1bor

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1bor, 1 NMR models ()
Ligands:
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


Contents

TRANSCRIPTION FACTOR PML, A PROTO-ONCOPROTEIN, NMR, 1 REPRESENTATIVE STRUCTURE AT PH 7.5, 30 C, IN THE PRESENCE OF ZINC

Publication Abstract from PubMed

Acute promyelocytic leukaemia (APL) has been ascribed to a chromosomal translocation event which results in a fusion protein comprising the PML protein and the retinoic acid receptor alpha. PML is normally a component of a nuclear multiprotein complex (termed ND10, Kr bodies, nuclear bodies, PML oncogenic domains or PODs) which is disrupted in the APL disease state. PML contains a number of characterized motifs including a Zn2+ binding domain called the RING or C3HC4 finger. Here we describe the solution structure of the PML RING finger as solved by 1H NMR methods at physiological pH with r.m.s. deviations for backbone atoms of 0.88 and 1.39 A for all atoms. Additional biophysical studies including CD and optical spectroscopy, show that the PML RING finger requires Zn2+ for autonomous folding and that cysteines are used in metal ligation. A comparison of the structure with the previously solved equine herpes virus IE110 RING finger, shows significant differences suggesting that the RING motif is structurally diverse. The role of the RING domain in PML nuclear body formation was tested in vivo, by using site-directed mutagenesis and immunofluorescence on transiently transfected NIH 3T3 cells. Independently mutating two pairs of cysteines in each of the Zn2+ binding sites prevents PML nuclear body formation, suggesting that a fully folded RING domain is necessary for this process. These results suggest that the PML RING domain is probably involved in protein-protein interactions, a feature which may be common to other RING finger domains.

The solution structure of the RING finger domain from the acute promyelocytic leukaemia proto-oncoprotein PML., Borden KL, Boddy MN, Lally J, O'Reilly NJ, Martin S, Howe K, Solomon E, Freemont PS, EMBO J. 1995 Apr 3;14(7):1532-41. PMID:7729428

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

Disease

[PML_HUMAN] Note=A chromosomal aberration involving PML may be a cause of acute promyelocytic leukemia (APL). Translocation t(15;17)(q21;q21) with RARA. The PML breakpoints (type A and type B) lie on either side of an alternatively spliced exon.[1][2]

Function

[PML_HUMAN] Key component of PML nuclear bodies that regulate a large number of cellular processes by facilitating post-translational modification of target proteins, promoting protein-protein contacts, or by sequestering proteins. Functions as tumor suppressor. Required for normal, caspase-dependent apoptosis in response to DNA damage, FAS, TNF, or interferons. Plays a role in transcription regulation, DNA damage response, DNA repair and chromatin organization. Plays a role in processes regulated by retinoic acid, regulation of cell division, terminal differentiation of myeloid precursor cells and differentiation of neural progenitor cells. Required for normal immunity to microbial infections. Plays a role in antiviral response. In the cytoplasm, plays a role in TGFB1-dependent processes. Regulates p53/TP53 levels by inhibiting its ubiquitination and proteasomal degradation. Regulates activation of p53/TP53 via phosphorylation at 'Ser-20'. Sequesters MDM2 in the nucleolus after DNA damage, and thereby inhibits ubiquitination and degradation of p53/TP53. Regulates translation of HIF1A by sequestering MTOR, and thereby plays a role in neoangiogenesis and tumor vascularization. Regulates RB1 phosphorylation and activity. Required for normal development of the brain cortex during embryogenesis. Can sequester herpes virus and varicella virus proteins inside PML bodies, and thereby inhibit the formation of infectious viral particles. Regulates phosphorylation of ITPR3 and plays a role in the regulation of calcium homeostasis at the endoplasmic reticulum (By similarity). Regulates transcription activity of ELF4. Inhibits specifically the activity of the tetrameric form of PKM. Together with SATB1, involved in local chromatin-loop remodeling and gene expression regulation at the MHC-I locus. Regulates PTEN compartmentalization through the inhibition of USP7-mediated deubiquitination.[3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20]

About this Structure

1bor is a 1 chain structure with sequence from Homo sapiens. Full experimental information is available from OCA.

Reference

  • Borden KL, Boddy MN, Lally J, O'Reilly NJ, Martin S, Howe K, Solomon E, Freemont PS. The solution structure of the RING finger domain from the acute promyelocytic leukaemia proto-oncoprotein PML. EMBO J. 1995 Apr 3;14(7):1532-41. PMID:7729428
  • Feig M, Im W, Brooks CL 3rd. Implicit solvation based on generalized Born theory in different dielectric environments. J Chem Phys. 2004 Jan 8;120(2):903-11. PMID:15267926 doi:10.1063/1.1631258
  1. de The H, Lavau C, Marchio A, Chomienne C, Degos L, Dejean A. The PML-RAR alpha fusion mRNA generated by the t(15;17) translocation in acute promyelocytic leukemia encodes a functionally altered RAR. Cell. 1991 Aug 23;66(4):675-84. PMID:1652369
  2. Goddard AD, Borrow J, Freemont PS, Solomon E. Characterization of a zinc finger gene disrupted by the t(15;17) in acute promyelocytic leukemia. Science. 1991 Nov 29;254(5036):1371-4. PMID:1720570
  3. Kamitani T, Kito K, Nguyen HP, Wada H, Fukuda-Kamitani T, Yeh ET. Identification of three major sentrinization sites in PML. J Biol Chem. 1998 Oct 9;273(41):26675-82. PMID:9756909
  4. Zhong S, Delva L, Rachez C, Cenciarelli C, Gandini D, Zhang H, Kalantry S, Freedman LP, Pandolfi PP. A RA-dependent, tumour-growth suppressive transcription complex is the target of the PML-RARalpha and T18 oncoproteins. Nat Genet. 1999 Nov;23(3):287-95. PMID:10610177 doi:10.1038/15463
  5. Zhong S, Salomoni P, Ronchetti S, Guo A, Ruggero D, Pandolfi PP. Promyelocytic leukemia protein (PML) and Daxx participate in a novel nuclear pathway for apoptosis. J Exp Med. 2000 Feb 21;191(4):631-40. PMID:10684855
  6. Guo A, Salomoni P, Luo J, Shih A, Zhong S, Gu W, Pandolfi PP. The function of PML in p53-dependent apoptosis. Nat Cell Biol. 2000 Oct;2(10):730-6. PMID:11025664 doi:10.1038/35036365
  7. Regad T, Saib A, Lallemand-Breitenbach V, Pandolfi PP, de The H, Chelbi-Alix MK. PML mediates the interferon-induced antiviral state against a complex retrovirus via its association with the viral transactivator. EMBO J. 2001 Jul 2;20(13):3495-505. PMID:11432836 doi:10.1093/emboj/20.13.3495
  8. Yang S, Kuo C, Bisi JE, Kim MK. PML-dependent apoptosis after DNA damage is regulated by the checkpoint kinase hCds1/Chk2. Nat Cell Biol. 2002 Nov;4(11):865-70. PMID:12402044 doi:10.1038/ncb869
  9. Blondel D, Regad T, Poisson N, Pavie B, Harper F, Pandolfi PP, De The H, Chelbi-Alix MK. Rabies virus P and small P products interact directly with PML and reorganize PML nuclear bodies. Oncogene. 2002 Nov 14;21(52):7957-70. PMID:12439746 doi:10.1038/sj.onc.1205931
  10. Louria-Hayon I, Grossman T, Sionov RV, Alsheich O, Pandolfi PP, Haupt Y. The promyelocytic leukemia protein protects p53 from Mdm2-mediated inhibition and degradation. J Biol Chem. 2003 Aug 29;278(35):33134-41. Epub 2003 Jun 16. PMID:12810724 doi:10.1074/jbc.M301264200
  11. Suico MA, Yoshida H, Seki Y, Uchikawa T, Lu Z, Shuto T, Matsuzaki K, Nakao M, Li JD, Kai H. Myeloid Elf-1-like factor, an ETS transcription factor, up-regulates lysozyme transcription in epithelial cells through interaction with promyelocytic leukemia protein. J Biol Chem. 2004 Apr 30;279(18):19091-8. Epub 2004 Feb 19. PMID:14976184 doi:10.1074/jbc.M312439200
  12. Bernardi R, Scaglioni PP, Bergmann S, Horn HF, Vousden KH, Pandolfi PP. PML regulates p53 stability by sequestering Mdm2 to the nucleolus. Nat Cell Biol. 2004 Jul;6(7):665-72. Epub 2004 Jun 13. PMID:15195100 doi:10.1038/ncb1147
  13. Lin HK, Bergmann S, Pandolfi PP. Cytoplasmic PML function in TGF-beta signalling. Nature. 2004 Sep 9;431(7005):205-11. PMID:15356634 doi:10.1038/nature02783
  14. Dellaire G, Ching RW, Ahmed K, Jalali F, Tse KC, Bristow RG, Bazett-Jones DP. Promyelocytic leukemia nuclear bodies behave as DNA damage sensors whose response to DNA double-strand breaks is regulated by NBS1 and the kinases ATM, Chk2, and ATR. J Cell Biol. 2006 Oct 9;175(1):55-66. PMID:17030982 doi:10.1083/jcb.200604009
  15. Shimada N, Shinagawa T, Ishii S. Modulation of M2-type pyruvate kinase activity by the cytoplasmic PML tumor suppressor protein. Genes Cells. 2008 Mar;13(3):245-54. doi: 10.1111/j.1365-2443.2008.01165.x. PMID:18298799 doi:10.1111/j.1365-2443.2008.01165.x
  16. Song MS, Salmena L, Carracedo A, Egia A, Lo-Coco F, Teruya-Feldstein J, Pandolfi PP. The deubiquitinylation and localization of PTEN are regulated by a HAUSP-PML network. Nature. 2008 Oct 9;455(7214):813-7. doi: 10.1038/nature07290. Epub 2008 Aug 20. PMID:18716620 doi:10.1038/nature07290
  17. Kumar PP, Bischof O, Purbey PK, Notani D, Urlaub H, Dejean A, Galande S. Functional interaction between PML and SATB1 regulates chromatin-loop architecture and transcription of the MHC class I locus. Nat Cell Biol. 2007 Jan;9(1):45-56. Epub 2006 Dec 17. PMID:17173041 doi:10.1038/ncb1516
  18. Oh W, Ghim J, Lee EW, Yang MR, Kim ET, Ahn JH, Song J. PML-IV functions as a negative regulator of telomerase by interacting with TERT. J Cell Sci. 2009 Aug 1;122(Pt 15):2613-22. doi: 10.1242/jcs.048066. Epub 2009 Jun, 30. PMID:19567472 doi:10.1242/jcs.048066
  19. Cuchet D, Sykes A, Nicolas A, Orr A, Murray J, Sirma H, Heeren J, Bartelt A, Everett RD. PML isoforms I and II participate in PML-dependent restriction of HSV-1 replication. J Cell Sci. 2011 Jan 15;124(Pt 2):280-91. doi: 10.1242/jcs.075390. Epub 2010 Dec , 20. PMID:21172801 doi:10.1242/jcs.075390
  20. Reichelt M, Wang L, Sommer M, Perrino J, Nour AM, Sen N, Baiker A, Zerboni L, Arvin AM. Entrapment of viral capsids in nuclear PML cages is an intrinsic antiviral host defense against varicella-zoster virus. PLoS Pathog. 2011 Feb 3;7(2):e1001266. doi: 10.1371/journal.ppat.1001266. PMID:21304940 doi:10.1371/journal.ppat.1001266

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