1xf7

From Proteopedia

Jump to: navigation, search
1xf7, 40 NMR models ()
Ligands:
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


Contents

High Resolution NMR Structure of the Wilms' Tumor Suppressor Protein (WT1) Finger 3

Publication Abstract from PubMed

The zinc finger, a motif of protein-nucleic acid recognition broadly conserved among eukaryotes, is a globular minidomain containing a tetrahedral metal-binding site. Preferential coordination of Zn(2+) (relative to Co(2+)) is proposed to reflect differences in ligand-field stabilization energies (LFSEs) due to complete or incomplete occupancy of d orbitals. LFSE predicts that the preference for Zn(2+) should be purely enthalpic in accord with calorimetric studies of a high-affinity consensus peptide (CP-1; Blasie, C. A., and Berg, J. (2002) Biochemistry 41, 15068-73). Despite its elegance, the general predominance of LFSE is unclear as (i) the magnitude by which CP-1 prefers Zn(2+) is greater than that expected and (ii) the analogous metal ion selectivity of a zinc metalloenzyme (carbonic anhydrase) is driven by changes in entropy rather than enthalpy. Because CP-1 was designed to optimize zinc binding, we have investigated the NMR structure and metal ion selectivity of a natural finger of lower stability derived from human tumor-suppressor protein WT1. Raman spectroscopy suggests that the structure of the WT1 domain is unaffected by interchange of Zn(2+) and Co(2+). As in CP-1, preferential binding of Zn(2+) (relative to Co(2+)) is driven predominantly by differences in enthalpy, but in this case the enthalpic advantage is less than that predicted by LFSE. A theoretical framework is presented to define the relationship between LFSE and other thermodynamic factors, such as metal ion electroaffinities, enthalpies of hydration, and the topography of the underlying folding landscape. The contribution of environmental coupling to entropy-enthalpy compensation is delineated in a formal thermodynamic cycle. Together, these considerations indicate that LFSE provides an important but incomplete description of the stringency and thermodynamic origin of metal-ion selectivity.

Why zinc fingers prefer zinc: ligand-field symmetry and the hidden thermodynamics of metal ion selectivity., Lachenmann MJ, Ladbury JE, Dong J, Huang K, Carey P, Weiss MA, Biochemistry. 2004 Nov 9;43(44):13910-25. PMID:15518539

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

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]

About this Structure

1xf7 is a 1 chain structure. Full experimental information is available from OCA.

Reference

  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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools