2rpc

From Proteopedia

(Difference between revisions)

Current revision

Solution structure of the tandem zf-C2H2 domains from the human zinc finger protein ZIC 3

Structural highlights

2rpc is a 1 chain structure with sequence from Homo sapiens. 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

ZIC3_HUMAN Defects in ZIC3 are the cause of visceral heterotaxy X-linked type 1 (HTX1) [MIM:306955. A form of visceral heterotaxy, a complex disorder due to disruption of the normal left-right asymmetry of the thoracoabdominal organs. It results in an abnormal arrangement of visceral organs, and a wide variety of congenital defects. Clinical features of visceral heterotaxy X-linked type 1 include dextrocardia, corrected transposition of great arteries, ventricular septal defect, patent ductus arteriosus, pulmonic stenosis, situs inversus viscerum, and asplenia and/or polysplenia.^[1] ^[2] ^[3] ^[4] ^[5] Defects in ZIC3 are a cause of VACTERL association X-linked with or without hydrocephalus (VACTERLX) [MIM:314390. A syndrome characterized by vertebral anomalies, anal atresia, cardiac malformations, tracheoesophageal fistula, renal anomalies (urethral atresia with hydronephrosis), and limb anomalies (hexadactyly, humeral hypoplasia, radial aplasia, and proximally placed thumb). Some patients may have hydrocephalus. Some cases of VACTERL-H are associated with increased chromosome breakage and rearrangement.^[6] Defects in ZIC3 are the cause of congenital heart defects, multiple types, 1, X-linked (CHTD1) [MIM:306955. A disorder characterized by congenital developmental abnormalities involving structures of the heart. Common defects include transposition of the great arteries, aortic stenosis, atrial septal defect, ventricular septal defect, pulmonic stenosis, and patent ductus arteriosus. The etiology of CHTD is complex, with contributions from environmental exposure, chromosomal abnormalities, and gene defects. Some patients with CHTD1 also have cardiac arrhythmias, which may be due to the anatomic defect itself or to surgical interventions.^[7] ^[8]

Function

ZIC3_HUMAN Acts as transcriptional activator. Required in the earliest stages in both axial midline development and left-right (LR) asymmetry specification. Binds to the minimal GLI-consensus sequence 5'-GGGTGGTC-3'.^[9]

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

Disruptions in ZIC3 cause heterotaxy, a congenital anomaly of the left-right axis. ZIC3 encodes a nuclear protein with a zinc finger (ZF) domain that contains five tandem C2H2 ZF motifs. Missense mutations in the first ZF motif (ZF1) result in defective nuclear localization, which may underlie the pathogenesis of heterotaxy. Here we revealed the structural and functional basis of the nuclear localization signal (NLS) of ZIC3 and investigated its relationship to the defect caused by ZF1 mutation. The ZIC3 NLS was located in the ZF2 and ZF3 regions, rather than ZF1. Several basic residues interspersed throughout these regions were responsible for the nuclear localization, but R320, K337 and R350 were particularly important. NMR structure analysis revealed that ZF1-4 had a similar structure to GLI ZF, and the basic side chains of the NLS clustered together in two regions on the protein surface, similar to classical bipartite NLSs. Among the residues for the ZF1 mutations, C253 and H286 were positioned for the metal chelation, whereas W255 was positioned in the hydrophobic core formed by ZF1 and ZF2. Tryptophan 255 was a highly conserved inter-finger connector and formed part of a structural motif (tandem CXW-C-H-H) that is shared with GLI, Glis and some fungal ZF proteins. Furthermore, we found that knockdown of Karyopherin alpha1/alpha6 impaired ZIC3 nuclear localization, and physical interactions between the NLS and the nuclear import adapter proteins were disturbed by mutations in the NLS but not by W255G. These results indicate that ZIC3 is imported into the cell nucleus by the Karyopherin (Importin) system and that the impaired nuclear localization by the ZF1 mutation is not due to a direct influence on the NLS.

Functional and structural basis of the nuclear localization signal in the ZIC3 zinc finger domain.,Hatayama M, Tomizawa T, Sakai-Kato K, Bouvagnet P, Kose S, Imamoto N, Yokoyama S, Utsunomiya-Tate N, Mikoshiba K, Kigawa T, Aruga J Hum Mol Genet. 2008 Nov 15;17(22):3459-73. Epub 2008 Aug 20. PMID:18716025^[10]

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

References

↑ Zhu L, Zhou G, Poole S, Belmont JW. Characterization of the interactions of human ZIC3 mutants with GLI3. Hum Mutat. 2008 Jan;29(1):99-105. PMID:17764085 doi:10.1002/humu.20606
↑ Hatayama M, Tomizawa T, Sakai-Kato K, Bouvagnet P, Kose S, Imamoto N, Yokoyama S, Utsunomiya-Tate N, Mikoshiba K, Kigawa T, Aruga J. Functional and structural basis of the nuclear localization signal in the ZIC3 zinc finger domain. Hum Mol Genet. 2008 Nov 15;17(22):3459-73. Epub 2008 Aug 20. PMID:18716025 doi:ddn239
↑ Gebbia M, Ferrero GB, Pilia G, Bassi MT, Aylsworth A, Penman-Splitt M, Bird LM, Bamforth JS, Burn J, Schlessinger D, Nelson DL, Casey B. X-linked situs abnormalities result from mutations in ZIC3. Nat Genet. 1997 Nov;17(3):305-8. PMID:9354794 doi:10.1038/ng1197-305
↑ Ware SM, Peng J, Zhu L, Fernbach S, Colicos S, Casey B, Towbin J, Belmont JW. Identification and functional analysis of ZIC3 mutations in heterotaxy and related congenital heart defects. Am J Hum Genet. 2004 Jan;74(1):93-105. Epub 2003 Dec 16. PMID:14681828 doi:S0002-9297(07)61948-X
↑ Chhin B, Hatayama M, Bozon D, Ogawa M, Schon P, Tohmonda T, Sassolas F, Aruga J, Valard AG, Chen SC, Bouvagnet P. Elucidation of penetrance variability of a ZIC3 mutation in a family with complex heart defects and functional analysis of ZIC3 mutations in the first zinc finger domain. Hum Mutat. 2007 Jun;28(6):563-70. PMID:17295247 doi:10.1002/humu.20480
↑ Wessels MW, Kuchinka B, Heydanus R, Smit BJ, Dooijes D, de Krijger RR, Lequin MH, de Jong EM, Husen M, Willems PJ, Casey B. Polyalanine expansion in the ZIC3 gene leading to X-linked heterotaxy with VACTERL association: a new polyalanine disorder? J Med Genet. 2010 May;47(5):351-5. doi: 10.1136/jmg.2008.060913. PMID:20452998 doi:10.1136/jmg.2008.060913
↑ Zhu L, Zhou G, Poole S, Belmont JW. Characterization of the interactions of human ZIC3 mutants with GLI3. Hum Mutat. 2008 Jan;29(1):99-105. PMID:17764085 doi:10.1002/humu.20606
↑ Ware SM, Peng J, Zhu L, Fernbach S, Colicos S, Casey B, Towbin J, Belmont JW. Identification and functional analysis of ZIC3 mutations in heterotaxy and related congenital heart defects. Am J Hum Genet. 2004 Jan;74(1):93-105. Epub 2003 Dec 16. PMID:14681828 doi:S0002-9297(07)61948-X
↑ Zhu L, Zhou G, Poole S, Belmont JW. Characterization of the interactions of human ZIC3 mutants with GLI3. Hum Mutat. 2008 Jan;29(1):99-105. PMID:17764085 doi:10.1002/humu.20606
↑ Hatayama M, Tomizawa T, Sakai-Kato K, Bouvagnet P, Kose S, Imamoto N, Yokoyama S, Utsunomiya-Tate N, Mikoshiba K, Kigawa T, Aruga J. Functional and structural basis of the nuclear localization signal in the ZIC3 zinc finger domain. Hum Mol Genet. 2008 Nov 15;17(22):3459-73. Epub 2008 Aug 20. PMID:18716025 doi:ddn239

1 Structural highlights
2 Disease
3 Function
4 Evolutionary Conservation
5 Publication Abstract from PubMed
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2rpc"

Categories: Homo sapiens | Large Structures | Kigawa T | Tomizawa T | Yokoyama S

@@ Line 1: / Line 1: @@
 ==Solution structure of the tandem zf-C2H2 domains from the human zinc finger protein ZIC 3==
-<StructureSection load='2rpc' size='340' side='right'caption='[[2rpc]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2rpc' size='340' side='right'caption='[[2rpc]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2rpc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RPC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2rpc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RPC 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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ZIC3 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=2rpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rpc OCA], [https://pdbe.org/2rpc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rpc RCSB], [https://www.ebi.ac.uk/pdbsum/2rpc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rpc ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[https://www.uniprot.org/uniprot/ZIC3_HUMAN ZIC3_HUMAN]] Defects in ZIC3 are the cause of visceral heterotaxy X-linked type 1 (HTX1) [MIM:[https://omim.org/entry/306955 306955]]. A form of visceral heterotaxy, a complex disorder due to disruption of the normal left-right asymmetry of the thoracoabdominal organs. It results in an abnormal arrangement of visceral organs, and a wide variety of congenital defects. Clinical features of visceral heterotaxy X-linked type 1 include dextrocardia, corrected transposition of great arteries, ventricular septal defect, patent ductus arteriosus, pulmonic stenosis, situs inversus viscerum, and asplenia and/or polysplenia.<ref>PMID:17764085</ref> <ref>PMID:18716025</ref> <ref>PMID:9354794</ref> <ref>PMID:14681828</ref> <ref>PMID:17295247</ref>   Defects in ZIC3 are a cause of VACTERL association X-linked with or without hydrocephalus (VACTERLX) [MIM:[https://omim.org/entry/314390 314390]]. A syndrome characterized by vertebral anomalies, anal atresia, cardiac malformations, tracheoesophageal fistula, renal anomalies (urethral atresia with hydronephrosis), and limb anomalies (hexadactyly, humeral hypoplasia, radial aplasia, and proximally placed thumb). Some patients may have hydrocephalus. Some cases of VACTERL-H are associated with increased chromosome breakage and rearrangement.<ref>PMID:20452998</ref>   Defects in ZIC3 are the cause of congenital heart defects, multiple types, 1, X-linked (CHTD1) [MIM:[https://omim.org/entry/306955 306955]]. A disorder characterized by congenital developmental abnormalities involving structures of the heart. Common defects include transposition of the great arteries, aortic stenosis, atrial septal defect, ventricular septal defect, pulmonic stenosis, and patent ductus arteriosus. The etiology of CHTD is complex, with contributions from environmental exposure, chromosomal abnormalities, and gene defects. Some patients with CHTD1 also have cardiac arrhythmias, which may be due to the anatomic defect itself or to surgical interventions.<ref>PMID:17764085</ref> <ref>PMID:14681828</ref>
+[https://www.uniprot.org/uniprot/ZIC3_HUMAN ZIC3_HUMAN] Defects in ZIC3 are the cause of visceral heterotaxy X-linked type 1 (HTX1) [MIM:[https://omim.org/entry/306955 306955]. A form of visceral heterotaxy, a complex disorder due to disruption of the normal left-right asymmetry of the thoracoabdominal organs. It results in an abnormal arrangement of visceral organs, and a wide variety of congenital defects. Clinical features of visceral heterotaxy X-linked type 1 include dextrocardia, corrected transposition of great arteries, ventricular septal defect, patent ductus arteriosus, pulmonic stenosis, situs inversus viscerum, and asplenia and/or polysplenia.<ref>PMID:17764085</ref> <ref>PMID:18716025</ref> <ref>PMID:9354794</ref> <ref>PMID:14681828</ref> <ref>PMID:17295247</ref>   Defects in ZIC3 are a cause of VACTERL association X-linked with or without hydrocephalus (VACTERLX) [MIM:[https://omim.org/entry/314390 314390]. A syndrome characterized by vertebral anomalies, anal atresia, cardiac malformations, tracheoesophageal fistula, renal anomalies (urethral atresia with hydronephrosis), and limb anomalies (hexadactyly, humeral hypoplasia, radial aplasia, and proximally placed thumb). Some patients may have hydrocephalus. Some cases of VACTERL-H are associated with increased chromosome breakage and rearrangement.<ref>PMID:20452998</ref>   Defects in ZIC3 are the cause of congenital heart defects, multiple types, 1, X-linked (CHTD1) [MIM:[https://omim.org/entry/306955 306955]. A disorder characterized by congenital developmental abnormalities involving structures of the heart. Common defects include transposition of the great arteries, aortic stenosis, atrial septal defect, ventricular septal defect, pulmonic stenosis, and patent ductus arteriosus. The etiology of CHTD is complex, with contributions from environmental exposure, chromosomal abnormalities, and gene defects. Some patients with CHTD1 also have cardiac arrhythmias, which may be due to the anatomic defect itself or to surgical interventions.<ref>PMID:17764085</ref> <ref>PMID:14681828</ref>
 == Function ==
-[[https://www.uniprot.org/uniprot/ZIC3_HUMAN ZIC3_HUMAN]] Acts as transcriptional activator. Required in the earliest stages in both axial midline development and left-right (LR) asymmetry specification. Binds to the minimal GLI-consensus sequence 5'-GGGTGGTC-3'.<ref>PMID:17764085</ref>
+[https://www.uniprot.org/uniprot/ZIC3_HUMAN ZIC3_HUMAN] Acts as transcriptional activator. Required in the earliest stages in both axial midline development and left-right (LR) asymmetry specification. Binds to the minimal GLI-consensus sequence 5'-GGGTGGTC-3'.<ref>PMID:17764085</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 35: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Kigawa, T]]
+[[Category: Kigawa T]]
-[[Category: Structural genomic]]
+[[Category: Tomizawa T]]
-[[Category: Tomizawa, T]]
+[[Category: Yokoyama S]]
-[[Category: Yokoyama, S]]
-[[Category: Disease mutation]]
-[[Category: Dna-binding]]
-[[Category: Metal-binding]]
-[[Category: National project on protein structural and functional analyse]]
-[[Category: Nppsfa]]
-[[Category: Nucleus]]
-[[Category: Polymorphism]]
-[[Category: Rsgi]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Zf-c2h2]]
-[[Category: Zic3]]
-[[Category: Zinc]]
-[[Category: Zinc finger protein of the cerebellum 3]]
-[[Category: Zinc-finger]]

2rpc

From Proteopedia

Current revision

Solution structure of the tandem zf-C2H2 domains from the human zinc finger protein ZIC 3

Structural highlights

Disease

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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