3hm3

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[[Image:3hm3.png|left|200px]]
 
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==The Structure and conformation of Lys-63 linked tetra-ubiquitin==
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The line below this paragraph, containing "STRUCTURE_3hm3", creates the "Structure Box" on the page.
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<StructureSection load='3hm3' size='340' side='right'caption='[[3hm3]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3hm3]] is a 4 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=3HM3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HM3 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.96&#8491;</td></tr>
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<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>
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{{STRUCTURE_3hm3| PDB=3hm3 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3hm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hm3 OCA], [https://pdbe.org/3hm3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hm3 RCSB], [https://www.ebi.ac.uk/pdbsum/3hm3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hm3 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/UBC_HUMAN UBC_HUMAN] 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.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hm/3hm3_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3hm3 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Ubiquitination involves the covalent attachment of the ubiquitin (Ub) C-terminus to the lysine side chain of a substrate protein by an isopeptide bond. The modification can comprise a single Ub moiety or a chain of Ub molecules joined by isopeptide bonds between the C-terminus of one Ub with one of the seven lysine residues in the next Ub. Modification of substrate proteins with Lys63-linked poly-Ub plays a key nondegradative signaling role in many biological processes, including DNA repair and nuclear factor-kappaB activation, whereas substrates modified by Lys48-linked chains are targeted to the proteasome for degradation. The distinct signaling properties of alternatively linked Ub chains presumably stem from structural differences that can be distinguished by effector proteins. We have determined the crystal structure of Lys63 tetra-Ub at a resolution of 1.96 A and performed small-angle X-ray scattering experiments and molecular dynamics simulations to probe the conformation of Lys63 tetra-Ub in solution. The chain adopts a highly extended conformation in the crystal, in contrast with the compact globular fold of Lys48 tetra-Ub. Small-angle X-ray scattering experiments show that the Lys63 tetra-Ub chain is dynamic in solution, adopting an ensemble of conformations that are more compact than the extended form in the crystal. The results of these studies provide a basis for understanding the differences in the behavior and recognition of Lys63 poly-Ub chains.
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===The Structure and conformation of Lys-63 linked tetra-ubiquitin===
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The structure and conformation of Lys63-linked tetraubiquitin.,Datta AB, Hura GL, Wolberger C J Mol Biol. 2009 Oct 9;392(5):1117-24. Epub 2009 Aug 4. PMID:19664638<ref>PMID:19664638</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3hm3" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_19664638}}, adds the Publication Abstract to the page
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*[[3D structures of ubiquitin|3D structures of ubiquitin]]
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(as it appears on PubMed at http://www.pubmed.gov), where 19664638 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19664638}}
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__TOC__
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</StructureSection>
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==About this Structure==
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3HM3 is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HM3 OCA].
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==Reference==
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<ref group="xtra">PMID:19664638</ref><references group="xtra"/>
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Datta, A B.]]
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[[Category: Large Structures]]
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[[Category: Hura, G L.]]
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[[Category: Datta AB]]
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[[Category: Wolberger, C.]]
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[[Category: Hura GL]]
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[[Category: Cytoplasm]]
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[[Category: Wolberger C]]
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[[Category: Isopeptide bond]]
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[[Category: Lys63-linked]]
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[[Category: Nucleus]]
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[[Category: Phosphoprotein]]
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[[Category: Signaling protein]]
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[[Category: Tetrameric ubiquitin]]
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[[Category: Ubiquitin chain]]
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[[Category: Ubl conjugation]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Sep 21 19:27:54 2009''
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Current revision

The Structure and conformation of Lys-63 linked tetra-ubiquitin

PDB ID 3hm3

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