2jp9: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2jp9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JP9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JP9 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2jp9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JP9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JP9 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2jp9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jp9 OCA], [https://pdbe.org/2jp9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jp9 RCSB], [https://www.ebi.ac.uk/pdbsum/2jp9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jp9 ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2jp9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jp9 OCA], [https://pdbe.org/2jp9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jp9 RCSB], [https://www.ebi.ac.uk/pdbsum/2jp9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jp9 ProSAT]</span></td></tr>
</table>
</table>

Latest revision as of 12:40, 9 May 2024

Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to DNAStructure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to DNA

Structural highlights

2jp9 is a 3 chain structure with sequence from Homo sapiens and Synthetic construct. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

WT1_HUMAN Defects in WT1 are the cause of Frasier syndrome (FS) [MIM:136680. FS is characterized by a slowly progressing nephropathy leading to renal failure in adolescence or early adulthood, male pseudohermaphroditism, and no Wilms tumor. As for histological findings of the kidneys, focal glomerular sclerosis is often observed. There is phenotypic overlap with Denys-Drash syndrome. Inheritance is autosomal dominant.[1] Defects in WT1 are the cause of Wilms tumor 1 (WT1) [MIM:194070. WT is an embryonal malignancy of the kidney that affects approximately 1 in 10'000 infants and young children. It occurs both in sporadic and hereditary forms.[2] [3] [4] [5] Defects in WT1 are the cause of Denys-Drash syndrome (DDS) [MIM:194080. DDS is a typical nephropathy characterized by diffuse mesangial sclerosis, genital abnormalities, and/or Wilms tumor. There is phenotypic overlap with WAGR syndrome and Frasier syndrome. Inheritance is autosomal dominant, but most cases are sporadic.[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] Defects in WT1 are the cause of nephrotic syndrome type 4 (NPHS4) [MIM:256370. A renal disease characterized clinically by proteinuria, hypoalbuminemia, hyperlipidemia and edema. Kidney biopsies show non-specific histologic changes such as focal segmental glomerulosclerosis and diffuse mesangial proliferation. Some affected individuals have an inherited steroid-resistant form and progress to end-stage renal failure. Most patients with NPHS4 show diffuse mesangial sclerosis on renal biopsy, which is a pathologic entity characterized by mesangial matrix expansion with no mesangial hypercellularity, hypertrophy of the podocytes, vacuolized podocytes, thickened basement membranes, and diminished patency of the capillary lumen.[23] [24] [25] [26] Defects in WT1 are a cause of Meacham syndrome (MEACHS) [MIM:608978. Meacham syndrome is a rare sporadically occurring multiple malformation syndrome characterized by male pseudohermaphroditism with abnormal internal female genitalia comprising a uterus and double or septate vagina, complex congenital heart defect and diaphragmatic abnormalities.[27] Note=A chromosomal aberration involving WT1 may be a cause of desmoplastic small round cell tumor (DSRCT). Translocation t(11;22)(p13;q12) with EWSR1. Defects in WT1 may be a cause of mesothelioma malignant (MESOM) [MIM:156240. An aggressive neoplasm of the serosal lining of the chest. It appears as broad sheets of cells, with some regions containing spindle-shaped, sarcoma-like cells and other regions showing adenomatous patterns. Pleural mesotheliomas have been linked to exposure to asbestos.[28]

Function

WT1_HUMAN Transcription factor that plays an important role in cellular development and cell survival. Regulates the expression of numerous target genes, including EPO. Plays an essential role for development of the urogenital system. Recognizes and binds to the DNA sequence 5'-CGCCCCCGC-3'. It has a tumor suppressor as well as an oncogenic role in tumor formation. Function may be isoform-specific: isoforms lacking the KTS motif may act as transcription factors. Isoforms containing the KTS motif may bind mRNA and play a role in mRNA metabolism or splicing. Isoform 1 has lower affinity for DNA, and can bind RNA.[29] [30]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The zinc finger domain of the Wilms tumor suppressor protein (WT1) contains four canonical Cys(2)His(2) zinc fingers. WT1 binds preferentially to DNA sequences that are closely related to the EGR-1 consensus site. We report the structure determination by both X-ray crystallography and NMR spectroscopy of the WT1 zinc finger domain in complex with DNA. The X-ray structure was determined for the complex with a cognate 14 base-pair oligonucleotide, and composite X-ray/NMR structures were determined for complexes with both the 14 base-pair and an extended 17 base-pair DNA. This combined approach allowed unambiguous determination of the position of the first zinc finger, which is influenced by lattice contacts in the crystal structure. The crystal structure shows the second, third and fourth zinc finger domains inserted deep into the major groove of the DNA where they make base-specific interactions. The DNA duplex is distorted in the vicinity of the first zinc finger, with a cytidine twisted and tilted out of the base stack to pack against finger 1 and the tip of finger 2. By contrast, the composite X-ray/NMR structures show that finger 1 continues to follow the major groove in the solution complexes. However, the orientation of the helix is non-canonical, and the fingertip and the N terminus of the helix project out of the major groove; as a consequence, the zinc finger side-chains that are commonly involved in base recognition make no contact with the DNA. We conclude that finger 1 helps to anchor WT1 to the DNA by amplifying the binding affinity although it does not contribute significantly to binding specificity. The structures provide molecular level insights into the potential consequences of mutations in zinc fingers 2 and 3 that are associated with Denys-Drash syndrome and nephritic syndrome. The mutations are of two types, and either destabilize the zinc finger structure or replace key base contact residues.

Structure of the Wilms tumor suppressor protein zinc finger domain bound to DNA.,Stoll R, Lee BM, Debler EW, Laity JH, Wilson IA, Dyson HJ, Wright PE J Mol Biol. 2007 Oct 5;372(5):1227-45. Epub 2007 Jul 21. PMID:17716689[31]

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

References

  1. ↑ Kohsaka T, Tagawa M, Takekoshi Y, Yanagisawa H, Tadokoro K, Yamada M. Exon 9 mutations in the WT1 gene, without influencing KTS splice isoforms, are also responsible for Frasier syndrome. Hum Mutat. 1999;14(6):466-70. PMID:10571943 doi:<466::AID-HUMU4>3.0.CO;2-6 10.1002/(SICI)1098-1004(199912)14:6<466::AID-HUMU4>3.0.CO;2-6
  2. ↑ Little MH, Prosser J, Condie A, Smith PJ, Van Heyningen V, Hastie ND. Zinc finger point mutations within the WT1 gene in Wilms tumor patients. Proc Natl Acad Sci U S A. 1992 Jun 1;89(11):4791-5. PMID:1317572
  3. ↑ Schumacher V, Schneider S, Figge A, Wildhardt G, Harms D, Schmidt D, Weirich A, Ludwig R, Royer-Pokora B. Correlation of germ-line mutations and two-hit inactivation of the WT1 gene with Wilms tumors of stromal-predominant histology. Proc Natl Acad Sci U S A. 1997 Apr 15;94(8):3972-7. PMID:9108089
  4. ↑ Jeanpierre C, Denamur E, Henry I, Cabanis MO, Luce S, Cecille A, Elion J, Peuchmaur M, Loirat C, Niaudet P, Gubler MC, Junien C. Identification of constitutional WT1 mutations, in patients with isolated diffuse mesangial sclerosis, and analysis of genotype/phenotype correlations by use of a computerized mutation database. Am J Hum Genet. 1998 Apr;62(4):824-33. PMID:9529364 doi:S0002-9297(07)60974-4
  5. ↑ Royer-Pokora B, Beier M, Henzler M, Alam R, Schumacher V, Weirich A, Huff V. Twenty-four new cases of WT1 germline mutations and review of the literature: genotype/phenotype correlations for Wilms tumor development. Am J Med Genet A. 2004 Jun 15;127A(3):249-57. PMID:15150775 doi:10.1002/ajmg.a.30015
  6. ↑ Jeanpierre C, Denamur E, Henry I, Cabanis MO, Luce S, Cecille A, Elion J, Peuchmaur M, Loirat C, Niaudet P, Gubler MC, Junien C. Identification of constitutional WT1 mutations, in patients with isolated diffuse mesangial sclerosis, and analysis of genotype/phenotype correlations by use of a computerized mutation database. Am J Hum Genet. 1998 Apr;62(4):824-33. PMID:9529364 doi:S0002-9297(07)60974-4
  7. ↑ Pelletier J, Bruening W, Kashtan CE, Mauer SM, Manivel JC, Striegel JE, Houghton DC, Junien C, Habib R, Fouser L, et al.. Germline mutations in the Wilms' tumor suppressor gene are associated with abnormal urogenital development in Denys-Drash syndrome. Cell. 1991 Oct 18;67(2):437-47. PMID:1655284
  8. ↑ Bruening W, Bardeesy N, Silverman BL, Cohn RA, Machin GA, Aronson AJ, Housman D, Pelletier J. Germline intronic and exonic mutations in the Wilms' tumour gene (WT1) affecting urogenital development. Nat Genet. 1992 May;1(2):144-8. PMID:1302008 doi:http://dx.doi.org/10.1038/ng0592-144
  9. ↑ Baird PN, Santos A, Groves N, Jadresic L, Cowell JK. Constitutional mutations in the WT1 gene in patients with Denys-Drash syndrome. Hum Mol Genet. 1992 Aug;1(5):301-5. PMID:1338906
  10. ↑ Little MH, Williamson KA, Mannens M, Kelsey A, Gosden C, Hastie ND, van Heyningen V. Evidence that WT1 mutations in Denys-Drash syndrome patients may act in a dominant-negative fashion. Hum Mol Genet. 1993 Mar;2(3):259-64. PMID:8388765
  11. ↑ Baird PN, Cowell JK. A novel zinc finger mutation in a patient with Denys-Drash syndrome. Hum Mol Genet. 1993 Dec;2(12):2193-4. PMID:8111391
  12. ↑ Tsuda M, Sakiyama T, Kitagawa T, Watanabe S, Watanabe T, Takahashi S, Kawaguchi H, Ito K. Molecular analysis of two Japanese cases of Denys-Drash syndrome. J Inherit Metab Dis. 1993;16(5):876-80. PMID:8295405
  13. ↑ Clarkson PA, Davies HR, Williams DM, Chaudhary R, Hughes IA, Patterson MN. Mutational screening of the Wilms's tumour gene, WT1, in males with genital abnormalities. J Med Genet. 1993 Sep;30(9):767-72. PMID:8411073
  14. ↑ Nordenskjold A, Friedman E, Anvret M. WT1 mutations in patients with Denys-Drash syndrome: a novel mutation in exon 8 and paternal allele origin. Hum Genet. 1994 Feb;93(2):115-20. PMID:8112732
  15. ↑ Tsuda M, Sakiyama T, Owada M, Chiba Y. A newly identified exonic mutation of the WT1 gene in a patient with Denys-Drash syndrome. Acta Paediatr Jpn. 1996 Jun;38(3):265-6. PMID:8741319
  16. ↑ Ghahremani M, Chan CB, Bistritzer T, Aladjem MM, Tieder M, Pelletier J. A novel mutation H373Y in the Wilms' tumor suppressor gene, WT1, associated with Denys-Drash syndrome. Hum Hered. 1996 Nov-Dec;46(6):336-8. PMID:8956030
  17. ↑ Kikuchi H, Takata A, Akasaka Y, Fukuzawa R, Yoneyama H, Kurosawa Y, Honda M, Kamiyama Y, Hata J. Do intronic mutations affecting splicing of WT1 exon 9 cause Frasier syndrome? J Med Genet. 1998 Jan;35(1):45-8. PMID:9475094
  18. ↑ Little M, Carman G, Donaldson E. Novel WT1 exon 9 mutation (D396Y) in a patient with early onset Denys Drash syndrome. Hum Mutat. 2000 Apr;15(4):389. PMID:10738002 doi:<389::AID-HUMU29>3.0.CO;2-E 10.1002/(SICI)1098-1004(200004)15:4<389::AID-HUMU29>3.0.CO;2-E
  19. ↑ Takata A, Kikuchi H, Fukuzawa R, Ito S, Honda M, Hata J. Constitutional WT1 correlate with clinical features in children with progressive nephropathy. J Med Genet. 2000 Sep;37(9):698-701. PMID:11182928
  20. ↑ Ohta S, Ozawa T, Izumino K, Sakuragawa N, Fuse H. A novel missense mutation of the Wt1 gene causing Denys-Drash syndrome with exceptionally mild renal manifestations. J Urol. 2000 Jun;163(6):1857-8. PMID:10799199
  21. ↑ Swiatecka-Urban A, Mokrzycki MH, Kaskel F, Da Silva F, Denamur E. Novel WT1 mutation (C388Y) in a female child with Denys-Drash syndrome. Pediatr Nephrol. 2001 Aug;16(8):627-30. PMID:11519891
  22. ↑ Hu M, Craig J, Howard N, Kan A, Chaitow J, Little D, Alexander SI. A novel mutation of WT1 exon 9 in a patient with Denys-Drash syndrome and pyloric stenosis. Pediatr Nephrol. 2004 Oct;19(10):1160-3. Epub 2004 Jul 28. PMID:15349765 doi:10.1007/s00467-004-1564-3
  23. ↑ Jeanpierre C, Denamur E, Henry I, Cabanis MO, Luce S, Cecille A, Elion J, Peuchmaur M, Loirat C, Niaudet P, Gubler MC, Junien C. Identification of constitutional WT1 mutations, in patients with isolated diffuse mesangial sclerosis, and analysis of genotype/phenotype correlations by use of a computerized mutation database. Am J Hum Genet. 1998 Apr;62(4):824-33. PMID:9529364 doi:S0002-9297(07)60974-4
  24. ↑ Takata A, Kikuchi H, Fukuzawa R, Ito S, Honda M, Hata J. Constitutional WT1 correlate with clinical features in children with progressive nephropathy. J Med Genet. 2000 Sep;37(9):698-701. PMID:11182928
  25. ↑ Schumacher V, Scharer K, Wuhl E, Altrogge H, Bonzel KE, Guschmann M, Neuhaus TJ, Pollastro RM, Kuwertz-Broking E, Bulla M, Tondera AM, Mundel P, Helmchen U, Waldherr R, Weirich A, Royer-Pokora B. Spectrum of early onset nephrotic syndrome associated with WT1 missense mutations. Kidney Int. 1998 Jun;53(6):1594-600. PMID:9607189 doi:10.1046/j.1523-1755.1998.00948.x
  26. ↑ Ruf RG, Schultheiss M, Lichtenberger A, Karle SM, Zalewski I, Mucha B, Everding AS, Neuhaus T, Patzer L, Plank C, Haas JP, Ozaltin F, Imm A, Fuchshuber A, Bakkaloglu A, Hildebrandt F. Prevalence of WT1 mutations in a large cohort of patients with steroid-resistant and steroid-sensitive nephrotic syndrome. Kidney Int. 2004 Aug;66(2):564-70. PMID:15253707 doi:10.1111/j.1523-1755.2004.00775.x
  27. ↑ Suri M, Kelehan P, O'neill D, Vadeyar S, Grant J, Ahmed SF, Tolmie J, McCann E, Lam W, Smith S, Fitzpatrick D, Hastie ND, Reardon W. WT1 mutations in Meacham syndrome suggest a coelomic mesothelial origin of the cardiac and diaphragmatic malformations. Am J Med Genet A. 2007 Oct 1;143A(19):2312-20. PMID:17853480 doi:10.1002/ajmg.a.31924
  28. ↑ Park S, Schalling M, Bernard A, Maheswaran S, Shipley GC, Roberts D, Fletcher J, Shipman R, Rheinwald J, Demetri G, et al.. The Wilms tumour gene WT1 is expressed in murine mesoderm-derived tissues and mutated in a human mesothelioma. Nat Genet. 1993 Aug;4(4):415-20. PMID:8401592 doi:http://dx.doi.org/10.1038/ng0893-415
  29. ↑ Weiss TC, Romaniuk PJ. Contribution of individual amino acids to the RNA binding activity of the Wilms' tumor suppressor protein WT1. Biochemistry. 2009 Jan 13;48(1):148-55. doi: 10.1021/bi801586a. PMID:19123921 doi:10.1021/bi801586a
  30. ↑ Rivera MN, Kim WJ, Wells J, Stone A, Burger A, Coffman EJ, Zhang J, Haber DA. The tumor suppressor WTX shuttles to the nucleus and modulates WT1 activity. Proc Natl Acad Sci U S A. 2009 May 19;106(20):8338-43. doi:, 10.1073/pnas.0811349106. Epub 2009 May 4. PMID:19416806 doi:10.1073/pnas.0811349106
  31. ↑ Stoll R, Lee BM, Debler EW, Laity JH, Wilson IA, Dyson HJ, Wright PE. Structure of the Wilms tumor suppressor protein zinc finger domain bound to DNA. J Mol Biol. 2007 Oct 5;372(5):1227-45. Epub 2007 Jul 21. PMID:17716689 doi:10.1016/j.jmb.2007.07.017
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