Generic placeholder image

Current Proteomics


ISSN (Print): 1570-1646
ISSN (Online): 1875-6247

Research Article

Computational Analysis of Therapeutic Enzyme Uricase from Different Source Organisms

Author(s): Anand Kumar Nelapati and JagadeeshBabu PonnanEttiyappan*

Volume 17, Issue 1, 2020

Page: [59 - 77] Pages: 19

DOI: 10.2174/1570164616666190617165107

Price: $65


Background: Hyperuricemia and gout are the conditions, which is a response of accumulation of uric acid in the blood and urine. Uric acid is the product of purine metabolic pathway in humans. Uricase is a therapeutic enzyme that can enzymatically reduces the concentration of uric acid in serum and urine into more a soluble allantoin. Uricases are widely available in several sources like bacteria, fungi, yeast, plants and animals.

Objective: The present study is aimed at elucidating the structure and physiochemical properties of uricase by insilico analysis.

Methods: A total number of sixty amino acid sequences of uricase belongs to different sources were obtained from NCBI and different analysis like Multiple Sequence Alignment (MSA), homology search, phylogenetic relation, motif search, domain architecture and physiochemical properties including pI, EC, Ai, Ii, and were performed.

Results: Multiple sequence alignment of all the selected protein sequences has exhibited distinct difference between bacterial, fungal, plant and animal sources based on the position-specific existence of conserved amino acid residues. The maximum homology of all the selected protein sequences is between 51-388. In singular category, homology is between 16-337 for bacterial uricase, 14-339 for fungal uricase, 12-317 for plants uricase, and 37-361 for animals uricase. The phylogenetic tree constructed based on the amino acid sequences disclosed clusters indicating that uricase is from different source. The physiochemical features revealed that the uricase amino acid residues are in between 300- 338 with a molecular weight as 33-39kDa and theoretical pI ranging from 4.95-8.88. The amino acid composition results showed that valine amino acid has a high average frequency of 8.79 percentage compared to different amino acids in all analyzed species.

Conclusion: In the area of bioinformatics field, this work might be informative and a stepping-stone to other researchers to get an idea about the physicochemical features, evolutionary history and structural motifs of uricase that can be widely used in biotechnological and pharmaceutical industries. Therefore, the proposed in silico analysis can be considered for protein engineering work, as well as for gout therapy.

Keywords: Uricase, homology, MSA, phylogenetic tree, motifs, domains, physicochemical properties.

Graphical Abstract
El Ridi, R.; Tallima, H. Physiological functions and pathogenic potential of uric acid: a review. J. Adv. Res., 2017, 8(5), 487-493.
[] [PMID: 28748115]
Yang, X.; Yuan, Y.; Zhan, C.G.; Liao, F. Uricases as therapeutic agents to treat refractory gout: current states and future directions. Drug Dev. Res., 2012, 73(2), 66-72.
[] [PMID: 22665944]
Kang, D-H.; Chen, W. Uric acid and chronic kidney disease: new understanding of an old problem. Semin. Nephrol., 2011, 31(5), 447-452.
[] [PMID: 22000652]
Sharaf-El-Din, U.A.A.; Salem, M.M.; Abdulazim, D.O.; Abdulazim, D.O. Uric acid in the pathogenesis of metabolic, renal, and cardiovascular diseases: a review. J. Adv. Res., 2017, 8(5), 537-548.
[] [PMID: 28748119]
Sherman, M.R.; Saifer, M.G.P.; Perez-Ruiz, F. PEG-uricase in the management of treatment-resistant gout and hyperuricemia. Adv. Drug Deliv. Rev., 2008, 60(1), 59-68.
[] [PMID: 17826865]
Khade, S.; Srivastava, S.K. Uricase and its clinical applications. Int. J. Biol. Med. Res., 2015, 6, 5211-5215.
Colloc’h, N.; Prangé, T. Functional relevance of the internal hydrophobic cavity of urate oxidase. FEBS Lett., 2014, 588(9), 1715-1719.
[] [PMID: 24657440]
Kahn, K.; Serfozo, P.; Tipton, P.A. Identification of the true product of the urate oxidase reaction. J. Am. Chem. Soc., 1997, 119, 5435-5442.
Bongaerts, G.P.; Uitzetter, J.; Brouns, R.; Vogels, G.D. Uricase of Bacillus fastidiosus. Properties and regulation of synthesis. Biochim. Biophys. Acta, 1978, 527(2), 348-358.
[] [PMID: 728443]
Motojima, K.; Kanaya, S.; Goto, S. Cloning and sequence analysis of cDNA for rat liver uricase. J. Biol. Chem., 1988, 263(32), 16677-16681.
[PMID: 3182808]
Nanda, P.; Babu, P.E. Isolation, screening and production studies of uricase producing bacteria from poultry sources. Prep. Biochem. Biotechnol., 2014, 44(8), 811-821.
[] [PMID: 24279683]
Chen, Z.; Wang, Z.; He, X.; Guo, X.; Li, W.; Zhang, B. Uricase production by a recombinant Hansenula polymorpha strain harboring Candida utilis uricase gene. Appl. Microbiol. Biotechnol., 2008, 79(4), 545-554.
[] [PMID: 18437374]
Yazdi, M.T.; Zarrini, G.; Mohit, E.; Faramarzi, M.A.; Setayesh, N.; Sedighi, N.; Mohseni, F.A. Mucor hiemalis: a new source for uricase production. World J. Microbiol. Biotechnol., 2006, 22, 325-330.
Ishikawa, J.; Yamashita, A.; Mikami, Y.; Hoshino, Y.; Kurita, H.; Hotta, K.; Shiba, T.; Hattori, M. The complete genomic sequence of Nocardia farcinica IFM 10152. Proc. Natl. Acad. Sci. USA, 2004, 101(41), 14925-14930.
[] [PMID: 15466710]
Tanaka, A.; Yamamura, M.; Kawamoto, S.; Fukui, S. Production of uricase by Candida tropicalis using n-alkane as a substrate. Appl. Environ. Microbiol., 1977, 34(4), 342-346.
[PMID: 200173]
Zhou, X.L.; Ma, X.H.; Sun, G.Q.; Li, X.; Guo, K.P. Isolation of a thermostable uricase-producing bacterium and study on its enzyme production conditions. Process Biochem., 2005, 40, 3749-3753.
Liu, J.; Li, G.; Liu, H.; Zhou, X. Purification and properties of uricase from Candida sp. and its application in uric acid analysis in serum. Appl. Biochem. Biotechnol., 1994, 47(1), 57-63.
[] [PMID: 8203871]
Shaaban, M.I.; Abdelmegeed, E.; Ali, Y.M. Cloning, expression, and purification of recombinant uricase enzyme from pseudomonas aeruginosa Ps43 using Escherichia coli. J. Microbiol. Biotechnol., 2015, 25(6), 887-892.
[] [PMID: 25588559]
Rainbird, R.M.; Atkins, C.A. Purification and some properties of urate oxidase from nitrogen-fixing nodules of cowpea. Biochim. Biophys. Acta, 1981, 659(1), 132-140.
[] [PMID: 7248313]
Lucas, K.; Boland, M.J.; Schubert, K.R. Uricase from soybean root nodules: purification, properties, and comparison with the enzyme from cowpea. Arch. Biochem. Biophys., 1983, 226(1), 190-197.
[] [PMID: 6685457]
Bergmann, H.; Preddie, E.; Verma, D.P. Nodulin-35: a subunit of specific uricase (uricase II) induced and localized in the uninfected cells of soybean nodules. EMBO J., 1983, 2(12), 2333-2339.
[] [PMID: 16453488]
Sanchez, F.; Campos, F.; Padilla, J.; Bonneville, J.; Enriquez, C.; Caput, D. Purification, CDNA cloning, and developmental expression of the nodule-specific uricase from Phaseolus vulgaris L. Plant Physiol., 1987, 1, 1143-1147.
[] [PMID: 16665575]
Montalbini, P.; Redondo, J.; Caballero, J.L.; Cárdenas, J.; Pineda, M. Uricase from leaves: its purification and characterization from three different higher plants. Planta, 1997, 202, 277-283.
Adámek, V.; Králová, B.; Süchová, M.; Valentová, O.; Demnerová, K. Purification of microbial uricase. J. Chromatogr. A, 1989, 497, 268-275.
[] [PMID: 2625463]
Schiavon, O.; Caliceti, P.; Ferruti, P.; Veronese, F.M. Therapeutic proteins: a comparison of chemical and biological properties of uricase conjugated to linear or branched poly(ethylene glycol) and poly(N-acryloylmorpholine). Farmaco, 2000, 55(4), 264-269.
[] [PMID: 10966157]
Dabbagh, F.; Moradpour, Z.; Ghasemian, A.; Ghasemi, Y. Phylogeny of urate oxidase producing bacteria on the basis of gene sequences of 16S RRNA and uricase protein. Iran. J. Pharm. Sci., 2012, 8, 99-102.
Keebaugh, A.C.; Thomas, J.W. The evolutionary fate of the genes encoding the purine catabolic enzymes in hominoids, birds, and reptiles. Mol. Biol. Evol., 2010, 27(6), 1359-1369.
[] [PMID: 20106906]
Oda, M.; Satta, Y.; Takenaka, O.; Takahata, N. Loss of urate oxidase activity in hominoids and its evolutionary implications. Mol. Biol. Evol., 2002, 19(5), 640-653.
[] [PMID: 11961098]
Kahn, K.; Tipton, P.A. Kinetic mechanism and cofactor content of soybean root nodule urate oxidase. Biochemistry, 1997, 36(16), 4731-4738.
[] [PMID: 9125493]
Imhoff, R.D.; Power, N.P.; Borrok, M.J.; Tipton, P.A. General base catalysis in the urate oxidase reaction: evidence for a novel Thr - Lys catalytic diad. Biochemistry, 2003, 4094-4100.
[] [PMID: 12680763]
Arslan, F. An amperometric biosensor for uric acid determination prepared from uricase immobilized in polyaniline-polypyrrole film. Sensors (Basel), 2008, 8(9), 5492-5500.
[] [PMID: 27873826]
Nakagawa, S.; Oda, H.; Anazawa, H. High cell density cultivation and high recombinant protein production of Escherichia coli strain expressing uricase. Biosci. Biotechnol. Biochem., 1995, 59(12), 2263-2267.
[] [PMID: 8611749]
Colloc’h, N.; el Hajji, M.; Bachet, B.; L’Hermite, G.; Schiltz, M.; Prangé, T.; Castro, B.; Mornon, J.P. Crystal structure of the protein drug urate oxidase-inhibitor complex at 2.05 a resolution. Nat. Struct. Biol., 1997, 4(11), 947-952.
[] [PMID: 9360612]
Nyborg, A.C.; Ward, C.; Zacco, A.; Chacko, B.; Grinberg, L.; Geoghegan, J.C.; Bean, R.; Wendeler, M.; Bartnik, F.; O’Connor, E.; Gruia, F.; Iyer, V.; Feng, H.; Roy, V.; Berge, M.; Miner, J.N.; Wilson, D.M.; Zhou, D.; Nicholson, S.; Wilker, C.; Wu, C.Y.; Wilson, S.; Jermutus, L.; Wu, H.; Owen, D.A.; Osbourn, J.; Coats, S.; Baca, M. A therapeutic uricase with reduced immunogenicity risk and improved development properties. PLoS One, 2016, 11(12)e0167935
[] [PMID: 28002433]
Nanda, P.; Jagadeeshbabu, P.E.; Fernandes, J.; Hazarika, P.; Dhabre, R. Studies on production, optimization and purification of uricase from Gliocladium viride. Res. Biotechnol., 2012, 3, 35-46.
Garay, R.P.; El-Gewely, M.R.; Labaune, J-P.; Richette, P. Therapeutic perspectives on uricases for gout. Joint Bone Spine, 2012, 79(3), 237-242.
[] [PMID: 22366146]
Apweiler, R.; Bairoch, A.; Wu, C.H.; Barker, W.C.; Boeckmann, B.; Ferro, S.; Gasteiger, E.; Huang, H.; Lopez, R.; Magrane, M.; Martin, M.J.; Natale, D.A.; O’Donovan, C.; Redaschi, N.; Yeh, L-S.L. UniProt: the universal protein knowledgebase. Nucleic Acids Res., 2004, 32(Database issue), D115-D119.
[] [PMID: 14681372]
Artimo, P.; Jonnalagedda, M.; Arnold, K.; Baratin, D.; Csardi, G.; de Castro, E.; Duvaud, S.; Flegel, V.; Fortier, A.; Gasteiger, E.; Grosdidier, A.; Hernandez, C.; Ioannidis, V.; Kuznetsov, D.; Liechti, R.; Moretti, S.; Mostaguir, K.; Redaschi, N.; Rossier, G.; Xenarios, I.; Stockinger, H. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res., 2012, 40(Web Server issue), W597-603.
[PMID: 22661580]
Kumar, S.; Stecher, G.; Tamura, K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol., 2016, 33(7), 1870-1874.
[] [PMID: 27004904]
Larkin, M.A.; Blackshields, G.; Brown, N.P.; Chenna, R.; McGettigan, P.A.; McWilliam, H.; Valentin, F.; Wallace, I.M.; Wilm, A.; Lopez, R.; Thompson, J.D.; Gibson, T.J.; Higgins, D.G.; Clustal, W.; Clustal, X. Version 2.0. Bioinformatics, 2007, 23(21), 2947-2948.
[] [PMID: 17846036]
Saitou, N.; Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 1987, 4(4), 406-425.
[PMID: 3447015]
Bailey, T.L.; Boden, M.; Buske, F.A.; Frith, M.; Grant, C.E.; Clementi, L.; Ren, J.; Li, W.W.; Noble, W.S. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res., 2009, 37(Web Server issue), W202-208.
[] [PMID: 19458158]
Bailey, T.L.; Gribskov, M. Combining evidence using p-values: application to sequence homology searches. Bioinformatics, 1998, 14(1), 48-54.
[] [PMID: 9520501]
Gasteiger, E.; Hoogland, C.; Gattiker, A.; Duvaud, S.; Wilkins, M.R.; Appel, R.D.; Bairoch, A. Protein identification and analysis tools on the expasy server; Proteomics Proto. Handbook, 2005, pp. 571-607.
Bjellqvist, B.; Hughes, G.J.; Pasquali, C.; Paquet, N.; Ravier, F.; Sanchez, J.C.; Frutiger, S.; Hochstrasser, D. The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis, 1993, 14(10), 1023-1031.
[] [PMID: 8125050]
Bjellqvist, B.; Basse, B.; Olsen, E.; Celis, J.E. Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis, 1994, 15(3-4), 529-539.
[] [PMID: 8055880]
Vivek, D.D.; Sharma, T.; Pandey, A.; Kumar, S. Insights to sequence information of alpha amylase enzyme from different source organisms. Int. J. Adv. Biotechnol. Bioinforma., 2012, 1, 87-91.
Mathew, A.; Verma, A.; Gaur, S. An in-silico insight into the characteristics of β-propeller phytase. Interdiscip. Sci., 2014, 6(2), 133-139.
[] [PMID: 25172451]
Bose, R.; Arora, S.; Dwivedi, V.D.; Pandey, A. Amino acid sequence based in silico analysis of β- Galactosidases. Int. J. Bioinforma. Biosci., 2013, 3, 37-44.
Alméciga-Díaz, C.J.; Gutierrez, Á.M.; Bahamon, I.; Rodríguez, A.; Rodríguez, M.A.; Sánchez, O.F. Computational analysis of the fructosyltransferase enzymes in plants, fungi and bacteria. Gene, 2011, 484(1-2), 26-34.
[] [PMID: 21679751]
Irajie, C.; Mohkam, M.; Nezafat, N.; Hosseinzadeh, S.; Aminlari, M.; Ghasemi, Y. In silico analysis of glutaminase from different species of Escherichia and Bacillus. Iran. J. Med. Sci., 2016, 41(5), 406-414.
[PMID: 27582590]
Kumar, V. Singh, G.; Verma, A.K.; Agrawal, S. In Silico characterization of histidine acid phytase sequences. Enzyme Res, 2012, 2012
Dwivedi, V.D.; Mishra, S.K. In silico analysis of L-asparaginase from different source organisms. Interdiscip. Sci., 2014, 6(2), 93-99.
[] [PMID: 25172447]
Yadav, M.; Yadav, S.; Yadav, D.; Yadav, K. In- Silico analysis of manganese peroxidases from different fungal sources. Curr. Proteomics, 2017, 14, 201-213.
Verma, A.; Singh, V.K.; Gaur, S. Computational based functional analysis of Bacillus phytases. Comput. Biol. Chem., 2016, 60, 53-58.
[] [PMID: 26672917]
Morya, V.K.; Yadav, S.; Kim, E.K.; Yadav, D. In silico characterization of alkaline proteases from different species of Aspergillus. Appl. Biochem. Biotechnol., 2012, 166(1), 243-257.
[] [PMID: 22072140]
Rahmatabadi, S.S.; Sadeghian, I.; Nezafat, N.; Negahdaripour, M.; Hajighahramani, N.; Hemmati, S.; Ghasemi, Y. In Silico investigation of Pullulanase enzymes from various Bacillus species. Curr. Proteomics, 2017, 14, 175-185.
Yadav, P.K.; Singh, V.K.; Yadav, S.; Yadav, K.D.S.; Yadav, D. In silico analysis of pectin lyase and pectinase sequences. Biochemistry (Mosc.), 2009, 74(9), 1049-1055.
[] [PMID: 19916917]
Dubey, A.K.; Yadav, S.; Kumar, M.; Singh, V.K.; Sarangi, B.K.; Yadav, D. In silico characterization of pectate lyase protein sequences from different source organisms. Enzyme Res., 2010. 2010950230
[] [PMID: 21048874]
Malviya, N.; Srivastava, M.; Diwakar, S.K.; Mishra, S.K. Insights to sequence information of polyphenol oxidase enzyme from different source organisms. Appl. Biochem. Biotechnol., 2011, 165(2), 397-405.
[] [PMID: 21523355]
Dwivedi, V.D.; Arora, S.; Kumar, A.; Mishra, S.K. Computational analysis of xanthine dehydrogenase enzyme from different source organisms. Netw. Model. Anal. Health Inform. Bioinform., 2013, 2, 185-189.
Morya, V.K.; Yadav, V.K.; Yadav, S.; Yadav, D. Active site characterization of proteases sequences from different species of aspergillus. Cell Biochem. Biophys., 2016, 74(3), 327-335.
[] [PMID: 27358183]
Ramya, L.N.; Pulicherla, K.K. Molecular insights into cold active polygalacturonase enzyme for its potential application in food processing. J. Food Sci. Technol., 2015, 52(9), 5484-5496.
[] [PMID: 26344963]
Ikai, A. Thermostability and aliphatic index of globular proteins. J. Biochem., 1980, 88(6), 1895-1898.
[PMID: 7462208]
Rawlings, N.D.; Morton, F.R.; Kok, C.Y.; Kong, J.; Barrett, A.J. MEROPS: the peptidase database. Nucleic Acids Res., 2008, 36(Database issue), D320-D325.
[PMID: 17991683]

Rights & Permissions Print Export Cite as
© 2022 Bentham Science Publishers | Privacy Policy