Oxidase: pH and Solvent Isotope Effects and Identification of Key Active Site Residues. Biochemistry 2017; 56:869-875. [PMID: 28080034 PMCID: PMC5312672 DOI: 10.1021/acs.biochem.6b01160] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The flavoenzyme l-6-hydroxynicotine oxidase is a member of the monoamine oxidase family that catalyzes the oxidation of (S)-6-hydroxynicotine to 6-hydroxypseudooxynicotine during microbial catabolism of nicotine. While the enzyme has long been understood to catalyze oxidation of the carbon-carbon bond, it has recently been shown to catalyze oxidation of a carbon-nitrogen bond [Fitzpatrick, P. F., et al. (2016) Biochemistry 55, 697-703]. The effects of pH and mutagenesis of active site residues have now been utilized to study the mechanism and roles of active site residues. Asn166 and Tyr311 bind the substrate, while Lys287 forms a water-mediated hydrogen bond with flavin N5. The N166A and Y311F mutations result in ∼30- and ∼4-fold decreases in kcat/Km and kred for (S)-6-hydroxynicotine, respectively, with larger effects on the kcat/Km value for (S)-6-hydroxynornicotine. The K287M mutation results in ∼10-fold decreases in these parameters and a 6000-fold decrease in the kcat/Km value for oxygen. The shapes of the pH profiles are not altered by the N166A and Y311F mutations. There is no solvent isotope effect on the kcat/Km value for amines. The results are consistent with a model in which both the charged and neutral forms of the amine can bind, with the former rapidly losing a proton to a hydrogen bond network of water and amino acids in the active site prior to the transfer of hydride to the flavin.
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Affiliation(s)
- Paul F. Fitzpatrick
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229
| | - Fatemeh Chadegani
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229
| | - Shengnan Zhang
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229
| | - Vi Dougherty
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229
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12
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Sjögren T, Wassvik CM, Snijder A, Aagaard A, Kumanomidou T, Barlind L, Kaminski TP, Kashima A, Yokota T, Fjellström O. The Structure of Murine N 1-Acetylspermine Oxidase Reveals Molecular Details of Vertebrate Polyamine Catabolism. Biochemistry 2017; 56:458-467. [PMID: 28029774 DOI: 10.1021/acs.biochem.6b01140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
N1-Acetylspermine oxidase (APAO) catalyzes the conversion of N1-acetylspermine or N1-acetylspermidine to spermidine or putrescine, respectively, with concomitant formation of N-acetyl-3-aminopropanal and hydrogen peroxide. Here we present the structure of murine APAO in its oxidized holo form and in complex with substrate. The structures provide a basis for understanding molecular details of substrate interaction in vertebrate APAO, highlighting a key role for an asparagine residue in coordinating the N1-acetyl group of the substrate. We applied computational methods to the crystal structures to rationalize previous observations with regard to the substrate charge state. The analysis suggests that APAO features an active site ideally suited for binding of charged polyamines. We also reveal the structure of APAO in complex with the irreversible inhibitor MDL72527. In addition to the covalent adduct, a second MDL72527 molecule is bound in the active site. Binding of MDL72527 is accompanied by altered conformations in the APAO backbone. On the basis of structures of APAO, we discuss the potential for development of specific inhibitors.
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Affiliation(s)
- Tove Sjögren
- Discovery Sciences, Innovative Medicines and Early Development, AstraZeneca , Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - Carola M Wassvik
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development, AstraZeneca , Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - Arjan Snijder
- Discovery Sciences, Innovative Medicines and Early Development, AstraZeneca , Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - Anna Aagaard
- Discovery Sciences, Innovative Medicines and Early Development, AstraZeneca , Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - Taichi Kumanomidou
- Discovery Technology Laboratories, Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation , 1000, Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Louise Barlind
- Discovery Sciences, Innovative Medicines and Early Development, AstraZeneca , Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - Tim P Kaminski
- Discovery Sciences, Innovative Medicines and Early Development, AstraZeneca , Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - Akiko Kashima
- Discovery Technology Laboratories, Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation , 1000, Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Takehiro Yokota
- Discovery Technology Laboratories, Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation , 1000, Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Ola Fjellström
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development, AstraZeneca , Pepparedsleden 1, SE-431 83 Mölndal, Sweden
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13
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Tormos JR, Suarez MB, Fitzpatrick PF. 13C kinetic isotope effects on the reaction of a flavin amine oxidase determined from whole molecule isotope effects. Arch Biochem Biophys 2016; 612:115-119. [PMID: 27815088 PMCID: PMC5257176 DOI: 10.1016/j.abb.2016.10.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 12/14/2022]
Abstract
A large number of flavoproteins catalyze the oxidation of amines. Because of the importance of these enzymes in metabolism, their mechanisms have previously been studied using deuterium, nitrogen, and solvent isotope effects. While these results have been valuable for computational studies to distinguish among proposed mechanisms, a measure of the change at the reacting carbon has been lacking. We describe here the measurement of a 13C kinetic isotope effect for a representative amine oxidase, polyamine oxidase. The isotope effect was determined by analysis of the isotopic composition of the unlabeled substrate, N, N'-dibenzyl-1,4-diaminopropane, to obtain a pH-independent value of 1.025. The availability of a 13C isotope effect for flavoprotein-catalyzed amine oxidation provides the first measure of the change in bond order at the carbon involved in this carbon-hydrogen bond cleavage and will be of value to understanding the transition state structure for this class of enzymes.
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Affiliation(s)
- José R Tormos
- Department of Chemistry and Biochemistry, St. Mary's University, San Antonio, TX 78228, United States
| | - Marina B Suarez
- Department of Geological Sciences, University of Texas-San Antonio, San Antonio, TX 78249, United States
| | - Paul F Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, United States.
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14
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Burg JM, Link JE, Morgan BS, Heller FJ, Hargrove AE, McCafferty DG. KDM1 class flavin-dependent protein lysine demethylases. Biopolymers 2015; 104:213-46. [PMID: 25787087 PMCID: PMC4747437 DOI: 10.1002/bip.22643] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/02/2015] [Accepted: 03/07/2015] [Indexed: 12/11/2022]
Abstract
Flavin-dependent, lysine-specific protein demethylases (KDM1s) are a subfamily of amine oxidases that catalyze the selective posttranslational oxidative demethylation of methyllysine side chains within protein and peptide substrates. KDM1s participate in the widespread epigenetic regulation of both normal and disease state transcriptional programs. Their activities are central to various cellular functions, such as hematopoietic and neuronal differentiation, cancer proliferation and metastasis, and viral lytic replication and establishment of latency. Interestingly, KDM1s function as catalytic subunits within complexes with coregulatory molecules that modulate enzymatic activity of the demethylases and coordinate their access to specific substrates at distinct sites within the cell and chromatin. Although several classes of KDM1-selective small molecule inhibitors have been recently developed, these pan-active site inhibition strategies lack the ability to selectively discriminate between KDM1 activity in specific, and occasionally opposing, functional contexts within these complexes. Here we review the discovery of this class of demethylases, their structures, chemical mechanisms, and specificity. Additionally, we review inhibition of this class of enzymes as well as emerging interactions with coregulatory molecules that regulate demethylase activity in highly specific functional contexts of biological and potential therapeutic importance.
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15
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Bonaiuto E, Grancara S, Martinis P, Stringaro A, Colone M, Agostinelli E, Macone A, Stevanato R, Vianello F, Toninello A, Di Paolo ML. A novel enzyme with spermine oxidase properties in bovine liver mitochondria: identification and kinetic characterization. Free Radic Biol Med 2015; 81:88-99. [PMID: 25591967 DOI: 10.1016/j.freeradbiomed.2015.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 12/19/2014] [Accepted: 01/04/2015] [Indexed: 01/31/2023]
Abstract
The uptake of spermine into mammalian mitochondria indicated the need to identify its catabolic pathway in these organelles. Bovine liver mitochondria were therefore purified and their capacity for natural polyamine uptake was verified. A kinetic approach was then used to determine the presence of an MDL 72527-sensitive enzyme with spermine oxidase activity in the matrix of bovine liver mitochondria. Western blot analysis of mitochondrial fractions and immunogold electron microscopy observations of purified mitochondria unequivocally confirmed the presence of a protein recognized by anti-spermine oxidase antibodies in the mitochondrial matrix. Preliminary kinetic characterization showed that spermine is the preferred substrate of this enzyme; lower activity was detected with spermidine and acetylated polyamines. Catalytic efficiency comparable to that of spermine was also found for 1-aminododecane. The considerable effect of ionic strength on the Vmax/KM ratio suggested the presence of more than one negatively charged zone inside the active site cavity of this mitochondrial enzyme, which is probably involved in the docking of positively charged substrates. These findings indicate that the bovine liver mitochondrial matrix contains an enzyme belonging to the spermine oxidase class. Because H2O2 is generated by spermine oxidase activity, the possible involvement of the latter as an important signaling transducer under both physiological and pathological conditions should be considered.
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Affiliation(s)
- Emanuela Bonaiuto
- Department of Molecular Medicine, University of Padova, Via G. Colombo 3, 35131 Padova, Italy
| | - Silvia Grancara
- Department of Biomedical Sciences, University of Padova, Via G. Colombo 3, 35131 Padova, Italy
| | - Pamela Martinis
- Department of Biomedical Sciences, University of Padova, Via G. Colombo 3, 35131 Padova, Italy
| | - Annarita Stringaro
- Department of Technology and Health, Italian Institute of Health, 00161 Roma, Italy
| | - Marisa Colone
- Department of Technology and Health, Italian Institute of Health, 00161 Roma, Italy
| | - Enzo Agostinelli
- Istituto Pasteur-Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli," Sapienza University of Rome and Institute of Biology and Molecular Pathology, Italian Research Council, P.le Aldo Moro 5, 00185 Roma, Italy
| | - Alberto Macone
- Istituto Pasteur-Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli," Sapienza University of Rome and Institute of Biology and Molecular Pathology, Italian Research Council, P.le Aldo Moro 5, 00185 Roma, Italy
| | - Roberto Stevanato
- Department of Molecular Science and Nanosystems, Università Ca' Foscari, Dorsoduro 2137, 30123 Venezia, Italy
| | - Fabio Vianello
- Department of Comparative Biomedicine and Food Science, Polo Agripolis, Viale dell'Università 16, University of Padova, 35020 Legnaro, Italy; Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University in Olomouc, 17 Listopadu 1192/12, 771 46 Olomouc, Czech Republic
| | - Antonio Toninello
- Department of Biomedical Sciences, University of Padova, Via G. Colombo 3, 35131 Padova, Italy.
| | - Maria Luisa Di Paolo
- Department of Molecular Medicine, University of Padova, Via G. Colombo 3, 35131 Padova, Italy; Consorzio Interuniversitario "Istituto Nazionale Biostrutture e Biosistemi," Viale delle medaglie d'Oro 305, 00136 Roma, Italy.
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16
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O’Sullivan MC, Durham TB, Valdes HE, Dauer KL, Karney NJ, Forrestel AC, Bacchi CJ, Baker JF. Dibenzosuberyl substituted polyamines and analogs of clomipramine as effective inhibitors of trypanothione reductase; molecular docking, and assessment of trypanocidal activities. Bioorg Med Chem 2015; 23:996-1010. [DOI: 10.1016/j.bmc.2015.01.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 01/04/2015] [Accepted: 01/09/2015] [Indexed: 12/15/2022]
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17
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Roberts KM, Tormos JR, Fitzpatrick PF. Characterization of unstable products of flavin- and pterin-dependent enzymes by continuous-flow mass spectrometry. Biochemistry 2014; 53:2672-9. [PMID: 24713088 PMCID: PMC4010283 DOI: 10.1021/bi500267c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
![]()
Continuous-flow mass spectrometry
(CFMS) was used to monitor the
products formed during the initial 0.25–20 s of the reactions
catalyzed by the flavoprotein N-acetylpolyamine oxidase
(PAO) and the pterin-dependent enzymes phenylalanine hydroxylase (PheH)
and tyrosine hydroxylase (TyrH). N,N′-Dibenzyl-1,4-diaminobutane (DBDB) is a substrate for PAO
for which amine oxidation is rate-limiting. CFMS of the reaction showed
formation of an initial imine due to oxidation of an exo-carbon–nitrogen bond. Nonenzymatic hydrolysis of the imine
formed benzaldehyde and N-benzyl-1,4-diaminobutane;
the subsequent oxidation by PAO of the latter to an additional imine
could also be followed. Measurement of the deuterium kinetic isotope
effect on DBDB oxidation by CFMS yielded a value of 7.6 ± 0.3,
in good agreement with a value of 6.7 ± 0.6 from steady-state
kinetic analyses. In the PheH reaction, the transient formation of
the 4a-hydroxypterin product was readily detected; tandem mass spectrometry
confirmed attachment of the oxygen to C(4a). With wild-type TyrH,
the 4a-hydroxypterin was also the product. In contrast, no product
other than a dihydropterin could be detected in the reaction of the
mutant protein E332A TyrH.
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Affiliation(s)
- Kenneth M Roberts
- Department of Biochemistry, University of Texas Health Science Center , San Antonio, Texas 78229, United States
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18
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Abstract
Polyamines are ubiquitous and essential components of mammalian cells. They have multiple functions including critical roles in nucleic acid and protein synthesis, gene expression, protein function, protection from oxidative damage, the regulation of ion channels, and maintenance of the structure of cellular macromolecules. It is essential to maintain a correct level of polyamines, and this amount is tightly regulated at the levels of transport, synthesis, and degradation. Catabolic pathways generate reactive aldehydes including acrolein and hydrogen peroxide via a number of oxidases. These metabolites, particularly those from spermine, can cause significant toxicity with damage to proteins, DNA, and other cellular components. Their production can be increased as a result of infection or cell damage that releases free polyamines and activates the oxidative catabolic pathways. Since polyamines also have an important physiological role in protection from oxidative damage, the reduction in polyamine content may exacerbate the toxic potential of these agents. Increases in polyamine catabolism have been implicated in the development of diseases including stroke, other neurological diseases, renal failure, liver disease, and cancer. These results provide new opportunities for the early diagnosis, prevention, and treatment of disease.
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Affiliation(s)
- Anthony E Pegg
- Department of Cellular and Molecular Physiology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine , Hershey, Pennsylvania 17033, United States
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19
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Karasulu B, Patil M, Thiel W. Amine oxidation mediated by lysine-specific demethylase 1: quantum mechanics/molecular mechanics insights into mechanism and role of lysine 661. J Am Chem Soc 2013; 135:13400-13. [PMID: 23988016 DOI: 10.1021/ja403582u] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report classical molecular dynamics (MD) simulations and combined quantum mechanics/molecular mechanics (QM/MM) calculations to elucidate the catalytic mechanism of the rate-determining amine oxidation step in the lysine-specific demethylase 1 (LSD1)-catalyzed demethylation of the histone tail lysine (H3K4), with flavin adenine dinucleotide (FAD) acting as cofactor. The oxidation of substrate lysine (sLys) involves the cleavage of an α-CH bond accompanied by the transfer of a hydride ion equivalent to FAD, leading to an imine intermediate. This hydride transfer pathway is shown to be clearly favored for sLys oxidation over other proposed mechanisms, including the radical (or single-electron transfer) route as well as carbanion and polar-nucleophilic mechanisms. MD simulations on six NVT ensembles (covering different protonation states of sLys and K661 as well as the K661M mutant) identify two possible orientations of the reacting sLys and FAD subunits (called "downward" and "upward"). Calculations at the QM(B3LYP-D/6-31G*)/CHARMM22 level provide molecular-level insights into the mechanism, helping to understand how LSD1 achieves the activation of the rather inert methyl-CH bond in a metal-free environment. Factors such as proper alignment of sLys (downward orientation), transition-state stabilization (due to the protein environment and favorable orbital interactions), and product stabilization via adduct formation are found to be crucial for facilitating the oxidative α-CH bond cleavage. The current study also sheds light on the role of important active-site residues (Y761, K661, and W695) and of the conserved water-bridge motif. The steric influence of Y761 helps to position the reaction partners properly, K661 is predicted to get deprotonated prior to substrate binding and to act as an active-site base that accepts a proton from sLys to enable the subsequent amine oxidation, and the water bridge that is stabilized by K661 and W695 mediates this proton transfer.
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Affiliation(s)
- Bora Karasulu
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim, Germany
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20
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Gaweska HM, Taylor AB, Hart PJ, Fitzpatrick PF. Structure of the flavoprotein tryptophan 2-monooxygenase, a key enzyme in the formation of galls in plants. Biochemistry 2013; 52:2620-6. [PMID: 23521653 DOI: 10.1021/bi4001563] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The flavoprotein tryptophan 2-monooxygenase catalyzes the oxidative decarboxylation of tryptophan to yield indole-3-acetamide. This is the initial step in the biosynthesis of the plant growth hormone indole-acetic acid by bacterial pathogens that cause crown gall and related diseases. The structure of the enzyme from Pseudomonas savastanoi has been determined by X-ray diffraction methods to a resolution of 1.95 Å. The overall structure of the protein shows that it has the same fold as members of the monoamine oxidase family of flavoproteins, with the greatest similarities to the l-amino acid oxidases. The location of bound indole-3-acetamide in the active site allows identification of residues responsible for substrate binding and specificity. Two residues in the enzyme are conserved in all members of the monoamine oxidase family, Lys365 and Trp466. The K365M mutation decreases the kcat and kcat/KTrp values by 60000- and 2 million-fold, respectively. The deuterium kinetic isotope effect increases to 3.2, consistent with carbon-hydrogen bond cleavage becoming rate-limiting in the mutant enzyme. The W466F mutation decreases the kcat value <2-fold and the kcat/KTrp value only 5-fold, while the W466M mutation results in an enzyme lacking flavin and detectable activity. This is consistent with a role for Trp466 in maintaining the structure of the flavin-binding site in the more conserved FAD domain.
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Affiliation(s)
- Helena M Gaweska
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229, USA
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21
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Tormos JR, Pozzi MH, Fitzpatrick PF. Mechanistic studies of the role of a conserved histidine in a mammalian polyamine oxidase. Arch Biochem Biophys 2012; 528:45-9. [PMID: 22959971 PMCID: PMC3483376 DOI: 10.1016/j.abb.2012.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 08/13/2012] [Accepted: 08/14/2012] [Indexed: 11/21/2022]
Abstract
Polyamine oxidases are peroxisomal flavoproteins that catalyze the oxidation of an endo carbon nitrogen bond of N1-acetylspermine in the catabolism of polyamines. While no structure has been reported for a mammalian polyamine oxidase, sequence alignments of polyamine oxidizing flavoproteins identify a conserved histidine residue. Based on the structure of a yeast polyamine oxidase, Saccharomyces cerevisiae Fms1, this residue has been proposed to hydrogen bond to the reactive nitrogen in the polyamine substrate. The corresponding histidine in mouse polyamine oxidase, His64, has been mutated to glutamine, asparagine, and alanine to determine if this residue plays a similar role in the mammalian enzymes. The kinetics of the mutant enzymes were examined with N1-acetylspermine and the slow substrates spermine and N,N'-dibenzyl-1,4-diaminobutane. On average the mutations result in a decrease of ~15-fold in the rate constant for amine oxidation. Rapid-reaction kinetic analyses established that amine oxidation is rate-limiting with spermine as substrate for the wild-type and mutant enzymes and for the H64N enzyme with N1-acetylspermine as substrate. The k(cat)/K(O(2)) value was unaffected by the mutations with N1-acetylspermine as substrate, but decreased ~55-fold with the two slower substrates. The results are consistent with this residue assisting in properly positioning the amine substrate for oxidation.
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Affiliation(s)
- José R. Tormos
- Department of Biochemistry, University of Texas Health Science Center, San Antonio TX 78229
| | | | - Paul F. Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center, San Antonio TX 78229
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22
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Adachi MS, Taylor AB, Hart PJ, Fitzpatrick PF. Mechanistic and structural analyses of the roles of active site residues in yeast polyamine oxidase Fms1: characterization of the N195A and D94N enzymes. Biochemistry 2012; 51:8690-7. [PMID: 23034052 PMCID: PMC3548949 DOI: 10.1021/bi3011434] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Flavoprotein Fms1 from Saccharomyces cerevisiae catalyzes the oxidation of spermine in the biosynthetic pathway for pantothenic acid. The same reaction is catalyzed by the mammalian polyamine and spermine oxidases. The active site of Fms1 contains three amino acid residues positioned to interact with the polyamine substrate, His67, Asn195, and Asp94. These three residues form a hydrogen-bonding triad with Asn195 being the central residue. Previous studies of the effects of mutating His67 are consistent with that residue being important both for interacting with the substrate and for maintaining the hydrogen bonds in the triad [Adachi, M. S., Taylor, A. B., Hart, P. J., and Fitzpatrick, P. F. (2012) Biochemistry 51, 4888-4897]. The N195A and D94N enzymes have now been characterized to evaluate their roles in catalysis. Both mutations primarily affect the reductive half-reaction. With N(1)-acetylspermine as the substrate, the rate constant for flavin reduction decreases ~450-fold for both mutations; the effects with spermine as the substrate are smaller, 20-40-fold. The k(cat)/K(amine)- and k(cat)-pH profiles with N(1)-acetylspermine are only slightly changed from the profiles for the wild-type enzyme, consistent with the pK(a) values arising from the amine substrate or product and not from active site residues. The structure of the N195A enzyme was determined at a resolution of 2.0 Å. The structure shows a molecule of tetraethylene glycol in the active site and establishes that the mutation has no effect on the protein structure. Overall, the results are consistent with the role of Asn195 and Asp94 being to properly position the polyamine substrate for oxidation.
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Affiliation(s)
- Mariya S. Adachi
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
| | - Alexander B. Taylor
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
| | - P. John Hart
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
- Department of Veterans Affairs, Audie Murphy Division, Geriatric Research, Education, and Clinical Center, South Texas Veterans Health Care System, San Antonio, TX 78229
| | - Paul F. Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
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23
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Adachi MS, Taylor AB, Hart PJ, Fitzpatrick PF. Mechanistic and structural analyses of the role of His67 in the yeast polyamine oxidase Fms1. Biochemistry 2012; 51:4888-97. [PMID: 22642831 DOI: 10.1021/bi300517s] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The flavoprotein oxidase Fms1 from Saccharomyces cerevisiae catalyzes the oxidation of spermine and N(1)-acetylspermine to spermidine and 3-aminopropanal or N-acetyl-3-aminopropanal. Within the active site of Fms1, His67 is positioned to form hydrogen bonds with the polyamine substrate. This residue is also conserved in other polyamine oxidases. The catalytic properties of H67Q, H67N, and H67A Fms1 have been characterized to evaluate the role of this residue in catalysis. With both spermine and N(1)-acetylspermine as the amine substrate, the value of the first-order rate constant for flavin reduction decreases 2-3 orders of magnitude, with the H67Q mutation having the smallest effect and H67N the largest. The k(cat)/K(O2) value changes very little upon mutation with N(1)-acetylspermine as the amine substrate and decreases only an order of magnitude with spermine. The k(cat)/K(M)-pH profiles with N(1)-acetylspermine are bell-shaped for all the mutants; the similarity to the profile of the wild-type enzyme rules out His67 as being responsible for either of the pK(a) values. The pH profiles for the rate constant for flavin reduction for all the mutant enzymes similarly show the same pK(a) as wild-type Fms1, about ∼7.4; this pK(a) is assigned to the substrate N4. The k(cat)/K(O2)-pH profiles for wild-type Fms1 and the H67A enzyme both show a pK(a) of about ∼6.9; this suggests His67 is not responsible for this pH behavior. With the H67Q, H67N, and H67A enzymes the k(cat) value decreases when a single residue is protonated, as is the case with the wild-type enzyme. The structure of H67Q Fms1 has been determined at a resolution of 2.4 Å. The structure shows that the mutation disrupts a hydrogen bond network in the active site, suggesting that His67 is important both for direct interactions with the substrate and to maintain the overall active site structure.
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Affiliation(s)
- Mariya S Adachi
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229, USA
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24
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Cervelli M, Amendola R, Polticelli F, Mariottini P. Spermine oxidase: ten years after. Amino Acids 2012; 42:441-50. [PMID: 21809080 DOI: 10.1007/s00726-011-1014-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 05/25/2011] [Indexed: 12/13/2022]
Abstract
Spermine oxidase (SMO) was discovered much more recently than other enzymes involved in polyamine metabolism; this review summarizes 10 years of researches on this enzyme. Spermine oxidase (SMO) is a FAD-dependent enzyme that specifically oxidizes spermine (Spm) and plays a dominant role in the highly regulated mammalian polyamines catabolism. SMO participates in drug response, apoptosis, response to stressful stimuli and etiology of several pathological conditions, including cancer. SMO is a highly inducible enzyme, its deregulation can alter polyamine homeostasis, and dysregulation of polyamine catabolism is often associated with several disease states. The oxidative products of SMO activity are spermidine, and the reactive oxygen species H(2)O(2) and the aldehyde 3-aminopropanal each with the potential to produce cellular damages and pathologies. The SMO substrate Spm is a tetramine that plays mandatory roles in several cell functions, such as DNA synthesis, cellular proliferation, modulation of ion channels function, cellular signaling, nitric oxide synthesis and inhibition of immune responses. The goal of this review is to cover the main biochemical, cellular and physiological processes in which SMO is involved.
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25
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Gaweska H, Fitzpatrick PF. Structures and Mechanism of the Monoamine Oxidase Family. Biomol Concepts 2011; 2:365-377. [PMID: 22022344 DOI: 10.1515/bmc.2011.030] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Members of the monoamine oxidase family of flavoproteins catalyze the oxidation of primary and secondary amines, polyamines, amino acids, and methylated lysine side chains in proteins. The enzymes have similar overall structures, with conserved FAD-binding domains and varied substrate-binding sites. Multiple mechanisms have been proposed for the catalytic reactions of these enzymes. The present review compares the structures of different members of the family and the various mechanistic proposals.
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Affiliation(s)
- Helena Gaweska
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
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26
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Kong X, Ouyang S, Liang Z, Lu J, Chen L, Shen B, Li D, Zheng M, Li KK, Luo C, Jiang H. Catalytic mechanism investigation of lysine-specific demethylase 1 (LSD1): a computational study. PLoS One 2011; 6:e25444. [PMID: 21984927 PMCID: PMC3184146 DOI: 10.1371/journal.pone.0025444] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 09/05/2011] [Indexed: 12/13/2022] Open
Abstract
Lysine-specific demethylase 1 (LSD1), the first identified histone demethylase, is a flavin-dependent amine oxidase which specifically demethylates mono- or dimethylated H3K4 and H3K9 via a redox process. It participates in a broad spectrum of biological processes and is of high importance in cell proliferation, adipogenesis, spermatogenesis, chromosome segregation and embryonic development. To date, as a potential drug target for discovering anti-tumor drugs, the medical significance of LSD1 has been greatly appreciated. However, the catalytic mechanism for the rate-limiting reductive half-reaction in demethylation remains controversial. By employing a combined computational approach including molecular modeling, molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations, the catalytic mechanism of dimethylated H3K4 demethylation by LSD1 was characterized in details. The three-dimensional (3D) model of the complex was composed of LSD1, CoREST, and histone substrate. A 30-ns MD simulation of the model highlights the pivotal role of the conserved Tyr761 and lysine-water-flavin motif in properly orienting flavin adenine dinucleotide (FAD) with respect to substrate. The synergy of the two factors effectively stabilizes the catalytic environment and facilitated the demethylation reaction. On the basis of the reasonable consistence between simulation results and available mutagenesis data, QM/MM strategy was further employed to probe the catalytic mechanism of the reductive half-reaction in demethylation. The characteristics of the demethylation pathway determined by the potential energy surface and charge distribution analysis indicates that this reaction belongs to the direct hydride transfer mechanism. Our study provides insights into the LSD1 mechanism of reductive half-reaction in demethylation and has important implications for the discovery of regulators against LSD1 enzymes.
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Affiliation(s)
- Xiangqian Kong
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Sisheng Ouyang
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Zhongjie Liang
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Junyan Lu
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Liang Chen
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Bairong Shen
- Center for Systems Biology, Soochow University, Jiangsu, China
| | - Donghai Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Jiangsu Diabetes Research Center, Nanjing University, Nanjing, China
| | - Mingyue Zheng
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Keqin Kathy Li
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- * E-mail: (CL); (KKL)
| | - Cheng Luo
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Center for Systems Biology, Soochow University, Jiangsu, China
- * E-mail: (CL); (KKL)
| | - Hualiang Jiang
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
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Tavladoraki P, Cervelli M, Antonangeli F, Minervini G, Stano P, Federico R, Mariottini P, Polticelli F. Probing mammalian spermine oxidase enzyme-substrate complex through molecular modeling, site-directed mutagenesis and biochemical characterization. Amino Acids 2011; 40:1115-26. [PMID: 20839014 DOI: 10.1007/s00726-010-0735-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Accepted: 08/26/2010] [Indexed: 10/19/2022]
Abstract
Spermine oxidase (SMO) and acetylpolyamine oxidase (APAO) are FAD-dependent enzymes that are involved in the highly regulated pathways of polyamine biosynthesis and degradation. Polyamine content is strictly related to cell growth, and dysfunctions in polyamine metabolism have been linked with cancer. Specific inhibitors of SMO and APAO would allow analyzing the precise role of these enzymes in polyamine metabolism and related pathologies. However, none of the available polyamine oxidase inhibitors displays the desired characteristics of selective affinity and specificity. In addition, repeated efforts to obtain structural details at the atomic level on these two enzymes have all failed. In the present study, in an effort to better understand structure-function relationships, SMO enzyme-substrate complex has been probed through a combination of molecular modeling, site-directed mutagenesis and biochemical studies. Results obtained indicate that SMO binds spermine in a similar conformation as that observed in the yeast polyamine oxidase FMS1-spermine complex and demonstrate a major role for residues His82 and Lys367 in substrate binding and catalysis. In addition, the SMO enzyme-substrate complex highlights the presence of an active site pocket with highly polar characteristics, which may explain the different substrate specificity of SMO with respect to APAO and provide the basis for the design of specific inhibitors for SMO and APAO.
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Affiliation(s)
- Paraskevi Tavladoraki
- Department of Biology, University Roma Tre, Viale Guglielmo Marconi 446, 00146, Rome, Italy
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Fiorillo A, Federico R, Polticelli F, Boffi A, Mazzei F, Di Fusco M, Ilari A, Tavladoraki P. The structure of maize polyamine oxidase K300M mutant in complex with the natural substrates provides a snapshot of the catalytic mechanism of polyamine oxidation. FEBS J 2011; 278:809-21. [PMID: 21205212 DOI: 10.1111/j.1742-4658.2010.08000.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Polyamine oxidases are FAD-dependent enzymes catalyzing the oxidation of polyamines at the secondary amino groups. Zea mays PAO (ZmPAO) oxidizes the carbon on the endo-side of the N5-nitrogen of spermidine (Spd) and spermine (Spm). The structure of ZmPAO revealed that the active site is formed by a catalytic tunnel in which the N5 atom of FAD lies in close proximity to the K300 side chain, the only active-site residue conserved in all PAOs. A water molecule, (HOH309), is hydrogen-bound to the amino group of K300 and mutation of this residue results in a 1400-fold decrease in the rate of flavin reduction. The structural studies on the catalytically impaired ZmPAO-K300M mutant described here show that substrates are bound in an 'out-of-register' mode and the HOH309 water molecule is absent in the enzyme-substrate complexes. Moreover, K300 mutation brings about a 60 mV decrease in the FAD redox potential and a 30-fold decrease in the FAD reoxidation rate, within a virtually unaltered geometry of the catalytic pocket. Taken together, these results indicate that the HOH309-K300 couple plays a major role in multiple steps of ZmPAO catalytic mechanism, such as correct substrate binding geometry as well as FAD reduction and reoxidation kinetics.
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Affiliation(s)
- Annarita Fiorillo
- Department of Science and Biomedical Technology, University of L'Aquila, Italy
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29
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Adachi MS, Torres JM, Fitzpatrick PF. Mechanistic studies of the yeast polyamine oxidase Fms1: kinetic mechanism, substrate specificity, and pH dependence. Biochemistry 2010; 49:10440-8. [PMID: 21067138 PMCID: PMC2999662 DOI: 10.1021/bi1016099] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The flavoprotein oxidase Fms1 from Saccharomyces cerevisiae catalyzes the oxidation of spermine and N(1)-acetylspermine to yield spermidine and 3-aminopropanal or N-acetyl-3-aminopropanal. The kinetic mechanism of the enzyme has been determined with both substrates. The initial velocity patterns are ping-pong, consistent with reduction being kinetically irreversible. Reduction of Fms1 by either substrate is biphasic. The rate constant for the rapid phase varies with the substrate concentration, with limiting rates for reduction of the enzyme of 126 and 1410 s(-1) and apparent K(d) values of 24.3 and 484 μM for spermine and N(1)-acetylspermine, respectively. The rapid phase is followed by a concentration-independent phase that is slower than turnover. The reaction of the reduced enzyme with oxygen is monophasic, with a rate constant of 402 mM(-1) s(-1) with spermine at 25 °C and 204 mM(-1) s(-1) with N(1)-acetylspermine at 4 °C and pH 9.0. This step is followed by rate-limiting product dissociation. The k(cat)/K(amine)-pH profiles are bell-shaped, with an average pK(a) value of 9.3 with spermine and pK(a) values of 8.3 and 9.6 with N(1)-acetylspermine. Both profiles are consistent with the active forms of substrates having two charged nitrogens. The pH profiles for the rate constant for flavin reduction show pK(a) values of 8.3 and 7.2 for spermine and N(1)-acetylspermine, respectively, for groups that must be unprotonated; these pK(a) values are assigned to the substrate N4. The k(cat)/K(O(2))-pH profiles show pK(a) values of 7.5 for spermine and 6.8 for N(1)-acetylspermine. With both substrates, the k(cat) value decreases when a single residue is protonated.
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Affiliation(s)
- Mariya S. Adachi
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
| | - Jason M. Torres
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
| | - Paul F. Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
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30
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Pozzi MH, Fitzpatrick PF. A lysine conserved in the monoamine oxidase family is involved in oxidation of the reduced flavin in mouse polyamine oxidase. Arch Biochem Biophys 2010; 498:83-8. [PMID: 20417173 PMCID: PMC2880204 DOI: 10.1016/j.abb.2010.04.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 04/19/2010] [Accepted: 04/20/2010] [Indexed: 10/19/2022]
Abstract
Lysine 315 of mouse polyamine amine oxidase corresponds to a lysine residue that is conserved in the flavoprotein amine oxidases of the monoamine oxidase structural family. In several structures, this lysine residue forms a hydrogen bond to a water molecule that is hydrogen-bonded to the flavin N(5). Mutation of Lys315 in polyamine oxidase to methionine was previously shown to have no effect on the kinetics of the reductive half-reaction of the enzyme (M. Henderson Pozzi, V. Gawandi, P.F. Fitzpatrick, Biochemistry 48 (2009) 1508-1516). In contrast, the mutation does affect steps in the oxidative half-reaction. The k(cat) value is unaffected by the mutation; this kinetic parameter likely reflects product release. At pH 10, the k(cat)/K(m) value for oxygen is 25-fold lower in the mutant enzyme. The k(cat)/K(O2) value is pH-dependent for the wild-type enzyme, decreasing below a pK(a) of 7.0, while this kinetic parameter for the mutant enzyme is pH-independent. This is consistent with the neutral form of Lys315 being required for more rapid flavin oxidation. The solvent isotope effect on the k(cat)/K(O2) value increases from 1.4 in the wild-type enzyme to 1.9 in the mutant protein, and the solvent inventory changes from linear to bowed. The effects of the mutation can be explained by the lysine orienting the bridging water so that it can accept the proton from the flavin N(5) during flavin oxidation. In the mutant enzyme the lysine amine would be replaced by a water chain.
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Affiliation(s)
| | - Paul F. Fitzpatrick
- Department of Biochemistry and Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, San Antonio TX 78229-3900
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31
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Szelke H, Schübel S, Harenberg J, Krämer R. Interaction of heparin with cationic molecular probes: Probe charge is a major determinant of binding stoichiometry and affinity. Bioorg Med Chem Lett 2010; 20:1445-7. [DOI: 10.1016/j.bmcl.2009.12.105] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 12/18/2009] [Accepted: 12/19/2009] [Indexed: 02/05/2023]
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32
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Adachi MS, Juarez PR, Fitzpatrick PF. Mechanistic studies of human spermine oxidase: kinetic mechanism and pH effects. Biochemistry 2010; 49:386-92. [PMID: 20000632 PMCID: PMC2810717 DOI: 10.1021/bi9017945] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In mammalian cells, the flavoprotein spermine oxidase (SMO) catalyzes the oxidation of spermine to spermidine and 3-aminopropanal. Mechanistic studies have been conducted with the recombinant human enzyme. The initial velocity pattern in which the ratio between the concentrations of spermine and oxygen is kept constant establishes the steady-state kinetic pattern as ping-pong. Reduction of SMO by spermine in the absence of oxygen is biphasic. The rate constant for the rapid phase varies with the substrate concentration, with a limiting value (k(3)) of 49 s(-1) and an apparent K(d) value of 48 microM at pH 8.3. The rate constant for the slow step is independent of the spermine concentration, with a value of 5.5 s(-1), comparable to the k(cat) value of 6.6 s(-1). The kinetics of the oxidative half-reaction depend on the aging time after the spermine and enzyme are mixed in a double-mixing experiment. At an aging time of 6 s, the reaction is monophasic with a second-order rate constant of 4.2 mM(-1) s(-1). At an aging time of 0.3 s, the reaction is biphasic with two second-order constants equal to 4.0 and 40 mM(-1) s(-1). Neither is equal to the k(cat)/K(O(2)) value of 13 mM(-1) s(-1). These results establish the existence of more than one pathway for the reaction of the reduced flavin intermediate with oxygen. The k(cat)/K(M) value for spermine exhibits a bell-shaped pH profile, with an average pK(a) value of 8.3. This profile is consistent with the active form of spermine having three charged nitrogens. The pH profile for k(3) shows a pK(a) value of 7.4 for a group that must be unprotonated. The pK(i)-pH profiles for the competitive inhibitors N,N'-dibenzylbutane-1,4-diamine and spermidine show that the fully protonated forms of the inhibitors and the unprotonated form of an amino acid residue with a pK(a) of approximately 7.4 in the active site are preferred for binding.
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Affiliation(s)
- Maria S. Adachi
- Department of Biochemistry and Center for Biomedical Neuroscience, University of Texas Health Science Center, San Antonio, TX 78229
| | - Paul R. Juarez
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Paul F. Fitzpatrick
- Department of Biochemistry and Center for Biomedical Neuroscience, University of Texas Health Science Center, San Antonio, TX 78229
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33
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Pozzi MH, Gawandi V, Fitzpatrick PF. Mechanistic studies of para-substituted N,N'-dibenzyl-1,4-diaminobutanes as substrates for a mammalian polyamine oxidase. Biochemistry 2009; 48:12305-13. [PMID: 19911805 PMCID: PMC2797579 DOI: 10.1021/bi901694s] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The kinetics of oxidation of a series of para-substituted N,N'-dibenzyl-1,4-diaminobutanes by the flavoprotein polyamine oxidase from mouse have been determined to gain insight into the mechanism of amine oxidation by this member of the monoamine oxidase structural family. The k(cat)/K(m) values are maximal at pH 9, consistent with the singly charged substrate being the active form. The rate constant for flavin reduction, k(red), by N,N'-dibenzyl-1,4-diaminobutane decreases about 5-fold below a pK(a) of approximately 8; this is attributed to the need for a neutral nitrogen at the site of oxidation. The k(red) and k(cat) values are comparable for each of the N,N'-dibenzyl-1,4-diaminobutanes, consistent with rate-limiting reduction. The deuterium kinetic isotope effects on k(red) and k(cat) are identical for each of the N,N'-dibenzyl-1,4-diaminobutanes, consistent with rate-limiting cleavage of the substrate CH bond. The k(red) values for seven different para-substituted N,N'-dibenzyl-1,4-diaminobutanes correlate with a combination of the van der Waals volume and sigma value of the substrates, with rho values of -0.59 at pH 8.6 and -0.09 at pH 6.6. These results are consistent with direct transfer of a hydride from the neutral CN bond of the substrate to the flavin as the mechanism of polyamine oxidase.
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Affiliation(s)
| | - Vijay Gawandi
- Department of Biochemistry and Biophysics Texas A&M University, College Station TX 77843-2128
| | - Paul F. Fitzpatrick
- Department of Biochemistry University of Texas Health Science Center at San Antonio, San Antonio TX 78229-3900
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Perdan-Pirkmajer K, Mavri J, Krzan M. Histamine (re)uptake by astrocytes: an experimental and computational study. J Mol Model 2009; 16:1151-8. [PMID: 20013137 DOI: 10.1007/s00894-009-0624-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Accepted: 10/26/2009] [Indexed: 10/20/2022]
Abstract
Astrocytes participate in the clearance of neurotransmitters by their uptake and subsequent enzymatic degradation. Histamine as a polar and/or protonated molecule must use a carrier to be transported across the cell membrane, although a specific histamine transporter has not been elucidated, yet. In this work we upgraded the kinetic studies of histamine uptake into neonatal rat cultured type 1 astrocytes with quantum chemical calculations of histamine pKa values in conjunction with Langevin dipoles solvation model as the first step toward microscopic simulation of transport. Our results indicate that astrocytes transport histamine by at least two carrier mediated processes, a concentration gradient dependent passive and a sodium-dependent and ATP-driven active transport. We also demonstrated that histamine protonation states depend on the polarity of the environment. In conclusion we suggest that histamine, a polar molecule at physiological pH uses at least two different mechanisms for its uptake into astrocytes -an electrodiffusion and Na(+)-dependent and ouabain sensitive active process. We emphasize relevance of knowledge of histamines protonation states at the rate limiting step of its transport for microscopic simulation that will be possible when structure of histamine transporter is known.
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Affiliation(s)
- Katja Perdan-Pirkmajer
- Department of Pharmacology and Experimental Toxicology, Faculty of Medicine, University of Ljubljana, Korytkova 2, Si-1001, Ljubljana, Slovenia.
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Abstract
Polyamines are ubiquitous small basic molecules that play multiple essential roles in mammalian physiology. Their cellular content is highly regulated and there is convincing evidence that altered metabolism is involvement in many disease states. Drugs altering polyamine levels may therefore have a variety of important targets. This review will summarize the current state of understanding of polyamine metabolism and function, the regulation of polyamine content, and heritable pathological conditions that may be derived from altered polyamine metabolism.
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Affiliation(s)
- Anthony E Pegg
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
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36
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Oxidation of amines by flavoproteins. Arch Biochem Biophys 2009; 493:13-25. [PMID: 19651103 DOI: 10.1016/j.abb.2009.07.019] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 07/27/2009] [Accepted: 07/29/2009] [Indexed: 11/21/2022]
Abstract
Many flavoproteins catalyze the oxidation of primary and secondary amines, with the transfer of a hydride equivalent from a carbon-nitrogen bond to the flavin cofactor. Most of these amine oxidases can be classified into two structural families, the D-amino acid oxidase/sarcosine oxidase family and the monoamine oxidase family. This review discusses the present understanding of the mechanisms of amine and amino acid oxidation by flavoproteins, focusing on these two structural families.
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Gaweska H, Henderson Pozzi M, Schmidt DMZ, McCafferty DG, Fitzpatrick PF. Use of pH and kinetic isotope effects to establish chemistry as rate-limiting in oxidation of a peptide substrate by LSD1. Biochemistry 2009; 48:5440-5. [PMID: 19408960 DOI: 10.1021/bi900499w] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The mechanism of oxidation of a peptide substrate by the flavoprotein lysine-specific demethylase (LSD1) has been examined using the effects of pH and isotopic substitution on steady-state and rapid-reaction kinetic parameters. The substrate contained the 21 N-terminal residues of histone H3, with a dimethylated lysyl residue at position 4. At pH 7.5, the rate constant for flavin reduction, k(red), equals k(cat), establishing the reductive half-reaction as rate-limiting at physiological pH. Deuteration of the lysyl methyls results in identical kinetic isotope effects of 3.1 +/- 0.2 on the k(red), k(cat), and k(cat)/K(m) values for the peptide, establishing C-H bond cleavage as rate-limiting with this substrate. No intermediates between oxidized and reduced flavin can be detected by stopped-flow spectroscopy, consistent with the expectation for a direct hydride transfer mechanism. The k(cat)/K(m) value for the peptide is bell-shaped, consistent with a requirement that the nitrogen at the site of oxidation be uncharged and that at least one of the other lysyl residues be charged for catalysis. The (D)(k(cat)/K(m)) value for the peptide is pH-independent, suggesting that the observed value is the intrinsic deuterium kinetic isotope effect for oxidation of this substrate.
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Affiliation(s)
- Helena Gaweska
- Department of Biochemistry and Biophysics and Johnson Research Foundation, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
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