3l1z

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "3l1z" [edit=sysop:move=sysop])
Current revision (08:28, 6 September 2023) (edit) (undo)
 
(4 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:3l1z.png|left|200px]]
 
-
<!--
+
==Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme==
-
The line below this paragraph, containing "STRUCTURE_3l1z", creates the "Structure Box" on the page.
+
<StructureSection load='3l1z' size='340' side='right'caption='[[3l1z]], [[Resolution|resolution]] 3.17&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'>[[3l1z]] is a 2 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=3L1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3L1Z 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]] 3.17&#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=3l1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l1z OCA], [https://pdbe.org/3l1z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3l1z RCSB], [https://www.ebi.ac.uk/pdbsum/3l1z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3l1z ProSAT]</span></td></tr>
-
{{STRUCTURE_3l1z| PDB=3l1z | SCENE= }}
+
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/UB2D3_HUMAN UB2D3_HUMAN] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-11'-, as well as 'Lys-48'-linked polyubiquitination. Cooperates with the E2 CDC34 and the SCF(FBXW11) E3 ligase complex for the polyubiquitination of NFKBIA leading to its subsequent proteasomal degradation. Acts as an initiator E2, priming the phosphorylated NFKBIA target at positions 'Lys-21' and/or 'Lys-22' with a monoubiquitin. Ubiquitin chain elongation is then performed by CDC34, building ubiquitin chains from the UBE2D3-primed NFKBIA-linked ubiquitin. Acts also as an initiator E2, in conjunction with RNF8, for the priming of PCNA. Monoubiquitination of PCNA, and its subsequent polyubiquitination, are essential events in the operation of the DNA damage tolerance (DDT) pathway that is activated after DNA damage caused by UV or chemical agents during S-phase. Associates with the BRCA1/BARD1 E3 ligase complex to perform ubiquitination at DNA damage sites following ionizing radiation leading to DNA repair. Targets DAPK3 for ubiquitination which influences promyelocytic leukemia protein nuclear body (PML-NB) formation in the nucleus. In conjunction with the MDM2 and TOPORS E3 ligases, functions ubiquitination of p53/TP53. Supports NRDP1-mediated ubiquitination and degradation of ERBB3 and of BRUCE which triggers apoptosis. In conjunction with the CBL E3 ligase, targets EGFR for polyubiquitination at the plasma membrane as well as during its internalization and transport on endosomes. In conjunction with the STUB1 E3 quality control E3 ligase, ubiquitinates unfolded proteins to catalyze their immediate destruction (By similarity).<ref>PMID:10329681</ref> <ref>PMID:11743028</ref> <ref>PMID:12646252</ref> <ref>PMID:15247280</ref> <ref>PMID:15280377</ref> <ref>PMID:15496420</ref> <ref>PMID:16628214</ref> <ref>PMID:18515077</ref> <ref>PMID:18948756</ref> <ref>PMID:18508924</ref> <ref>PMID:18284575</ref> <ref>PMID:20061386</ref> <ref>PMID:20347421</ref> <ref>PMID:21532592</ref>
 +
== 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/l1/3l1z_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=3l1z ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Human E4B, also called UFD2a, is a U box-containing protein that functions as an E3 ubiquitin ligase and an E4 polyubiquitin chain elongation factor. E4B is thought to participate in the proteasomal degradation of misfolded or damaged proteins through association with chaperones. The U box domain is an anchor site for E2 ubiquitin-conjugating enzymes, but little is known of the binding mechanism. Using X-ray crystallography and NMR spectroscopy, we determined the structures of E4B U box free and bound to UbcH5c and Ubc4 E2s. Whereas previously characterized U box domains are homodimeric, we show that E4B U box is a monomer stabilized by a network of hydrogen bonds identified from scalar coupling measurements. These structural studies, complemented by calorimetry- and NMR-based binding assays, suggest an allosteric regulation of UbcH5c and Ubc4 by E4B U box and provide a molecular basis to understand how the ubiquitylation machinery involving E4B assembles.
-
===Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme===
+
Molecular basis for the association of human E4B U box ubiquitin ligase with E2-conjugating enzymes UbcH5c and Ubc4.,Benirschke RC, Thompson JR, Nomine Y, Wasielewski E, Juranic N, Macura S, Hatakeyama S, Nakayama KI, Botuyan MV, Mer G Structure. 2010 Aug 11;18(8):955-65. PMID:20696396<ref>PMID:20696396</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 3l1z" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_20696396}}, adds the Publication Abstract to the page
+
*[[3D structures of ubiquitin conjugating enzyme|3D structures of ubiquitin conjugating enzyme]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 20696396 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_20696396}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
[[3l1z]] is a 2 chain structure with sequence 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=3L1Z OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:020696396</ref><references group="xtra"/>
+
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Ubiquitin--protein ligase]]
+
[[Category: Large Structures]]
-
[[Category: Benirschke, R.]]
+
[[Category: Benirschke R]]
-
[[Category: Mer, G.]]
+
[[Category: Mer G]]
-
[[Category: Thompson, J R.]]
+
[[Category: Thompson JR]]
-
[[Category: E2 ubiquitin conjugating enzyme]]
+
-
[[Category: E4b]]
+
-
[[Category: Ligase]]
+
-
[[Category: U-box ubiquitin ligase]]
+
-
[[Category: Ubch5c]]
+
-
[[Category: Ubl conjugation pathway]]
+
-
[[Category: Ufd2a]]
+

Current revision

Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme

PDB ID 3l1z

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3l1z"
Personal tools