GPS-ARM: Computational analysis of the APC/C recognition motif by predicting D-boxes and KEN-boxes

PLoS ONE

Volumn 7, Issue 3, 2012, Pages

  Liu, Zexian ^a,b   Yuan, Fang ^a   Ren, Jian ^c   Cao, Jun ^a   Zhou, Yanhong ^a   Yang, Qing ^a   Xue, Yu ^a  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^c SUN YAT SEN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ANAPHASE PROMOTING COMPLEX; CELL CYCLE PROTEIN; D BOX PROTEIN; KEN BOX PROTEIN; UNCLASSIFIED DRUG; ANAPHASE-PROMOTING COMPLEX; PROTEIN; UBIQUITIN PROTEIN LIGASE;

ALGORITHM; ARTICLE; COMPUTER ANALYSIS; CONTROLLED STUDY; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; ENZYME SUBSTRATE; MATHEMATICAL MODEL; MITOSIS; MOLECULAR RECOGNITION; PERFORMANCE MEASUREMENT SYSTEM; PREDICTIVE VALUE; PROTEIN DETERMINATION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; SYSTEM ANALYSIS; ANIMAL; BIOLOGICAL MODEL; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; ENZYME SPECIFICITY; HUMAN; METABOLISM; METHODOLOGY; PROTEIN BINDING; PROTEOMICS;

HOMO SAPIENS;

ALGORITHMS; AMINO ACID MOTIFS; ANIMALS; COMPUTER SIMULATION; HUMANS; MODELS, BIOLOGICAL; PROTEIN BINDING; PROTEINS; PROTEOMICS; SOFTWARE; SUBSTRATE SPECIFICITY; UBIQUITIN-PROTEIN LIGASE COMPLEXES;

EID: 84859078891     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0034370     Document Type: Article

References (36)

1. (2001) Milestones in cell division. Nat Cell Biol 3: E265.
2. Nasmyth K, (2001) A prize for proliferation. Cell 107: 689-701.
3. Barford D, (2011) Structure, function and mechanism of the anaphase promoting complex (APC/C). Q Rev Biophys 44: 153-190.
4. Thornton BR, Toczyski DP, (2006) Precise destruction: an emerging picture of the APC. Genes Dev 20: 3069-3078.
5. Peters JM, (2006) The anaphase promoting complex/cyclosome: a machine designed to destroy. Nat Rev Mol Cell Biol 7: 644-656.
6. Fang G, Yu H, Kirschner MW, (1999) Control of mitotic transitions by the anaphase-promoting complex. Philos Trans R Soc Lond B Biol Sci 354: 1583-1590.
7. Pagano M, (1997) Cell cycle regulation by the ubiquitin pathway. FASEB J 11: 1067-1075.
8. Peters JM, (1998) SCF and APC: the Yin and Yang of cell cycle regulated proteolysis. Curr Opin Cell Biol 10: 759-768.
9. Sudakin V, Ganoth D, Dahan A, Heller H, Hershko J, et al. (1995) The cyclosome, a large complex containing cyclin-selective ubiquitin ligase activity, targets cyclins for destruction at the end of mitosis. Mol Biol Cell 6: 185-197.
10. Liot C, Seguin L, Siret A, Crouin C, Schmidt S, et al. (2011) APC Mediates Degradation of the Oncogenic Rho-GEF Ect2 after Mitosis. PLoS One 6: e23676.
11. Naoe H, Araki K, Nagano O, Kobayashi Y, Ishizawa J, et al. (2010) The anaphase-promoting complex/cyclosome activator Cdh1 modulates Rho GTPase by targeting p190 RhoGAP for degradation. Mol Cell Biol 30: 3994-4005.
12. Kim AH, Bonni A, (2007) Thinking within the D box: initial identification of Cdh1-APC substrates in the nervous system. Mol Cell Neurosci 34: 281-287.
13. Silies M, Klambt C, (2010) APC/C(Fzr/Cdh1)-dependent regulation of cell adhesion controls glial migration in the Drosophila PNS. Nat Neurosci 13: 1357-1364.
14. Tudzarova S, Colombo SL, Stoeber K, Carcamo S, Williams GH, et al. (2011) Two ubiquitin ligases, APC/C-Cdh1 and SKP1-CUL1-F (SCF)-beta-TrCP, sequentially regulate glycolysis during the cell cycle. Proc Natl Acad Sci U S A 108: 5278-5283.
15. Colombo SL, Palacios-Callender M, Frakich N, De Leon J, Schmitt CA, et al. (2010) Anaphase-promoting complex/cyclosome-Cdh1 coordinates glycolysis and glutaminolysis with transition to S phase in human T lymphocytes. Proc Natl Acad Sci U S A 107: 18868-18873.
16. Glotzer M, Murray AW, Kirschner MW, (1991) Cyclin is degraded by the ubiquitin pathway. Nature 349: 132-138.
17. Owens TJ, Hoyt MA, (2005) The D box asserts itself. Mol Cell 18: 611-612.
18. King RW, Glotzer M, Kirschner MW, (1996) Mutagenic analysis of the destruction signal of mitotic cyclins and structural characterization of ubiquitinated intermediates. Mol Biol Cell 7: 1343-1357.
19. Fang G, Yu H, Kirschner MW, (1998) Direct binding of CDC20 protein family members activates the anaphase-promoting complex in mitosis and G1. Mol Cell 2: 163-171.
20. da Fonseca PC, Kong EH, Zhang Z, Schreiber A, Williams MA, et al. (2011) Structures of APC/C(Cdh1) with substrates identify Cdh1 and Apc10 as the D-box co-receptor. Nature 470: 274-278.
21. Gurden MD, Holland AJ, van Zon W, Tighe A, Vergnolle MA, et al. (2010) Cdc20 is required for the post-anaphase, KEN-dependent degradation of centromere protein F. J Cell Sci 123: 321-330.
22. Pfleger CM, Kirschner MW, (2000) The KEN box: an APC recognition signal distinct from the D box targeted by Cdh1. Genes Dev 14: 655-665.
23. Nguyen HG, Chinnappan D, Urano T, Ravid K, (2005) Mechanism of Aurora-B degradation and its dependency on intact KEN and A-boxes: identification of an aneuploidy-promoting property. Mol Cell Biol 25: 4977-4992.
24. Castro A, Vigneron S, Bernis C, Labbe JC, Lorca T, (2003) Xkid is degraded in a D-box, KEN-box, and A-box-independent pathway. Mol Cell Biol 23: 4126-4138.
25. Reis A, Levasseur M, Chang HY, Elliott DJ, Jones KT, (2006) The CRY box: a second APCcdh1-dependent degron in mammalian cdc20. EMBO Rep 7: 1040-1045.
26. Pfleger CM, Lee E, Kirschner MW, (2001) Substrate recognition by the Cdc20 and Cdh1 components of the anaphase-promoting complex. Genes Dev 15: 2396-2407.
27. Davey NE, Haslam NJ, Shields DC, Edwards RJ, (2011) SLiMSearch 2.0: biological context for short linear motifs in proteins. Nucleic Acids Res 39: W56-60.
28. Michael S, Trave G, Ramu C, Chica C, Gibson TJ, (2008) Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation. Bioinformatics 24: 453-457.
29. Liu Z, Ma Q, Cao J, Gao X, Ren J, et al. (2011) GPS-PUP: computational prediction of pupylation sites in prokaryotic proteins. Mol Biosyst 7: 2737-2740.
30. Dinkel H, Michael S, Weatheritt RJ, Davey NE, Van Roey K, et al. (2012) ELM-the database of eukaryotic linear motifs. Nucleic Acids Res 40: D242-251.
31. Schuster-Bockler B, Schultz J, Rahmann S, (2004) HMM Logos for visualization of protein families. BMC Bioinformatics 5: 7.
32. Liu Z, Cao J, Ma Q, Gao X, Ren J, et al. (2011) GPS-YNO2: computational prediction of tyrosine nitration sites in proteins. Mol Biosyst 7: 1197-1204.
33. Kurasawa Y, Todokoro K, (1999) Identification of human APC10/Doc1 as a subunit of anaphase promoting complex. Oncogene 18: 5131-5137.
34. Kallio MJ, Beardmore VA, Weinstein J, Gorbsky GJ, (2002) Rapid microtubule-independent dynamics of Cdc20 at kinetochores and centrosomes in mammalian cells. J Cell Biol 158: 841-847.
35. Zhou Y, Ching YP, Chun AC, Jin DY, (2003) Nuclear localization of the cell cycle regulator CDH1 and its regulation by phosphorylation. J Biol Chem 278: 12530-12536.
36. Ren J, Liu Z, Gao X, Jin C, Ye M, et al. (2010) MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore. Nucleic Acids Res 38: D155-160.