2prt
From Proteopedia
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|PDB= 2prt |SIZE=350|CAPTION= <scene name='initialview01'>2prt</scene>, resolution 3.15Å | |PDB= 2prt |SIZE=350|CAPTION= <scene name='initialview01'>2prt</scene>, resolution 3.15Å | ||
|SITE= <scene name='pdbsite=AC1:Zn+Binding+Site+For+Residue+A+201'>AC1</scene>, <scene name='pdbsite=AC2:Zn+Binding+Site+For+Residue+A+202'>AC2</scene>, <scene name='pdbsite=AC3:Zn+Binding+Site+For+Residue+A+203'>AC3</scene> and <scene name='pdbsite=AC4:Zn+Binding+Site+For+Residue+A+204'>AC4</scene> | |SITE= <scene name='pdbsite=AC1:Zn+Binding+Site+For+Residue+A+201'>AC1</scene>, <scene name='pdbsite=AC2:Zn+Binding+Site+For+Residue+A+202'>AC2</scene>, <scene name='pdbsite=AC3:Zn+Binding+Site+For+Residue+A+203'>AC3</scene> and <scene name='pdbsite=AC4:Zn+Binding+Site+For+Residue+A+204'>AC4</scene> | ||
| - | |LIGAND= <scene name='pdbligand=ZN:ZINC ION'>ZN</scene> | + | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= WT1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]) | |GENE= WT1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2prt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2prt OCA], [http://www.ebi.ac.uk/pdbsum/2prt PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2prt RCSB]</span> | ||
}} | }} | ||
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==Overview== | ==Overview== | ||
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. | 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. | ||
| + | |||
| + | ==Disease== | ||
| + | Known disease associated with this structure: Denys-Drash syndrome OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=607102 607102]], Frasier syndrome OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=607102 607102]], Mesangial sclerosis, isolated diffuse OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=607102 607102]], WAGR syndrome OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=607102 607102]], Wilms tumor, type 1 OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=607102 607102]] | ||
==About this Structure== | ==About this Structure== | ||
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[[Category: Wilson, I A.]] | [[Category: Wilson, I A.]] | ||
[[Category: Wright, P E.]] | [[Category: Wright, P E.]] | ||
| - | [[Category: ZN]] | ||
[[Category: protein-dna complex]] | [[Category: protein-dna complex]] | ||
[[Category: transcription/dna complex]] | [[Category: transcription/dna complex]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:39:56 2008'' |
Revision as of 01:39, 31 March 2008
| |||||||
| , resolution 3.15Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , , and | ||||||
| Ligands: | , , , , | ||||||
| Gene: | WT1 (Homo sapiens) | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to DNA
Contents |
Overview
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.
Disease
Known disease associated with this structure: Denys-Drash syndrome OMIM:[607102], Frasier syndrome OMIM:[607102], Mesangial sclerosis, isolated diffuse OMIM:[607102], WAGR syndrome OMIM:[607102], Wilms tumor, type 1 OMIM:[607102]
About this Structure
2PRT is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Mon Mar 31 04:39:56 2008
