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Retnoningrum DS, Yoshida H, Pajatiwi I, Muliadi R, Utami RA, Artarini A, Ismaya WT. Introducing Intermolecular Interaction to Strengthen the Stability of MnSOD Dimer. Appl Biochem Biotechnol 2023:10.1007/s12010-023-04347-7. [PMID: 36701098 DOI: 10.1007/s12010-023-04347-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2023] [Indexed: 01/27/2023]
Abstract
Manganese superoxide dismutase from Staphylococcus equorum (MnSODSeq) maintains its activity upon treatments like a wide range of pH, addition of detergent and denaturing agent, exposure to ultraviolet light, and heating up to 50 °C. The enzyme dimer dissociates at 52-55 °C, while its monomer unfolds at 63-67 °C. MnSOD dimeric form is indispensable for the enzyme activity; therefore, strengthening the interactions between the monomers is the most preferred strategy to improve the enzyme stability. However, to date, modification of MnSODSeq at the dimer interface has been unfruitful despite excluding the inner and outer sphere regions that are important to the enzyme activity. Here, a new strategy was developed and K38R-A121E/Y double substitutions were proposed. These mutants displayed similar enzyme activity to the wild type. K38R-A121E dimer was thermally more stable and its monomer stability was similar to the wild type. The thermal stability of K38R-A121Y dimer was similar to the wild type but its monomer was thermally less stable. In addition, the structure of the previously reported L169W mutant was also elucidated. The L169W mutant structure showed that intramolecular modification can decrease flexibility of the MnSODSeq monomer and leads to a less stable enzyme with similar activity to the wild type. Thus, while the enzyme activity depends on arrangement of residues in the dimer interface, the stability appears to depend more on its monomeric architecture. Furthermore, in the L169W structure in complex with azide, which is a specific inhibitor for MnSOD, one of the azide molecules was present in the dimer interface region that previously has been identified to involve in the enzymatic reaction. Nevertheless, the present results show that an MnSODSeq mutant with better thermal stability has been obtained.
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Affiliation(s)
- Debbie S Retnoningrum
- Laboratory of Pharmaceutical Biotechnology, Pharmaceutics Research Group, School of Pharmacy, Institut Teknologi Bandung, Ganesha 10, Bandung, 40132, West Java, Indonesia
| | - Hiromi Yoshida
- Department of Basic Life Science, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-Cho, Kita-Gun, Kagawa, 761-0793, Japan
| | - Ismiana Pajatiwi
- Laboratory of Pharmaceutical Biotechnology, Pharmaceutics Research Group, School of Pharmacy, Institut Teknologi Bandung, Ganesha 10, Bandung, 40132, West Java, Indonesia
| | - Rahmat Muliadi
- Laboratory of Pharmaceutical Biotechnology, Pharmaceutics Research Group, School of Pharmacy, Institut Teknologi Bandung, Ganesha 10, Bandung, 40132, West Java, Indonesia
| | - Ratna A Utami
- Laboratory of Pharmaceutical Biotechnology, Pharmaceutics Research Group, School of Pharmacy, Institut Teknologi Bandung, Ganesha 10, Bandung, 40132, West Java, Indonesia
| | - Anita Artarini
- Laboratory of Pharmaceutical Biotechnology, Pharmaceutics Research Group, School of Pharmacy, Institut Teknologi Bandung, Ganesha 10, Bandung, 40132, West Java, Indonesia.
| | - Wangsa T Ismaya
- Dexa Laboratories of Biomolecular Sciences, Dexa Medica, Industri Selatan V Blok PP-7, Cikarang, 17750, West Java, Indonesia
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2
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Zhou XE, Schultz CR, Suino Powell K, Henrickson A, Lamp J, Brunzelle JS, Demeler B, Vega IE, Bachmann AS, Melcher K. Structure and Enzymatic Activity of an Intellectual Disability-Associated Ornithine Decarboxylase Variant, G84R. ACS Omega 2022; 7:34665-34675. [PMID: 36188294 PMCID: PMC9520691 DOI: 10.1021/acsomega.2c04702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/30/2022] [Indexed: 06/13/2023]
Abstract
Ornithine decarboxylase (ODC) is a rate-limiting enzyme for the synthesis of polyamines (PAs). PAs are required for proliferation, and increased ODC activity is associated with cancer and neural over-proliferation. ODC levels and activity are therefore tightly regulated, including through the ODC-specific inhibitor, antizyme AZ1. Recently, ODC G84R has been reported as a partial loss-of-function variant that is associated with intellectual disability and seizures. However, G84 is distant from both the catalytic center and the ODC homodimerization interface. To understand how G84R modulates ODC activity, we have determined the crystal structure of ODC G84R in both the presence and the absence of the cofactor pyridoxal 5-phosphate. The structures show that the replacement of G84 by arginine leads to hydrogen bond formation of R84 with F420, the last residue of the ODC C-terminal helix, a structural element that is involved in the AZ1-mediated proteasomal degradation of ODC. In contrast, the catalytic center is essentially indistinguishable from that of wildtype ODC. We therefore reanalyzed the catalytic activity of ODC G84R and found that it is rescued when the protein is purified in the presence of a reducing agent to mimic the reducing environment of the cytoplasm. This suggests that R84 may exert its neurological effects not through reducing ODC catalytic activity but through misregulation of its AZ1-mediated proteasomal degradation.
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Affiliation(s)
- X. Edward Zhou
- Department
of Structural Biology, Van Andel Institute, Grand Rapids, Michigan 49503, United States
| | - Chad R. Schultz
- Department
of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49546, United States
| | - Kelly Suino Powell
- Department
of Structural Biology, Van Andel Institute, Grand Rapids, Michigan 49503, United States
| | - Amy Henrickson
- Department
of Chemistry and Biochemistry, The University
of Lethbridge, Lethbridge, AB T1K3M4, Canada
| | - Jared Lamp
- Department
of Translational Neuroscience, Integrated Mass Spectrometry Unit,
College of Human Medicine, Michigan State
University, Grand
Rapids, Michigan 49503, United States
| | - Joseph S. Brunzelle
- Northwestern
University Synchrotron Research Center, Life Sciences Collaborative
Access Team, Northwestern University, Argonne, Illinois 60439, United States
| | - Borries Demeler
- Department
of Chemistry and Biochemistry, The University
of Lethbridge, Lethbridge, AB T1K3M4, Canada
- Department
of Chemistry and Biochemistry, The University
of Montana, Missoula, Montana 59812, United
States
| | - Irving E. Vega
- Department
of Translational Neuroscience, Integrated Mass Spectrometry Unit,
College of Human Medicine, Michigan State
University, Grand
Rapids, Michigan 49503, United States
| | - André S. Bachmann
- Department
of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49546, United States
| | - Karsten Melcher
- Department
of Structural Biology, Van Andel Institute, Grand Rapids, Michigan 49503, United States
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3
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R A, C S, A P, R K. Spectroscopic and Molecular Docking Studies of a Novel Biologically Active Heterocyclic Compound 2-Chloro-6-Methoxypyridine-4-Carboxylic Acid by Quantum Computational Method. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2102664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Arivazhagan R
- Department of Physics, Thiruvalluvar Govt. Arts College, Rasipuram, India
| | - Sridevi C
- Department of Physics, Sri Sarada College for Women (Autonomous), Salem, India
| | - Prakasam A
- Department of Physics, Thiruvalluvar Govt. Arts College, Rasipuram, India
| | - Kumar R
- Department of Physics, Banaras Hindu University, Varanasi, India
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4
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Mothersole RG, Kolesnikov M, Chan ACK, Oduro E, Murphy MEP, Wolthers KR. Sequence Divergence in the Arginase Domain of Ornithine Decarboxylase/Arginase in Fusobacteriacea Leads to Loss of Function in Oral Associated Species. Biochemistry 2022; 61:1378-1391. [PMID: 35732022 DOI: 10.1021/acs.biochem.2c00197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A number of species within the Fusobacteriaceae family of Gram-negative bacteria uniquely encode for an ornithine decarboxylase/arginase (ODA) that ostensibly channels l-ornithine generated by hydrolysis of l-arginine to putrescine formation. However, two aspartate residues required for coordination to a catalytically obligatory manganese cluster of arginases are substituted for a serine and an asparagine. Curiously, these natural substitutions occur only in a clade of Fusobacterium species that inhabit the oral cavity. Herein, we expressed and isolated full-length ODA from the opportunistic oral pathogen Fusobacterium nucleatum along with the individual arginase and ornithine decarboxylase components. The crystal structure of the arginase domain reveals that it adopts the classical α/β arginase-fold, but metal ions are absent in the active site. As expected, the ureohydrolase activity with l-arginine was not detected for wild-type ODA or the isolated arginase domain. However, engineering of the complete metal coordination environment through site-directed mutagenesis restored Mn2+ binding capacity and arginase activity, although the catalytic efficiency for l-arginine was low (60-100 M-1 s-1). Full-length ODA and the isolated ODC component were able to decarboxylate both l-ornithine and l-arginine to form putrescine and agmatine, respectively, but kcat/KM of l-ornithine was ∼20-fold higher compared to l-arginine. We discuss environmental conditions that may have led to the natural selection of an inactive arginase in the oral associated species of Fusobacterium.
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Affiliation(s)
- Robert G Mothersole
- Department of Chemistry, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna V1V 1V7, Canada
| | - Maxim Kolesnikov
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Anson C K Chan
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Emmanuella Oduro
- Department of Chemistry, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna V1V 1V7, Canada
| | - Michael E P Murphy
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Kirsten R Wolthers
- Department of Chemistry, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna V1V 1V7, Canada
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Yang YF, Lee CY, Hsieh JY, Liu YL, Lin CL, Liu GY, Hung HC. Regulation of polyamine homeostasis through an antizyme citrullination pathway. J Cell Physiol 2021; 236:5646-5663. [PMID: 33432662 DOI: 10.1002/jcp.30252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/05/2020] [Accepted: 12/18/2020] [Indexed: 11/12/2022]
Abstract
This study reveals an uncovered mechanism for the regulation of polyamine homeostasis through protein arginyl citrullination of antizyme (AZ), a natural inhibitor of ornithine decarboxylase (ODC). ODC is critical for the cellular production of polyamines. AZ binds to ODC dimers and promotes the degradation of ODC via the 26S proteasome. This study demonstrates the protein citrullination of AZ catalyzed by peptidylarginine deiminase type 4 (PAD4) both in vitro and in cells. Upon PAD4 activation, the AZ protein was citrullinated and accumulated, leading to higher levels of ODC proteins in the cell. In the PAD4-overexpressing and activating cells, the levels of ODC enzyme activity and the product putrescine increased with the level of citrullinated AZ proteins and PAD4 activity. Suppressing cellular PAD4 activity reduces the cellular levels of ODC and downregulates cellular polyamines. Furthermore, citrullination of AZ in the C-terminus attenuates AZ function in the inhibition, binding, and degradation of ODC. This paper provides evidence to illustrate that PAD4-mediated AZ citrullination upregulates cellular ODC and polyamines by retarding ODC degradation, thus interfering with the homeostasis of cellular polyamines, which may be an important pathway regulating AZ functions that is relevant to cancer biology.
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Affiliation(s)
- Yi-Fang Yang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan.,Ph.D. Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Chien-Yun Lee
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan.,Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Ju-Yi Hsieh
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Liang Liu
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan.,Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Chi-Li Lin
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Guang-Yaw Liu
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Allergy Immunology and Rheumatology, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Hui-Chih Hung
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan.,Institute of Genomics & Bioinformatics, National Chung Hsing University, Taichung, Taiwan.,iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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6
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Liu YC, Liu YL, Hsieh JY, Wang CH, Lin CL, Liu GY, Hung HC. Baicalein, 7,8-Dihydroxyflavone and Myricetin as Potent Inhibitors of Human Ornithine Decarboxylase. Nutrients 2020; 12:E3867. [PMID: 33348871 DOI: 10.3390/nu12123867] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 11/23/2022] Open
Abstract
Background: Human ornithine decarboxylase (ODC) is a well-known oncogene, and the discovery of ODC enzyme inhibitors is a beneficial strategy for cancer therapy and prevention. Methods: We examined the inhibitory effects of a variety of flavone and flavonol derivatives on ODC enzymatic activity, and performed in silico molecular docking of baicalein, 7,8-dihydroxyflavone and myricetin to the whole dimer of human ODC to investigate the possible binding site of these compounds on ODC. We also examined the cytotoxic effects of these compounds with cell-based studies. Results: Baicalein, 7,8-dihydroxyflavone and myricetin exhibited significant ODC suppression activity with IC50 values of 0.88 µM, 2.54 µM, and 7.3 µM, respectively, which were much lower than that of the active-site irreversible inhibitor α-DL-difluoromethylornithine (IC50, the half maximal inhibitory concentration, of approximately 100 µM). Kinetic studies and molecular docking simulations suggested that baicalein, and 7,8-dihydroxyflavone act as noncompetitive inhibitors that are hydrogen-bonded to the region near the active site pocket in the dimer interface of the enzyme. Baicalein and myricetin suppress cell growth and induce cellular apoptosis, and both of these compounds suppress the ODC-evoked anti-apoptosis of cells. Conclusions: Therefore, we suggest that the flavone or flavonol derivatives baicalein, 7,8-dihydroxyflavone, and myricetin are potent chemopreventive and chemotherapeutic agents that target ODC.
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7
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Banerjee S, Garrigues RJ, Chanakira MN, Negron-Olivo JJ, Odeh YH, Spuches AM, Martin Roop R, Pitzer JE, Martin DW, Dasgupta S. Investigating the roles of the conserved Cu 2+-binding residues on Brucella FtrA in producing conformational stability and functionality. J Inorg Biochem 2020; 210:111162. [PMID: 32623149 PMCID: PMC7484176 DOI: 10.1016/j.jinorgbio.2020.111162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 06/07/2020] [Accepted: 06/11/2020] [Indexed: 11/17/2022]
Abstract
Brucella is a zoonotic pathogen requiring iron for its survival and acquires this metal through the expression of several high-affinity uptake systems. Of these, the newly discovered ferrous iron transporter, FtrABCD, is proposed to take part in ferrous iron uptake. Sequence homology shows that, FtrA, the proposed periplasmic ferrous-binding component, is a P19-type protein (a periplasmic protein from C. jejuni which shows Cu2+ dependent iron affinity). Previous structural and biochemical studies on other P19 systems have established a Cu2+ dependent Mn2+ affinity as well as formation of homodimers for these systems. The Cu2+ coordinating amino acids from these proteins are conserved in Brucella FtrA, hinting towards similar properties. However, there has been no experimental evidence, till date, establishing metal affinities and the possibility of dimer formation by Brucella FtrA. Using wild-type FtrA and Cu2+-binding mutants (H65A, E67A, H118A, and H151A) we investigated the metal affinities, folding stabilities, dimer forming abilities, and the molecular basis of the Cu2+ dependence for this P19-type protein employing homology modeling, analytical gel filtration, calorimetric, and spectroscopic methods. The data reported here confirm a Cu2+-dependent, low-μM Mn2+ (Fe2+ mimic) affinity for the wild-type FtrA. In addition, our data clearly show the loss of Mn2+ affinity, and the formation of less stable protein conformations as a result of mutating these conserved Cu2+-binding residues, indicating the important roles these residues play in producing a native and functional fold of Brucella FtrA.
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Affiliation(s)
- Sambuddha Banerjee
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA.
| | - Ryan J Garrigues
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
| | - Mina N Chanakira
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | | | - Yasmene H Odeh
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | - Anne M Spuches
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | - R Martin Roop
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
| | - Joshua Edison Pitzer
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
| | - Daniel W Martin
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
| | - Saumya Dasgupta
- Department of Chemistry, Amity Institute of Applied Sciences, Amity University Kolkata, WB, 700135, India
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8
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Abstract
Polyamines are multivalent and organic cations essential for cellular growth, proliferation, differentiation, and apoptosis. Increased levels of polyamines are closely associated with numerous forms of cancer. An autoregulatory circuit composed of ornithine decarboxylase (ODC), antizyme (AZ) and antizyme inhibitor (AZI) govern the intracellular level of polyamines. Antizyme binds with ODC to inhibit ODC activity and to promote the ubiquitin‐independent degradation of ODC. Antizyme inhibitor binds to AZ with a higher affinity than ODC. Consequently, ODC is released from the ODC–AZ complex to rescue its activity. Antizyme inhibitor increases the ODC activity to accelerate the formation of intracellular polyamines, triggering gastric and breast carcinogenesis as well as hepatocellular carcinoma and esophageal squamous cell carcinoma development. Antizyme inhibitor 1 (AZIN1), a primary member of the AZI family, has aroused more attention because of its contribution to cancer. Even though its conformation is changed by adenosine‐to‐inosine (A→I) RNA editing, it plays an important role in tumorigenesis through regulating intracellular polyamines. Encouragingly, AZIN1 has been revealed to have an additional function outside the polyamine pathway so as to bypass the deficiency of targeting the polyamine biosynthetic pathway, promising to become a critical target for cancer therapy. Here, we review the latest research advances into AZIN1 and its potential contribution to carcinogenesis.
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Affiliation(s)
- Shiqiao Qiu
- Department of Immunobiology, Institute of Tissue Transplantation and Immunology, Jinan University, Guangzhou, China.,Key Laboratory of Functional Protein Research of Guangdong, Higher Education Institutes, Jinan University, Guangzhou, China
| | - Jing Liu
- Department of Stomatology, Jinan University, Guangzhou, China
| | - Feiyue Xing
- Department of Immunobiology, Institute of Tissue Transplantation and Immunology, Jinan University, Guangzhou, China.,Key Laboratory of Functional Protein Research of Guangdong, Higher Education Institutes, Jinan University, Guangzhou, China
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9
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Sivashanmugam M, J J, V U, K N S. Ornithine and its role in metabolic diseases: An appraisal. Biomed Pharmacother 2016; 86:185-194. [PMID: 27978498 DOI: 10.1016/j.biopha.2016.12.024] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/16/2016] [Accepted: 12/04/2016] [Indexed: 11/28/2022] Open
Abstract
Ornithine is a non-essential amino acid produced as an intermediate molecule in urea cycle. It is a key substrate for the synthesis of proline, polyamines and citrulline. Ornithine also plays an important role in the regulation of several metabolic processes leading to diseases like hyperorithinemia, hyperammonemia, gyrate atrophy and cancer in humans. However, the mechanism of action behind the multi-faceted roles of ornithine is yet to be unraveled completely. Several types of cancers are also characterized by excessive polyamine synthesis from ornithine by different rate limiting enzymes. Hence, in this review we aim to provide extensive insights on potential roles of ornithine in many of the disease related cellular processes and also on the structural features of ornithine interacting proteins, enabling development of therapeutic modalities.
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Affiliation(s)
- Muthukumaran Sivashanmugam
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, India; School of Chemical and Biotechnology, SASTRA University, Thanjavur, India
| | - Jaidev J
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, India
| | - Umashankar V
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, India.
| | - Sulochana K N
- R.S. Mehta Jain Department of Biochemistry and Cell Biology, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, India.
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