1
|
Tararina MA, Allen KN. Bioinformatic Analysis of the Flavin-Dependent Amine Oxidase Superfamily: Adaptations for Substrate Specificity and Catalytic Diversity. J Mol Biol 2020; 432:3269-3288. [PMID: 32198115 DOI: 10.1016/j.jmb.2020.03.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/24/2020] [Accepted: 03/06/2020] [Indexed: 12/29/2022]
Abstract
The flavin-dependent amine oxidase (FAO) superfamily consists of over 9000 nonredundant sequences represented in all domains of life. Of the thousands of members identified, only 214 have been functionally annotated to date, and 40 unique structures are represented in the Protein Data Bank. The few functionally characterized members share a catalytic mechanism involving the oxidation of an amine substrate through transfer of a hydride to the FAD cofactor, with differences observed in substrate specificities. Previous studies have focused on comparing a subset of superfamily members. Here, we present a comprehensive analysis of the FAO superfamily based on reaction mechanism and substrate recognition. Using a dataset of 9192 sequences, a sequence similarity network, and subsequently, a genome neighborhood network were constructed, organizing the superfamily into eight subgroups that accord with substrate type. Likewise, through phylogenetic analysis, the evolutionary relationship of subgroups was determined, delineating the divergence between enzymes based on organism, substrate, and mechanism. In addition, using sequences and atomic coordinates of 22 structures from the Protein Data Bank to perform sequence and structural alignments, active-site elements were identified, showing divergence from the canonical aromatic-cage residues to accommodate large substrates. These specificity determinants are held in a structural framework comprising a core domain catalyzing the oxidation of amines with an auxiliary domain for substrate recognition. Overall, analysis of the FAO superfamily reveals a modular fold with cofactor and substrate-binding domains allowing for diversity of recognition via insertion/deletions. This flexibility allows facile evolution of new activities, as shown by reinvention of function between subfamilies.
Collapse
Affiliation(s)
- Margarita A Tararina
- Program in Biomolecular Pharmacology, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Karen N Allen
- Program in Biomolecular Pharmacology, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA; Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA.
| |
Collapse
|
2
|
Syatkin SP, Neborak EV, Khlebnikov AI, Komarova MV, Shevkun NA, Kravtsov EG, Blagonravov ML, Agostinelli E. The investigation of structure-activity relationship of polyamine-targeted synthetic compounds from different chemical groups. Amino Acids 2019; 52:199-211. [PMID: 31520286 DOI: 10.1007/s00726-019-02778-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 08/14/2019] [Indexed: 01/26/2023]
Abstract
The polyamine (PA) metabolism is involved in cell proliferation and differentiation. Increased cellular PA levels are observed in different types of cancers. Products of PA oxidation induce apoptosis in cancer cells. These observations open a perspective to exploit the enzymes of PA catabolism as a target for anticancer drug design. The substances capable to enhance PA oxidation may become potential anticancer agents. The goal of our study was to explore how the mode of ligand binding with a PA catabolic enzyme is associated with its stimulatory or inhibitory effect upon PA oxidation. Murine N1-acetylpolyamine oxidase (5LFO) crystalline structure was used for molecular docking with ligands of various chemical structures. In vitro experiments were carried out to evaluate the action of the tested compounds upon PA oxidative deamination in a cell-free test system from rat liver. Two amino acid residues (Aps211 and Tyr204) in the structure of 5LFO were found to be significant for binding with the tested compounds. 19 out of 51 screened compounds were activators and 17 were inhibitors of oxidative deamination of PA. Taken together, these results enabled to construct a recognition model with characteristic descriptors depicting activators and inhibitors. The general tendency indicated that a strong interaction with Asp211 or Tyr204 was rather typical for activators. The understanding of how the structure determines the binding mode of compounds with PA catabolic enzyme may help in explanation of their structure-activity relationship and thus promote structure-based drug design.
Collapse
Affiliation(s)
- Sergey P Syatkin
- Medical Institute, RUDN University (Peoples' Friendship University of Russia), Miklukho-Maklaya str.6, Moscow, 117198, Russia.
| | - Ekaterina V Neborak
- Medical Institute, RUDN University (Peoples' Friendship University of Russia), Miklukho-Maklaya str.6, Moscow, 117198, Russia
| | - Andrei I Khlebnikov
- Kizhner Research Center, National Research Tomsk Polytechnic University, Tomsk, 634050, Russia
- Scientific Research Institute of Biological Medicine, Altai State University, Barnaul, 656049, Russia
| | | | - Natalia A Shevkun
- Drug Product Division, Project Development Department, NEARMEDIC PHARMA LLC, Moscow, Russia
| | - Eduard G Kravtsov
- Medical Institute, RUDN University (Peoples' Friendship University of Russia), Miklukho-Maklaya str.6, Moscow, 117198, Russia
| | - Mikhail L Blagonravov
- Medical Institute, RUDN University (Peoples' Friendship University of Russia), Miklukho-Maklaya str.6, Moscow, 117198, Russia
| | - Enzo Agostinelli
- Department of Biochemical Sciences, SAPIENZA University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
- International Polyamines Foundation, ONLUS, Via del Forte Tiburtino, 98, 00159, Rome, Italy
| |
Collapse
|
3
|
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.
Collapse
|
4
|
Liu J, Zhao M, Song W, Ma L, Li X, Zhang F, Diao L, Pi Y, Jiang K. An amine oxidase gene from mud crab, Scylla paramamosain, regulates the neurotransmitters serotonin and dopamine in vitro. PLoS One 2018; 13:e0204325. [PMID: 30248122 PMCID: PMC6152983 DOI: 10.1371/journal.pone.0204325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 09/06/2018] [Indexed: 11/20/2022] Open
Abstract
Amine oxidase, which participates in the metabolic processing of biogenic amines, is widely found in organisms, including higher organisms and various microorganisms. In this study, the full-length cDNA of a novel amine oxidase gene was cloned from the mud crab, Scylla paramamosain, and termed SpAMO. The cDNA sequence was 2,599 bp in length, including an open reading frame of 1,521 bp encoding 506 amino acids. Two amino acid sequence motifs, a flavin adenine dinucleotide-binding domain and a flavin-containing amine oxidoreductase, were highly conserved in SpAMO. A quantitative real-time polymerase chain reaction analysis showed that the expression level of SpAMO after quercetin treatment was time- and concentration-dependent. The expression of SpAMO tended to decrease and then increase in the brain and haemolymph after treatment with 5 mg/kg/d quercetin; after treatment with 50 mg/kg/d quercetin, the expression of SpAMO declined rapidly and remained low in the brain and haemolymph. These results indicated that quercetin could inhibit the transcription of SpAMO, and the high dose (50 mg/kg/d) had a relatively significant inhibitory effect. SpAMO showed the highest catalytic activity on serotonin, followed by dopamine, β-phenylethylamine, and spermine, suggesting that the specific substrates of SpAMO are serotonin and dopamine. A bioinformatics analysis of SpAMO showed that it has molecular characteristics of spermine oxidase, but a quercetin test and enzyme activity study indicated that it also functions like monoamine oxidase. It is speculated that SpAMO might be a novel amine oxidase in S. paramamosain that has the functions of both spermine oxidase and monoamine oxidase.
Collapse
Affiliation(s)
- Junguo Liu
- Key Laboratory of Aquatic Genomics, Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Ming Zhao
- Key Laboratory of Aquatic Genomics, Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Wei Song
- Key Laboratory of Aquatic Genomics, Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Lingbo Ma
- Key Laboratory of Aquatic Genomics, Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- * E-mail: (KJ); (LM)
| | - Xiu Li
- Key Laboratory of Aquatic Genomics, Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Fengying Zhang
- Key Laboratory of Aquatic Genomics, Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Le Diao
- Key Laboratory of Aquatic Genomics, Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Yan Pi
- School of Life Sciences, Fudan University, Shanghai, China
| | - Keji Jiang
- Key Laboratory of Aquatic Genomics, Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- * E-mail: (KJ); (LM)
| |
Collapse
|
5
|
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.
Collapse
Affiliation(s)
- Kenneth M Roberts
- Department of Biochemistry, University of Texas Health Science Center , San Antonio, Texas 78229, United States
| | | | | |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|