Structural Insight into Anaphase Promoting Complex 3 Structure and Docking with a Natural Inhibitory Compound

Document Type : Original Article


1 Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran

2 National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, Iran

3 Department of Life Sciences, Barcelona Supercomputing Center, Barcelona, Spain; Department of Bioinformatics, Institute of Biophysics and Biochemistry, University of Tehran, Tehran, Iran

4 Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran


Background: Anaphase promoting complex (APC) is the biggest Cullin-RING E3 ligase and is very important in cell cycle control; many anti-cancer agents target this. APC controls the onset of chromosome separation and mitotic exit through securin and cyclin B degradation, respectively. Its APC3 subunit identifies the APC activators-Cdh1 and Cdc20. Materials and Methods: The structural model of the APC3 subunit of APC was developed by means of computational techniques; the binding of a natural inhibitory compound to APC3 was also investigated. Results: It was found that APC3 structure consists of numerous helices organized in anti-parallel and the overall model is superhelical of tetratrico-peptide repeat (TPR) domains. Furthermore, binding pocket of the natural inhibitory compound as APC3 inhibitor was shown. Conclusion: The findings are beneficial to understand the mechanism of the APC activation and design inhibitory compounds.


Rape M, Kirschner MW. Autonomous regulation of the anaphase-promoting complex couples mitosis to S-phase entry. Nature 2004;432:588-95.  Back to cited text no. 1
Mocciaro A, Rape M. Emerging regulatory mechanisms in ubiquitin-dependent cell cycle control. J Cell Sci 2012;125(Pt 2):255-63.  Back to cited text no. 2
Cooper KF, Strich R. Meiotic control of the APC/C: Similarities and differences from mitosis. Cell Div 2011;6:16.  Back to cited text no. 3
Izawa D, Pines J. How APC/C-Cdc20 changes its substrate specificity in mitosis. Nat Cell Biol 2011;13:223-33.  Back to cited text no. 4
Floyd S, Pines J, Lindon C. APC/C Cdh1 targets aurora kinase to control reorganization of the mitotic spindle at anaphase. Current Biol 2008;18:1649-58.  Back to cited text no. 5
Reddy SK, Rape M, Margansky WA, Kirschner MW. Ubiquitination by the anaphase-promoting complex drives spindle checkpoint inactivation. Nature 2007;446:921-5.  Back to cited text no. 6
Turnell AS, Stewart GS, Grand RJ, Rookes SM, Martin A, Yamano H, et al. The APC/C and CBP/p300 cooperate to regulate transcription and cell-cycle progression. Nature 2005;438:690-5.  Back to cited text no. 7
Mailand N, Diffley JF. CDKs promote DNA replication origin licensing in human cells by protecting Cdc6 from APC/C-dependent proteolysis. Cell 2005;122:915-26.  Back to cited text no. 8
De Boeck M, ten Dijke P. Key role for ubiquitin protein modification in TGFbeta signal transduction. Ups J Med Sci 2012;117:153-65.  Back to cited text no. 9
Garedew A, Andreassi C, Moncada S. Mitochondrial dynamics, biogenesis, and function are coordinated with the cell cycle by APC/C CDH1. Cell Metab 2012;15:466-79.  Back to cited text no. 10
Meyer HJ, Rape M. Processive ubiquitin chain formation by the anaphase-promoting complex. Semin Cell Dev Biol 2011;22:544-50.  Back to cited text no. 11
Rape M, Reddy SK, Kirschner MW. The processivity of multiubiquitination by the APC determines the order of substrate degradation. Cell 2006;124:89-103.  Back to cited text no. 12
Mathe E, Kraft C, Giet R, Deak P, Peters JM, Glover DM. The E2-C vihar is required for the correct spatiotemporal proteolysis of cyclin B and itself undergoes cyclical degradation. Curr Biol 2004;14:1723-33.  Back to cited text no. 13
Wu T, Merbl Y, Huo Y, Gallop JL, Tzur A, Kirschner MW. UBE2S drives elongation of K11-linked ubiquitin chains by the anaphase-promoting complex. Proc Natl Acad Sci U S A 2010;107:1355-60.  Back to cited text no. 14
Min M, Lindon C. Substrate targeting by the ubiquitin-proteasome system in mitosis. Semin Cell Dev Biol 2012;23:482-91.  Back to cited text no. 15
Kraft C, Herzog F, Gieffers C, Mechtler K, Hagting A, Pines J, et al. Mitotic regulation of the human anaphase-promoting complex by phosphorylation. EMBO J 2003;22:6598-609.  Back to cited text no. 16
Thornton BR, Toczyski DP. Precise destruction: An emerging picture of the APC. Genes Dev 2006;20:3069-78.  Back to cited text no. 17
Ban KH, Torres JZ, Miller JJ, Mikhailov A, Nachury MV, Tung JJ, et al. The END network couples spindle pole assembly to inhibition of the anaphase-promoting complex/cyclosome in early mitosis. Dev Cell 2007;13:29-42.  Back to cited text no. 18
Song MS, Song SJ, Ayad NG, Chang JS, Lee JH, Hong HK, et al. The tumour suppressor RASSF1A regulates mitosis by inhibiting the APC-Cdc20 complex. Nat Cell Biol 2004;6:129-37.  Back to cited text no. 19
Thornton BR, Ng TM, Matyskiela ME, Carroll CW, Morgan DO, Toczyski DP. An architectural map of the anaphase-promoting complex. Genes Dev 2006;20:449-60.  Back to cited text no. 20
Schreiber A, Stengel F, Zhang Z, Enchev RI, Kong EH, Morris EP, et al. Structural basis for the subunit assembly of the anaphase-promoting complex. Nature 2011;470:227-32.  Back to cited text no. 21
Matyskiela ME, Morgan DO. Analysis of activator-binding sites on the APC/C supports a cooperative substrate-binding mechanism. Mol Cell 2009;34:68-80.  Back to cited text no. 22
Herzog F, Primorac I, Dube P, Lenart P, Sander B, Mechtler K, et al. Structure of the anaphase-promoting complex/cyclosome interacting with a mitotic checkpoint complex. Science 2009;323:1477-81.  Back to cited text no. 23
Wang J, Dye BT, Rajashankar KR, Kurinov I, Schulman BA. Insights into anaphase promoting complex TPR subdomain assembly from a CDC26-APC6 structure. Nat Struct Mol Biol 2009;16:987-9.  Back to cited text no. 24
Han D, Kim K, Kim Y, Kang Y, Lee JY, Kim Y. Crystal structure of the N-terminal domain of anaphase-promoting complex subunit 7. J Biol Chem 2009;284:15137-46.  Back to cited text no. 25
Pal M, Nagy O, Menesi D, Udvardy A, Deak P. Structurally related TPR subunits contribute differently to the function of the anaphase-promoting complex in Drosophila melanogaster. J Cell Sci 2007;120:3238-48.  Back to cited text no. 26
Lamb JR, Michaud WA, Sikorski RS, Hieter PA. Cdc16p, Cdc23p AND Cdc27p form a complex essential for mitosis. EMBO J 1994;13:4321-8.  Back to cited text no. 27
Bolanos-Garcia VM. The N-terminal, TPR-containing domain of the mitotic checkpoint protein BUBR1 does not bind fatty acids. Comput Biol Chem 2008;32:139-40.  Back to cited text no. 28
Millson SH, Vaughan CK, Zhai C, Ali MM, Panaretou B, Piper PW, et al. Chaperone ligand-discrimination by the TPR-domain protein Tah1. Biochem J 2008;413:261-8.  Back to cited text no. 29
Lapouge K, Smith SJ, Walker PA, Gamblin SJ, Smerdon SJ, Rittinger K. Structure of the TPR domain of p67phox in complex with Rac.GTP. Mol Cell 2000;6:899-907.  Back to cited text no. 30
Taylor P, Dornan J, Carrello A, Minchin RF, Ratajczak T, Walkinshaw MD. Two structures of cyclophilin 40: Folding and fidelity in the TPR domains. Structure 2001;9:431-8.  Back to cited text no. 31
Blatch GL, Lassle M. The tetratricopeptide repeat: A structural motif mediating protein-protein interactions. Bioessays 1999;21:932-9.  Back to cited text no. 32
D'Andrea LD, Regan L. TPR proteins: The versatile helix. Trends Biochem Sci 2003;28:655-62.  Back to cited text no. 33
Vodermaier HC, Gieffers C, Maurer-Stroh S, Eisenhaber F, Peters JM. TPR subunits of the anaphase-promoting complex mediate binding to the activator protein CDH1. Curr Biol 2003;13:1459-68.  Back to cited text no. 34
Singh N, Wiltshire TD, Thompson JR, Mer G, Couch FJ. Molecular basis for the association of microcephalin (MCPH 1) protein with the cell division cycle protein 27 (Cdc27) subunit of the anaphase-promoting complex. J Biol Chem 2012;287:2854-62.  Back to cited text no. 35
Zeng X, Sigoillot F, Gaur S, Choi S, Pfaff KL, Oh DC, et al. Pharmacologic inhibition of the anaphase-promoting complex induces a spindle checkpoint-dependent mitotic arrest in the absence of spindle damage. Cancer Cell 2010;18:382-95.  Back to cited text no. 36
UniProt Consortium. The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res 2009;37:D169-74.  Back to cited text no. 37
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007;23:2947-8.  Back to cited text no. 38
Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ. Jalview Version 2: A multiple sequence alignment editor and analysis workbench. Bioinformatics 2009;25:1189-91.  Back to cited text no. 39
Cole C, Barber JD, Barton GJ. The Jpred 3 secondary structure prediction server. Nucleic Acids Res 2008;36:W197-201.  Back to cited text no. 40
Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, et al. Comparative protein structure modeling using modeller. Curr Protoc Bioinformatics 2006;Chapter 5:Unit 5.6.  Back to cited text no. 41
Söding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 2005;33:W244-8.  Back to cited text no. 42
Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ. GROMACS: Fast, flexible, and free. J Comput Chem 2005;26:1701-18.  Back to cited text no. 43
Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, Dror RO, et al. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins 2010;78:1950-8.  Back to cited text no. 44
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-35.  Back to cited text no. 45
Hess B, Bekker H, Berendsen HJ, Fraaije JG. LINCS: A linear constraint solver for molecular simulations. J Comput Chem 1997;18:1463-72.  Back to cited text no. 46
Berendsen HJ, Postma JP, Van der Gunsteren WF, Dinola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-90.  Back to cited text no. 47
Parrinello M, Rahman A. Crystal structure and pair potentials: Molecular dynamics study. Phys Rev Lett 1980;45:1196-9.  Back to cited text no. 48
Merlino A, Mazzarella L, Carannante A, Di Fiore A, Donato A, Notomista E, et al. The importance of dynamic effects on the enzyme activity: X-ray structure and molecular dynamics of onconase mutants. J Biol Chem 2005;280:17953-60.  Back to cited text no. 49
Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: A program to check the stereochemical quality of protein structures. J Appl Crystallogr 1993;26:283-91.  Back to cited text no. 50
Luthy R, Bowie JU, Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature 1992;356:83-5.  Back to cited text no. 51
Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, et al. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem 2009;30:2785-91.  Back to cited text no. 52
Laskowski RA, Swindells MB. LigPlot+: Multiple ligand-protein interaction diagrams for drug discovery. J Chem Inf Model 2011;51:2778-86.  Back to cited text no. 53
Jackson PK, Eldridge AG, Freed E, Furstenthal L, Hsu JY, Kaiser BK, et al. The lore of the RINGs: Substrate recognition and catalysis by ubiquitin ligases. Trends Cell Biol 2000;10:429-39.  Back to cited text no. 54
Brinker A, Scheufler C, Von Der Mulbe F, Fleckenstein B, Herrmann C, Jung G, et al. Ligand discrimination by TPR domains. Relevance and selectivity of EEVD-recognition in Hsp70×Hop×Hsp90 complexes. J Biol Chem 2002;277:19265-75.  Back to cited text no. 55
Kobayashi K, Sueyoshi T, Inoue K, Moore R, Negishi M. Cytoplasmic accumulation of the nuclear receptor CAR by a tetratricopeptide repeat protein in HepG2 cells. Mol Pharmacol 2003;64:1069-75.  Back to cited text no. 56
Magliery TJ, Regan L. Beyond consensus: Statistical free energies reveal hidden interactions in the design of a TPR motif. J Mol Biol 2004;343:731-45.  Back to cited text no. 57
Carrigan PE, Nelson GM, Roberts PJ, Stoffer J, Riggs DL, Smith DF. Multiple domains of the co-chaperone Hop are important for Hsp70 binding. J Biol Chem 2004;279:16185-93.  Back to cited text no. 58
Das AK, Cohen PW, Barford D. The structure of the tetratricopeptide repeats of protein phosphatase 5: Implications for TPR-mediated protein-protein interactions. EMBO J 1998;17:1192-9.  Back to cited text no. 59
Buschhorn BA, Petzold G, Galova M, Dube P, Kraft C, Herzog F, et al. Substrate binding on the APC/C occurs between the coactivator Cdh1 and the processivity factor Doc1. Nat Struct Mol Biol 2011;18:6-13.  Back to cited text no. 60
da Fonseca PC, Kong EH, Zhang Z, Schreiber A, Williams MA, Morris EP, et al. Structures of APC/CCdh1 with substrates identify Cdh1 and Apc10 as the D-box co-receptor. Nature 2011;470:274-8.  Back to cited text no. 61
Vodermaier H, Gieffers C, Maurer-Stroh S, Eisenhaber F, Peters JM, Gmachl M, inventors. Method of identifying compounds that specifically inhibit the anaphase promoting complex; 2005.  Back to cited text no. 62
Cliff MJ, Williams MA, Brooke-Smith J, Barford D, Ladbury JE. Molecular recognition via coupled folding and binding in a TPR domain. J Mol Biol 2005;346:717-32.  Back to cited text no. 63