Bioinformatic identification of novel protein phosphatases in the dog genome.
Protein kinases and protein phosphatases constitute about 2-4% of the genes in a typical eukaryotic genome. Protein phosphatases are important players in many cellular processes such as proliferation, differentiation, cell adhesion, and motility. In this study, we identified, classified, and analyzed protein phosphatase complement of the dog genome. In this article, we report the identification of at least 178 putative protein phosphatases in dog which include 51 PSTPs, 112 PTPs, and 15 Asp-based protein phosphatases. Interestingly, we found at least five novel protein phosphatases in dog, namely DUSP5L, DUSP18L, MTMR9L, MTMR12L, and PPP6CL which are not present in human, mouse, rat, and cow. In addition, we found PTP4A1-rt, a retro-transposed copy of the PTP4A1 gene, in chromosome 27. Furthermore, we modeled three-dimensional structures of the catalytic domains of these putative protein phosphatases and aligned them to see the structural similarities between them. We docked PPP2CA with okadaic acid and calculated the value of affinity energy as -8.8 kcal/mol. Our nucleotide substitution rate study revealed that apparently none of the phosphatase family is under significantly higher evolutionary pressure.
Biomedical Research Center for Signal Transduction Networks, Department of Chemistry, Inha University, Incheon 402-751, Korea.
Mrigendra B
MB
Karmacharya
Jae-Won
JW
Soh
D000818:Animals; D019295:Computational Biology; D004285:Dogs; D016678:Genome; D008958:Models, Molecular; D016366:Open Reading Frames; D010749:Phosphoprotein Phosphatases / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D013347:Subcellular Fractions / Q000201:enzymology
D010749:Phosphoprotein Phosphatases
Cell Mol Life Sci. 2005 Sep;62(18):2092-9
16132230
Nat Rev Mol Cell Biol. 2006 Nov;7(11):833-46
17057753
J Immunol. 2006 Dec 1;177(11):7497-504
17114416
Nucleic Acids Res. 2009 Jan;37(Database issue):D205-10
18984618
Curr Opin Pharmacol. 2002 Aug;2(4):458-62
12127881
Nucleic Acids Res. 2009 Jan;37(Database issue):D229-32
18978020
Am J Hum Genet. 1997 Sep;61(3):475-80
9326310
Bioinformatics. 2001 Apr;17(4):377-8
11301311
Nucleic Acids Res. 2007 Jan;35(Database issue):D237-40
17135202
Plant Physiol. 2008 Feb;146(2):351-67
18156295
Bioinformatics. 2006 Jul 15;22(14):e530-8
16873517
Nat Rev Drug Discov. 2002 Dec;1(12):961-76
12461518
Curr Opin Cell Biol. 2005 Apr;17(2):197-202
15780597
Science. 2002 Dec 6;298(5600):1912-34
12471243
J Vet Intern Med. 2000 Jan-Feb;14(1):1-9
10668810
Bioinformatics. 2007 Nov 1;23(21):2947-8
17846036
Bioinformatics. 2009 Jun 1;25(11):1451-2
19346325
Nat Rev Mol Cell Biol. 2007 Mar;8(3):234-44
17318227
Nat Protoc. 2007;2(4):953-71
17446895
Nat Rev Cancer. 2006 Apr;6(4):307-20
16557282
Biochem J. 2009 Jan 15;417(2):401-9
19099538
Cell. 2006 Oct 20;127(2):341-53
17055435
J Comput Chem. 2010 Jan 30;31(2):455-61
19499576
Cytogenet Cell Genet. 2001;95(1-2):60-3
11978971
J Bioinform Comput Biol. 2006 Feb;4(1):1-18
16568539
Protein Eng. 1998 Sep;11(9):739-47
9796821
Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31
18940867
Nucleic Acids Res. 2007 Jan;35(Database issue):D668-73
17142222
BMC Bioinformatics. 2005 Dec 01;6 Suppl 4:S20
16351747
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W407-10
17517781
Nucleic Acids Res. 2008 Jan;36(Database issue):D281-8
18039703
Trends Biochem Sci. 2000 Dec;25(12):596-601
11116185
Nucleic Acids Res. 2009 Jan;37(Database issue):D169-74
18836194
Bioinformatics. 1998;14(9):755-63
9918945
Genome Res. 2002 Apr;12(4):656-64
11932250
Brief Bioinform. 2004 Dec;5(4):378-88
15606974
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
9254694
Bioinformatics. 2006 Jul 15;22(14):e408-16
16873501
Curr Opin Chem Biol. 2001 Aug;5(4):416-23
11470605
Biochim Biophys Acta. 1999 Oct 12;1434(2):275-83
10525146
J Struct Funct Genomics. 2007 Sep;8(2-3):121-40
18058037