6pax: Difference between revisions

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-[[Image:6pax.gif|left|200px]]<br />
-<applet load="6pax" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="6pax, resolution 2.50&Aring;" />
-'''CRYSTAL STRUCTURE OF THE HUMAN PAX-6 PAIRED DOMAIN-DNA COMPLEX REVEALS A GENERAL MODEL FOR PAX PROTEIN-DNA INTERACTIONS'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF THE HUMAN PAX-6 PAIRED DOMAIN-DNA COMPLEX REVEALS A GENERAL MODEL FOR PAX PROTEIN-DNA INTERACTIONS==
-Pax6, a transcription factor containing the bipartite paired DNA-binding, domain, has critical roles in development of the eye, nose, pancreas, and, central nervous system. The 2.5 A structure of the human Pax6 paired, domain with its optimal 26-bp site reveals extensive DNA contacts from the, amino-terminal subdomain, the linker region, and the carboxy-terminal, subdomain. The Pax6 structure not only confirms the docking arrangement of, the amino-terminal subdomain as seen in cocrystals of the Drosophila Prd, Pax protein, but also reveals some interesting differences in this region, and helps explain the sequence specificity of paired domain-DNA, recognition. In addition, this structure gives the first detailed, information about how the paired linker region and carboxy-terminal, subdomain contact DNA. The extended linker makes minor groove contacts, over an 8-bp region, and the carboxy-terminal helix-turn-helix unit makes, base contacts in the major groove. The structure and docking arrangement, of the carboxy-terminal subdomain of Pax6 is remarkably similar to that of, the amino-terminal subdomain, and there is an approximate twofold symmetry, axis relating the polypeptide backbones of these two helix-turn-helix, units. Our structure of the Pax6 paired domain-DNA complex provides a, framework for understanding paired domain-DNA interactions, for analyzing, mutations that map in the linker and carboxy-terminal regions of the, paired domain, and for modeling protein-protein interactions of the Pax, family proteins.
+<StructureSection load='6pax' size='340' side='right'caption='[[6pax]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6pax]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PAX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PAX FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</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=6pax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pax OCA], [https://pdbe.org/6pax PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pax RCSB], [https://www.ebi.ac.uk/pdbsum/6pax PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pax ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/PAX6_HUMAN PAX6_HUMAN] Defects in PAX6 are the cause of aniridia (AN) [MIM:[https://omim.org/entry/106210 106210]. A congenital, bilateral, panocular disorder characterized by complete absence of the iris or extreme iris hypoplasia. Aniridia is not just an isolated defect in iris development but it is associated with macular and optic nerve hypoplasia, cataract, corneal changes, nystagmus. Visual acuity is generally low but is unrelated to the degree of iris hypoplasia. Glaucoma is a secondary problem causing additional visual loss over time.<ref>PMID:10346815</ref> <ref>PMID:8364574</ref> <ref>PMID:8640214</ref> <ref>PMID:9147640</ref> <ref>PMID:9281415</ref> <ref>PMID:9792406</ref> <ref>PMID:9856761</ref> <ref>PMID:10234503</ref> <ref>PMID:9931324</ref> <ref>PMID:7958875</ref> <ref>PMID:10955655</ref> <ref>PMID:10737978</ref> <ref>PMID:11553050</ref> <ref>PMID:11309364</ref> <ref>PMID:11826019</ref> <ref>PMID:12721955</ref> <ref>PMID:12634864</ref> <ref>PMID:12552561</ref> <ref>PMID:16493447</ref> <ref>PMID:21850189</ref>   Defects in PAX6 are a cause of Peters anomaly (PAN) [MIM:[https://omim.org/entry/604229 604229]. Peters anomaly consists of a central corneal leukoma, absence of the posterior corneal stroma and Descemet membrane, and a variable degree of iris and lenticular attachments to the central aspect of the posterior cornea.<ref>PMID:12721955</ref> <ref>PMID:8162071</ref> <ref>PMID:10441571</ref>   Defects in PAX6 are a cause of foveal hypoplasia (FOVHYP) [MIM:[https://omim.org/entry/136520 136520]. Foveal hypoplasia can be isolated or associated with presenile cataract. Inheritance is autosomal dominant.<ref>PMID:8640214</ref> <ref>PMID:9931324</ref>   Defects in PAX6 are a cause of keratitis hereditary (KERH) [MIM:[https://omim.org/entry/148190 148190]. An ocular disorder characterized by corneal opacification, recurrent stromal keratitis and vascularization.  Defects in PAX6 are a cause of coloboma of iris choroid and retina (COI) [MIM:[https://omim.org/entry/120200 120200]; also known as uveoretinal coloboma. Ocular colobomas are a set of malformations resulting from abnormal morphogenesis of the optic cup and stalk, and the fusion of the fetal fissure (optic fissure). Severe colobomatous malformations may cause as much as 10% of the childhood blindness. The clinical presentation of ocular coloboma is variable. Some individuals may present with minimal defects in the anterior iris leaf without other ocular defects. More complex malformations create a combination of iris, uveoretinal and/or optic nerve defects without or with microphthalmia or even anophthalmia.<ref>PMID:12721955</ref>   Defects in PAX6 are a cause of coloboma of optic nerve (COLON) [MIM:[https://omim.org/entry/120430 120430].  Defects in PAX6 are a cause of bilateral optic nerve hypoplasia (BONH) [MIM:[https://omim.org/entry/165550 165550]; also known as bilateral optic nerve aplasia. A congenital anomaly in which the optic disc appears abnormally small. It may be an isolated finding or part of a spectrum of anatomic and functional abnormalities that includes partial or complete agenesis of the septum pellucidum, other midline brain defects, cerebral anomalies, pituitary dysfunction, and structural abnormalities of the pituitary.<ref>PMID:12721955</ref>   Defects in PAX6 are a cause of aniridia cerebellar ataxia and mental deficiency (ACAMD) [MIM:[https://omim.org/entry/206700 206700]; also known as Gillespie syndrome. A rare condition consisting of partial rudimentary iris, cerebellar impairment of the ability to perform coordinated voluntary movements, and mental retardation.<ref>PMID:17595013</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/PAX6_HUMAN PAX6_HUMAN] Transcription factor with important functions in the development of the eye, nose, central nervous system and pancreas. Required for the differentiation of pancreatic islet alpha cells (By similarity). Competes with PAX4 in binding to a common element in the glucagon, insulin and somatostatin promoters. Regulates specification of the ventral neuron subtypes by establishing the correct progenitor domains (By similarity). Isoform 5a appears to function as a molecular switch that specifies target genes.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pa/6pax_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=6pax ConSurf].
+<div style="clear:both"></div>
-==Disease==
+==See Also==
-Known diseases associated with this structure: Aniridia, type II OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=607108 607108]], Cataract, congenital, with late-onset corneal dystrophy OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=607108 607108]], Coloboma, ocular OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=607108 607108]], Ectopia pupillae OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=607108 607108]], Eye anomalies, multiplex OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=607108 607108]], Foveal hypoplasia, isolated OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=607108 607108]], Keratitis OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=607108 607108]], Morning glory disc anomaly OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=607108 607108]], Optic nerve hypoplasia/aplasia OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=607108 607108]], Peters anomaly OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=607108 607108]]
+*[[Paired box protein|Paired box protein]]
+== References ==
-==About this Structure==
+<references/>
-PAX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=6PAX OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Crystal structure of the human Pax6 paired domain-DNA complex reveals specific roles for the linker region and carboxy-terminal subdomain in DNA binding., Xu HE, Rould MA, Xu W, Epstein JA, Maas RL, Pabo CO, Genes Dev. 1999 May 15;13(10):1263-75. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10346815 10346815]
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Epstein, J.A.]]
+[[Category: Epstein JA]]
-[[Category: Maas, R.L.]]
+[[Category: Maas RL]]
-[[Category: Pabo, C.O.]]
+[[Category: Pabo CO]]
-[[Category: Rould, M.A.]]
+[[Category: Rould MA]]
-[[Category: Xu, H.E.]]
+[[Category: Xu HE]]
-[[Category: Xu, W.]]
+[[Category: Xu W]]
-[[Category: paired domain]]
-[[Category: pax]]
-[[Category: protein-dna interactions]]
-[[Category: transcription]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 23:52:52 2007''