Structural and Functional Characterization of Arabidopsis thaliana WW Domain Containing Protein F4JC80
WW domains are the smallest known independently foldable protein structural motifs that are involved in cellular events like protein turnover, splicing, development, and tumor growth control. These motifs bind the polyproline rich ligands. While the WW domains of animal origin are well characterized, the same from plant origin are not well documented yet. Despite the small repertoire of WW proteome of plants (in comparison to animal WW proteome) functional diversity is reported to be equally vivid for plants also. Here, for the first time, we report the structural and functional properties of an Arabidopsis thaliana (At) WW domain containing protein F4JC80 by using homology modeling and docking techniques. Our findings report that the At F4JC80 protein contains two WW domains which bear the standard triple β sheet structure and structurally and functionally resemble Class I WW domains of E3 ubiquitin ligase family but their structural differences impact their polypeptide binding abilities differently.
KeywordsWW domain Arabidopsis thaliana Transcription Splicing Homology modeling Molecular docking
The authors would like to thank the members of RD and AB laboratory for their continuous support and critical assessments. AD and SB would like to thank CSIR (India) and UGC (India), respectively, for their Ph.D. fellowships.
Author Contributions AD and SB have performed the modeling and docking studies and drafted the manuscript. RD and AB have analyzed the results and prepared the final version of the manuscript. All the authors have read and approved the final version of the manuscript.
- 1.Salah Z, Alian A, Aqeilan RI (2012) WW domain-containing proteins: retrospectives and the future. Front Biosci (Landmark Ed) 17:331–348. doi:http://dx.doi.org/10.2741/3930
- 2.Sudol M (1996) Structure and function of the WW domain. Prog Biophys Mol Biol 65:113–32. doi:http://dx.doi.org/10.1016/S0079-6107(96)00008-9
- 3.Mouchantaf R, Azakir BA, McPherson PS, Millard SM, Wood SA, Angers A (2006) The ubiquitin ligase itch is auto-ubiquitylated in vivo and in vitro but is protected from degradation by interacting with the deubiquitylating enzyme FAM/USP9X. J Biol Chem 281:38738–38747. doi:http://dx.doi.org/10.1074/jbc.M605959200
- 7.Kato Y, Miyakawa T, Kurita J, Tanokura M (2006) Structure of FBP11 WW1-PL ligand complex reveals the mechanism of proline-rich ligand recognition by group II/III WW domains. J Biol Chem 281:40321–40329. doi:http://dx.doi.org/10.1074/jbc.M609321200
- 8.Lippens G, Landrieu I, Smet C (2007) Molecular mechanisms of the phospho-dependent prolyl cis/trans isomerase Pin1. FEBS J 274:5211–5222. doi:http://dx.doi.org/10.1111/j.1742-4658.2007.06057.x
- 9.Qin J, Barajas D, Nagy PD (2012) An inhibitory function of WW domain-containing host proteins in RNA virus replication. Virology 426:106–119. doi:http://dx.doi.org/10.1016/j.virol.2012.01.020
- 10.Wu R, Li S, He S, Wassmann F, Yu C, Qin G et al. (2011) CFL1, a WW domain protein, regulates cuticle development by modulating the function of HDG1, a class IV homeodomain transcription factor, in rice and Arabidopsis. Plant Cell 23:3392–3411. doi:http://dx.doi.org/10.1105/tpc.111.088625
- 12.Hong F, Attia K, Wei C, Li K, He G, Su W et al (2007) Overexpression of the rFCA RNA recognition motif affects morphologies modifications in rice (Oryza sativa L.). Biosci Rep 27:225–234. doi:http://dx.doi.org/10.1007/s10540-007-9047-y
- 14.Landrieu I, Wieruszeski JM, Wintjens R, Inzé D, Lippens G (2002) Solution structure of the single-domain prolyl cis/trans isomerase PIN1At from Arabidopsis thaliana. J Mol Biol 320:321–332. doi:http://dx.doi.org/10.1016/S0022-2836(02)00429-1
- 15.Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C et al (2012) The Pfam protein families database. Nucleic Acids Res (database issue) 40:D290–D301. doi:http://dx.doi.org/10.1093/nar/gkr1065
- 16.Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H et al. (2011) ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res (database issue) 39:D465–474. doi:http://dx.doi.org/10.1093/nar/gkq1091
- 17.Lüthy R, Bowie JU, Eisenberg D (1992) Assessment of protein models with three-dimensional profiles. Nature 356:83–85. doi:http://dx.doi.org/10.1038/356083a0
- 18.Bowie JU, Lüthy R, Eisenberg D (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science 253:164–170. doi:http://dx.doi.org/10.1126/science.1853201
- 19.Colovos C, Yeates TO (1993) Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 2:1511–1519. doi:http://dx.doi.org/10.1002/pro.5560020916
- 20.Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35:W407–410. doi:http://dx.doi.org/10.1093/nar/gkm290
- 21.Holm L, Rosenström P (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res 38:W545–549. doi:http://dx.doi.org/10.1093/nar/gkq366
- 22.Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 4:187–217. http://dx.doi.org/10.1002/jcc.540040211
- 23.Pierce BG, Hourai Y, Weng Z (2011) Accelerating protein docking in ZDOCK using an advanced 3D convolution library. PLoS One 6(9):e24657. doi:http://dx.doi.org/10.1371/journal.pone.0024657
- 25.Nguyen, BAN, Pogoutse A, Provart N, Moses AM (2009) NLStradamus: a simple Hidden Markov model for nuclear localization signal prediction. BMC Bioinformatics 10(1):202. doi:http://dx.doi.org/10.1186/1471-2105-10-202