1yd8: Difference between revisions

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-[[Image:1yd8.gif|left|200px]]
-<!--
+==COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN==
-The line below this paragraph, containing "STRUCTURE_1yd8", creates the "Structure Box" on the page.
+<StructureSection load='1yd8' size='340' side='right'caption='[[1yd8]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1yd8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YD8 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#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=1yd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd8 OCA], [https://pdbe.org/1yd8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yd8 RCSB], [https://www.ebi.ac.uk/pdbsum/1yd8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yd8 ProSAT]</span></td></tr>
-{{STRUCTURE_1yd8|  PDB=1yd8  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/UBC_BOVIN UBC_BOVIN] Ubiquitin: Exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling (By similarity).
+== 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/yd/1yd8_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=1yd8 ConSurf].
+<div style="clear:both"></div>
-'''COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN'''
+==See Also==
+*[[3D structures of ubiquitin|3D structures of ubiquitin]]
+__TOC__
-==Overview==
+</StructureSection>
-The Golgi-localized, gamma-ear-containing, Arf (ADP-ribosylation factor)-binding (GGA) proteins are clathrin adaptors that mediate the sorting of transmembrane-cargo molecules at the trans-Golgi network and endosomes. Cargo proteins can be directed into the GGA pathway by at least two different types of sorting signals: acidic cluster-dileucine motifs and covalent modification by ubiquitin. The latter modification is recognized by the GGAs through binding to their GAT [GGA and TOM (target of Myb)] domain. Here we report the crystal structure of the GAT domain of human GGA3 in a 1:1 complex with ubiquitin at 2.8-A resolution. Ubiquitin binds to a hydrophobic and acidic patch on helices alpha1 and alpha2 of the GAT three-helix bundle that includes Asn-223, Leu-227, Glu-230, Met-231, Asp-244, Glu-246, Leu-247, Glu-250, and Leu-251. The GAT-binding surface on ubiquitin is a hydrophobic patch centered on Ile-44 that is also responsible for binding most other ubiquitin effectors. The ubiquitin-binding site observed in the crystal is distinct from the Rabaptin-5-binding site on helices alpha2 and alpha3 of the GAT domain. Mutational analysis and modeling of the ubiquitin-Rabaptin-5-GAT ternary complex indicates that ubiquitin and Rabaptin-5 can bind to the GAT domain at two different sites without any steric conflict. This ability highlights the GAT domain as a hub for interactions with multiple partners in trafficking.
-==About this Structure==
-YD8 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD8 OCA].
-==Reference==
-Structural mechanism for ubiquitinated-cargo recognition by the Golgi-localized, gamma-ear-containing, ADP-ribosylation-factor-binding proteins., Prag G, Lee S, Mattera R, Arighi CN, Beach BM, Bonifacino JS, Hurley JH, Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2334-9. Epub 2005 Feb 8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15701688 15701688]
 [[Category: Bos taurus]]
 [[Category: Homo sapiens]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Arighi, C N.]]
+[[Category: Arighi CN]]
-[[Category: Beach, B M.]]
+[[Category: Beach BM]]
-[[Category: Bonifacino, J S.]]
+[[Category: Bonifacino JS]]
-[[Category: Hurley, J H.]]
+[[Category: Hurley JH]]
-[[Category: Lee, S.]]
+[[Category: Lee S]]
-[[Category: Mattera, R.]]
+[[Category: Mattera R]]
-[[Category: Prag, G.]]
+[[Category: Prag G]]
-[[Category: Mono-ubiquitination]]
-[[Category: Post translational modification]]
-[[Category: Protein transport;]]
-[[Category: Trafficking]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 16:10:42 2008''