4i9y

From Proteopedia

(Difference between revisions)

Current revision

Structure of the C-terminal domain of Nup358

Structural highlights

4i9y is a 6 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.75Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

RBP2_HUMAN Defects in RANBP2 are the cause of encephalopathy acute infection-induced type 3 (IIAE3) [MIM:608033. A rapidly progressive encephalopathy manifesting in susceptibile individuals with seizures and coma. It can occur within days in otherwise healthy children after common viral infections such as influenza and parainfluenza, without evidence of viral infection of the brain or inflammatory cell infiltration. Brain T2-weighted magnetic resonance imaging reveals characteristic symmetric lesions present in the thalami, pons and brainstem. Note=Mutations in the RANBP2 gene predispose to IIAE3, but by themselves are insufficient to make the phenotype fully penetrant; additional genetic and environmental factors are required (PubMed:19118815).^[1]

Function

RBP2_HUMAN E3 SUMO-protein ligase which facilitates SUMO1 and SUMO2 conjugation by UBE2I. Involved in transport factor (Ran-GTP, karyopherin)-mediated protein import via the F-G repeat-containing domain which acts as a docking site for substrates. Could also have isomerase or chaperone activity and may bind RNA or DNA. Component of the nuclear export pathway. Specific docking site for the nuclear export factor exportin-1.^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

The nuclear pore complex is the sole mediator of bidirectional transport between the nucleus and cytoplasm. Nup358 is a metazoan-specific nucleoporin that localizes to the cytoplasmic filaments and provides several binding sites for the mobile nucleocytoplasmic transport machinery. Here we present the crystal structure of the C-terminal domain (CTD) of Nup358 at 1.75A resolution. The structure reveals that the CTD adopts a cyclophilin-like fold with a non-canonical active-site configuration. We determined biochemically that the CTD possesses weak peptidyl-prolyl isomerase activity and show that the active-site cavity mediates a weak association with the human immunodeficiency virus-1 capsid protein, supporting its role in viral infection. Overall, the surface is evolutionarily conserved, suggesting that the CTD serves as a protein-protein interaction platform. However, we demonstrate that the CTD is dispensable for nuclear envelope localization of Nup358, suggesting that the CTD does not interact with other nucleoporins.

Structural and Functional Analysis of the C-Terminal Domain of Nup358/RanBP2.,Lin DH, Zimmermann S, Stuwe T, Stuwe E, Hoelz A J Mol Biol. 2013 Jan 23. pii: S0022-2836(13)00037-5. doi:, 10.1016/j.jmb.2013.01.021. PMID:23353830^[6]

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

References

↑ Neilson DE, Adams MD, Orr CM, Schelling DK, Eiben RM, Kerr DS, Anderson J, Bassuk AG, Bye AM, Childs AM, Clarke A, Crow YJ, Di Rocco M, Dohna-Schwake C, Dueckers G, Fasano AE, Gika AD, Gionnis D, Gorman MP, Grattan-Smith PJ, Hackenberg A, Kuster A, Lentschig MG, Lopez-Laso E, Marco EJ, Mastroyianni S, Perrier J, Schmitt-Mechelke T, Servidei S, Skardoutsou A, Uldall P, van der Knaap MS, Goglin KC, Tefft DL, Aubin C, de Jager P, Hafler D, Warman ML. Infection-triggered familial or recurrent cases of acute necrotizing encephalopathy caused by mutations in a component of the nuclear pore, RANBP2. Am J Hum Genet. 2009 Jan;84(1):44-51. doi: 10.1016/j.ajhg.2008.12.009. PMID:19118815 doi:10.1016/j.ajhg.2008.12.009
↑ Pichler A, Gast A, Seeler JS, Dejean A, Melchior F. The nucleoporin RanBP2 has SUMO1 E3 ligase activity. Cell. 2002 Jan 11;108(1):109-20. PMID:11792325
↑ Kirsh O, Seeler JS, Pichler A, Gast A, Muller S, Miska E, Mathieu M, Harel-Bellan A, Kouzarides T, Melchior F, Dejean A. The SUMO E3 ligase RanBP2 promotes modification of the HDAC4 deacetylase. EMBO J. 2002 Jun 3;21(11):2682-91. PMID:12032081 doi:10.1093/emboj/21.11.2682
↑ Pichler A, Knipscheer P, Saitoh H, Sixma TK, Melchior F. The RanBP2 SUMO E3 ligase is neither HECT- nor RING-type. Nat Struct Mol Biol. 2004 Oct;11(10):984-91. Epub 2004 Sep 19. PMID:15378033 doi:10.1038/nsmb834
↑ Reverter D, Lima CD. Insights into E3 ligase activity revealed by a SUMO-RanGAP1-Ubc9-Nup358 complex. Nature. 2005 Jun 2;435(7042):687-92. PMID:15931224 doi:10.1038/nature03588
↑ Lin DH, Zimmermann S, Stuwe T, Stuwe E, Hoelz A. Structural and Functional Analysis of the C-Terminal Domain of Nup358/RanBP2. J Mol Biol. 2013 Jan 23. pii: S0022-2836(13)00037-5. doi:, 10.1016/j.jmb.2013.01.021. PMID:23353830 doi:http://dx.doi.org/10.1016/j.jmb.2013.01.021

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4i9y"

@@ Line 1: / Line 1: @@
 ==Structure of the C-terminal domain of Nup358==
-<StructureSection load='4i9y' size='340' side='right' caption='[[4i9y]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
+<StructureSection load='4i9y' size='340' side='right'caption='[[4i9y]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4i9y]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I9Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I9Y FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4i9y]] is a 6 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=4I9Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4I9Y FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4if5|4if5]], [[4if6|4if6]], [[4ig9|4ig9]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RANBP2, NUP358 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4i9y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i9y OCA], [https://pdbe.org/4i9y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4i9y RCSB], [https://www.ebi.ac.uk/pdbsum/4i9y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4i9y ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4i9y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i9y OCA], [http://pdbe.org/4i9y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4i9y RCSB], [http://www.ebi.ac.uk/pdbsum/4i9y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4i9y ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[http://www.uniprot.org/uniprot/RBP2_HUMAN RBP2_HUMAN]] Defects in RANBP2 are the cause of encephalopathy acute infection-induced type 3 (IIAE3) [MIM:[http://omim.org/entry/608033 608033]]. A rapidly progressive encephalopathy manifesting in susceptibile individuals with seizures and coma. It can occur within days in otherwise healthy children after common viral infections such as influenza and parainfluenza, without evidence of viral infection of the brain or inflammatory cell infiltration. Brain T2-weighted magnetic resonance imaging reveals characteristic symmetric lesions present in the thalami, pons and brainstem. Note=Mutations in the RANBP2 gene predispose to IIAE3, but by themselves are insufficient to make the phenotype fully penetrant; additional genetic and environmental factors are required (PubMed:19118815).<ref>PMID:19118815</ref>
+[https://www.uniprot.org/uniprot/RBP2_HUMAN RBP2_HUMAN] Defects in RANBP2 are the cause of encephalopathy acute infection-induced type 3 (IIAE3) [MIM:[https://omim.org/entry/608033 608033]. A rapidly progressive encephalopathy manifesting in susceptibile individuals with seizures and coma. It can occur within days in otherwise healthy children after common viral infections such as influenza and parainfluenza, without evidence of viral infection of the brain or inflammatory cell infiltration. Brain T2-weighted magnetic resonance imaging reveals characteristic symmetric lesions present in the thalami, pons and brainstem. Note=Mutations in the RANBP2 gene predispose to IIAE3, but by themselves are insufficient to make the phenotype fully penetrant; additional genetic and environmental factors are required (PubMed:19118815).<ref>PMID:19118815</ref>
 == Function ==
-[[http://www.uniprot.org/uniprot/RBP2_HUMAN RBP2_HUMAN]] E3 SUMO-protein ligase which facilitates SUMO1 and SUMO2 conjugation by UBE2I. Involved in transport factor (Ran-GTP, karyopherin)-mediated protein import via the F-G repeat-containing domain which acts as a docking site for substrates. Could also have isomerase or chaperone activity and may bind RNA or DNA. Component of the nuclear export pathway. Specific docking site for the nuclear export factor exportin-1.<ref>PMID:11792325</ref> <ref>PMID:12032081</ref> <ref>PMID:15378033</ref> <ref>PMID:15931224</ref>
+[https://www.uniprot.org/uniprot/RBP2_HUMAN RBP2_HUMAN] E3 SUMO-protein ligase which facilitates SUMO1 and SUMO2 conjugation by UBE2I. Involved in transport factor (Ran-GTP, karyopherin)-mediated protein import via the F-G repeat-containing domain which acts as a docking site for substrates. Could also have isomerase or chaperone activity and may bind RNA or DNA. Component of the nuclear export pathway. Specific docking site for the nuclear export factor exportin-1.<ref>PMID:11792325</ref> <ref>PMID:12032081</ref> <ref>PMID:15378033</ref> <ref>PMID:15931224</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 25: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Hoelz, A]]
+[[Category: Large Structures]]
-[[Category: Lin, D H]]
+[[Category: Hoelz A]]
-[[Category: Stuwe, E]]
+[[Category: Lin DH]]
-[[Category: Stuwe, T]]
+[[Category: Stuwe E]]
-[[Category: Zimmermann, S]]
+[[Category: Stuwe T]]
-[[Category: Nuclear pore complex]]
+[[Category: Zimmermann S]]
-[[Category: Transport protein]]

4i9y

From Proteopedia

Current revision

Structure of the C-terminal domain of Nup358

Structural highlights

Disease

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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