6if1: Difference between revisions
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==Crystal structure of Ube2K and K48-linked di-ubiquitin complex== | |||
<StructureSection load='6if1' size='340' side='right'caption='[[6if1]], [[Resolution|resolution]] 2.47Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6if1]] 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=6IF1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IF1 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]] 2.466Å</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=6if1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6if1 OCA], [https://pdbe.org/6if1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6if1 RCSB], [https://www.ebi.ac.uk/pdbsum/6if1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6if1 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/UBE2K_HUMAN UBE2K_HUMAN] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro, in the presence or in the absence of BRCA1-BARD1 E3 ubiquitin-protein ligase complex, catalyzes the synthesis of 'Lys-48'-linked polyubiquitin chains. Does not transfer ubiquitin directly to but elongates monoubiquitinated substrate protein. Mediates the selective degradation of short-lived and abnormal proteins, such as the endoplasmic reticulum-associated degradation (ERAD) of misfolded lumenal proteins. Ubiquitinates huntingtin. May mediate foam cell formation by the suppression of apoptosis of lipid-bearing macrophages through ubiquitination and subsequence degradation of p53/TP53. Proposed to be involved in ubiquitination and proteolytic processing of NF-kappa-B; in vitro supports ubiquitination of NFKB1. In case of infection by cytomegaloviruses may be involved in the US11-dependent degradation of MHC class I heavy chains following their export from the ER to the cytosol. In case of viral infections may be involved in the HPV E7 protein-dependent degradation of RB1.<ref>PMID:8702625</ref> <ref>PMID:10634809</ref> <ref>PMID:10675012</ref> <ref>PMID:16714285</ref> <ref>PMID:16868077</ref> <ref>PMID:17873885</ref> <ref>PMID:20061386</ref> <ref>PMID:19906396</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Ubiquitin-conjugating enzymes (E2) form thioester bonds with ubiquitin (Ub), which are subsequently transferred to target proteins for cellular progress. Ube2K/E2-25K (a class II E2 enzyme) contains a C-terminal ubiquitin-associated (UBA) domain that has been suggested to control ubiquitin recognition, dimerization, or poly-ubiquitin chain formation. Ube2K is a special E2 because it synthesizes K48-linked poly-ubiquitin chains without E3 ubiquitin ligase. We found that a novel interaction between the acceptor di-Ub (Ub(2)) and the auxiliary Ube2K promotes the discharging reaction and production of tri-Ub (Ub(3)), probably by guiding and positioning the K48 (in the distal Ub) of the acceptor Ub(2) in the active site. We also determined the crystal structure of Ube2K-Ub(2) at 2.47â¯A resolution. Based on our structural and biochemical data, we proposed a structural model of Ub(3) synthesis by Ube2K without E3. | |||
Crystal structure of the Ube2K/E2-25K and K48-linked di-ubiquitin complex provides structural insight into the mechanism of K48-specific ubiquitin chain synthesis.,Lee JG, Youn HS, Kang JY, Park SY, Kidera A, Yoo YJ, Eom SH Biochem Biophys Res Commun. 2018 Nov 17;506(1):102-107. doi: , 10.1016/j.bbrc.2018.10.067. Epub 2018 Oct 16. PMID:30336976<ref>PMID:30336976</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 6if1" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[3D structures of ubiquitin|3D structures of ubiquitin]] | |||
*[[3D structures of ubiquitin conjugating enzyme|3D structures of ubiquitin conjugating enzyme]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Homo sapiens]] | |||
[[Category: Large Structures]] | |||
[[Category: An JY]] | |||
[[Category: Eom SH]] | |||
[[Category: Kang JY]] | |||
[[Category: Lee J-G]] | |||
[[Category: Lee Y]] | |||
[[Category: Lim JJ]] | |||
[[Category: Park KR]] | |||
[[Category: Youn H-S]] | |||
Latest revision as of 12:40, 22 November 2023
Crystal structure of Ube2K and K48-linked di-ubiquitin complexCrystal structure of Ube2K and K48-linked di-ubiquitin complex
Structural highlights
FunctionUBE2K_HUMAN Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro, in the presence or in the absence of BRCA1-BARD1 E3 ubiquitin-protein ligase complex, catalyzes the synthesis of 'Lys-48'-linked polyubiquitin chains. Does not transfer ubiquitin directly to but elongates monoubiquitinated substrate protein. Mediates the selective degradation of short-lived and abnormal proteins, such as the endoplasmic reticulum-associated degradation (ERAD) of misfolded lumenal proteins. Ubiquitinates huntingtin. May mediate foam cell formation by the suppression of apoptosis of lipid-bearing macrophages through ubiquitination and subsequence degradation of p53/TP53. Proposed to be involved in ubiquitination and proteolytic processing of NF-kappa-B; in vitro supports ubiquitination of NFKB1. In case of infection by cytomegaloviruses may be involved in the US11-dependent degradation of MHC class I heavy chains following their export from the ER to the cytosol. In case of viral infections may be involved in the HPV E7 protein-dependent degradation of RB1.[1] [2] [3] [4] [5] [6] [7] [8] Publication Abstract from PubMedUbiquitin-conjugating enzymes (E2) form thioester bonds with ubiquitin (Ub), which are subsequently transferred to target proteins for cellular progress. Ube2K/E2-25K (a class II E2 enzyme) contains a C-terminal ubiquitin-associated (UBA) domain that has been suggested to control ubiquitin recognition, dimerization, or poly-ubiquitin chain formation. Ube2K is a special E2 because it synthesizes K48-linked poly-ubiquitin chains without E3 ubiquitin ligase. We found that a novel interaction between the acceptor di-Ub (Ub(2)) and the auxiliary Ube2K promotes the discharging reaction and production of tri-Ub (Ub(3)), probably by guiding and positioning the K48 (in the distal Ub) of the acceptor Ub(2) in the active site. We also determined the crystal structure of Ube2K-Ub(2) at 2.47â¯A resolution. Based on our structural and biochemical data, we proposed a structural model of Ub(3) synthesis by Ube2K without E3. Crystal structure of the Ube2K/E2-25K and K48-linked di-ubiquitin complex provides structural insight into the mechanism of K48-specific ubiquitin chain synthesis.,Lee JG, Youn HS, Kang JY, Park SY, Kidera A, Yoo YJ, Eom SH Biochem Biophys Res Commun. 2018 Nov 17;506(1):102-107. doi: , 10.1016/j.bbrc.2018.10.067. Epub 2018 Oct 16. PMID:30336976[9] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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