5jpx

From Proteopedia

(Difference between revisions)

Revision as of 10:11, 14 June 2023

Solution structure of the TRIM21 B-box2 (B2)

Structural highlights

5jpx is a 1 chain structure with sequence from Homo sapiens. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RO52_HUMAN E3 ubiquitin-protein ligase whose activity is dependent on E2 enzymes, UBE2D1, UBE2D2, UBE2E1 and UBE2E2. Forms a ubiquitin ligase complex in cooperation with the E2 UBE2D2 that is used not only for the ubiquitination of USP4 and IKBKB but also for its self-ubiquitination. Component of cullin-RING-based SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complexes such as SCF(SKP2)-like complexes. A TRIM21-containing SCF(SKP2)-like complex is shown to mediate ubiquitination of CDKN1B ('Thr-187' phosphorylated-form), thereby promoting its degradation by the proteasome. Monoubiquitinates IKBKB that will negatively regulates Tax-induced NF-kappa-B signaling. Negatively regulates IFN-beta production post-pathogen recognition by polyubiquitin-mediated degradation of IRF3. Mediates the ubiquitin-mediated proteasomal degradation of IgG1 heavy chain, which is linked to the VCP-mediated ER-associated degradation (ERAD) pathway. Promotes IRF8 ubiquitination, which enhanced the ability of IRF8 to stimulate cytokine genes transcription in macrophages. Plays a role in the regulation of the cell cycle progression. Enhances the decapping activity of DCP2. Exists as a ribonucleoprotein particle present in all mammalian cells studied and composed of a single polypeptide and one of four small RNA molecules. At least two isoforms are present in nucleated and red blood cells, and tissue specific differences in RO/SSA proteins have been identified. The common feature of these proteins is their ability to bind HY RNAs.2. Involved in the regulation of innate immunity and the inflammatory response in response to IFNG/IFN-gamma. Organizes autophagic machinery by serving as a platform for the assembly of ULK1, Beclin 1/BECN1 and ATG8 family members and recognizes specific autophagy targets, thus coordinating target recognition with assembly of the autophagic apparatus and initiation of autophagy. Acts as an autophagy receptor for the degradation of IRF3, hence attenuating type I interferon (IFN)-dependent immune responses (PubMed:26347139).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10]

Publication Abstract from PubMed

Tripartite motif-containing (TRIM) proteins are defined by the sequential arrangement of RING, B-box and coiled-coil domains (RBCC), where the B-box domain is a unique feature of the TRIM protein family. TRIM21 is an E3 ubiquitin-protein ligase implicated in innate immune signaling by acting as an autoantigen and by modifying interferon regulatory factors. Here we report the three-dimensional solution structure of the TRIM21 B-box2 domain by nuclear magnetic resonance (NMR) spectroscopy. The structure of the B-box2 domain, comprising TRIM21 residues 86-130, consists of a short alpha-helical segment with an N-terminal short beta-strand and two anti-parallel beta-strands jointly found the core, and adopts a RING-like fold. This betabetaalphabeta core largely defines the overall fold of the TRIM21 B-box2 and the coordination of one Zn2+ ion stabilizes the tertiary structure of the protein. Using NMR titration experiments, we have identified an exposed interaction surface, a novel interaction patch where the B-box2 is likely to bind the N-terminal RING domain. Our structure together with comparisons with other TRIM B-box domains jointly reveal how its different surfaces are employed for various modular interactions, and provides extended understanding of how this domain relates to flanking domains in TRIM proteins.

Solution NMR structure of the TRIM21 B-box2 and identification of residues involved in its interaction with the RING domain.,Wallenhammar A, Anandapadamanaban M, Lemak A, Mirabello C, Lundstrom P, Wallner B, Sunnerhagen M PLoS One. 2017 Jul 28;12(7):e0181551. doi: 10.1371/journal.pone.0181551., eCollection 2017. PMID:28753623^[11]

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

References

↑ Wada K, Kamitani T. Autoantigen Ro52 is an E3 ubiquitin ligase. Biochem Biophys Res Commun. 2006 Jan 6;339(1):415-21. Epub 2005 Nov 14. PMID:16297862 doi:http://dx.doi.org/10.1016/j.bbrc.2005.11.029
↑ Wada K, Tanji K, Kamitani T. Oncogenic protein UnpEL/Usp4 deubiquitinates Ro52 by its isopeptidase activity. Biochem Biophys Res Commun. 2006 Jan 20;339(3):731-6. PMID:16316627 doi:10.1016/j.bbrc.2005.11.076
↑ Wada K, Kamitani T. UnpEL/Usp4 is ubiquitinated by Ro52 and deubiquitinated by itself. Biochem Biophys Res Commun. 2006 Mar 31;342(1):253-8. Epub 2006 Feb 6. PMID:16472766 doi:10.1016/j.bbrc.2006.01.144
↑ Sabile A, Meyer AM, Wirbelauer C, Hess D, Kogel U, Scheffner M, Krek W. Regulation of p27 degradation and S-phase progression by Ro52 RING finger protein. Mol Cell Biol. 2006 Aug;26(16):5994-6004. PMID:16880511 doi:http://dx.doi.org/10.1128/MCB.01630-05
↑ Takahata M, Bohgaki M, Tsukiyama T, Kondo T, Asaka M, Hatakeyama S. Ro52 functionally interacts with IgG1 and regulates its quality control via the ERAD system. Mol Immunol. 2008 Apr;45(7):2045-54. Epub 2007 Nov 26. PMID:18022694 doi:http://dx.doi.org/10.1016/j.molimm.2007.10.023
↑ Yamochi T, Ohnuma K, Hosono O, Tanaka H, Kanai Y, Morimoto C. SSA/Ro52 autoantigen interacts with Dcp2 to enhance its decapping activity. Biochem Biophys Res Commun. 2008 May 23;370(1):195-9. doi:, 10.1016/j.bbrc.2008.03.075. Epub 2008 Mar 24. PMID:18361920 doi:http://dx.doi.org/10.1016/j.bbrc.2008.03.075
↑ Higgs R, Ni Gabhann J, Ben Larbi N, Breen EP, Fitzgerald KA, Jefferies CA. The E3 ubiquitin ligase Ro52 negatively regulates IFN-beta production post-pathogen recognition by polyubiquitin-mediated degradation of IRF3. J Immunol. 2008 Aug 1;181(3):1780-6. PMID:18641315
↑ Espinosa A, Oke V, Elfving A, Nyberg F, Covacu R, Wahren-Herlenius M. The autoantigen Ro52 is an E3 ligase resident in the cytoplasm but enters the nucleus upon cellular exposure to nitric oxide. Exp Cell Res. 2008 Dec 10;314(20):3605-13. doi: 10.1016/j.yexcr.2008.09.011. Epub, 2008 Sep 25. PMID:18845142 doi:http://dx.doi.org/10.1016/j.yexcr.2008.09.011
↑ Wada K, Niida M, Tanaka M, Kamitani T. Ro52-mediated monoubiquitination of IKK{beta} down-regulates NF-{kappa}B signalling. J Biochem. 2009 Dec;146(6):821-32. doi: 10.1093/jb/mvp127. Epub 2009 Aug 12. PMID:19675099 doi:http://dx.doi.org/10.1093/jb/mvp127
↑ Kimura T, Jain A, Choi SW, Mandell MA, Schroder K, Johansen T, Deretic V. TRIM-mediated precision autophagy targets cytoplasmic regulators of innate immunity. J Cell Biol. 2015 Sep 14;210(6):973-89. PMID:26347139 doi:http://dx.doi.org/10.1083/jcb.201503023
↑ Wallenhammar A, Anandapadamanaban M, Lemak A, Mirabello C, Lundstrom P, Wallner B, Sunnerhagen M. Solution NMR structure of the TRIM21 B-box2 and identification of residues involved in its interaction with the RING domain. PLoS One. 2017 Jul 28;12(7):e0181551. doi: 10.1371/journal.pone.0181551., eCollection 2017. PMID:28753623 doi:http://dx.doi.org/10.1371/journal.pone.0181551

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5jpx"

Categories: Homo sapiens | Large Structures | Anandapadamanaban M | Sunnerhagen M | Wallenhammar A

@@ Line 1: / Line 1: @@
 ==Solution structure of the TRIM21 B-box2 (B2)==
-<StructureSection load='5jpx' size='340' side='right'caption='[[5jpx]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='5jpx' size='340' side='right'caption='[[5jpx]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5jpx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JPX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JPX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5jpx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JPX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JPX FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><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>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TRIM21, RNF81, RO52, SSA1 ([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=5jpx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jpx OCA], [https://pdbe.org/5jpx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jpx RCSB], [https://www.ebi.ac.uk/pdbsum/5jpx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jpx 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=5jpx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jpx OCA], [http://pdbe.org/5jpx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jpx RCSB], [http://www.ebi.ac.uk/pdbsum/5jpx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jpx ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RO52_HUMAN RO52_HUMAN]] E3 ubiquitin-protein ligase whose activity is dependent on E2 enzymes, UBE2D1, UBE2D2, UBE2E1 and UBE2E2. Forms a ubiquitin ligase complex in cooperation with the E2 UBE2D2 that is used not only for the ubiquitination of USP4 and IKBKB but also for its self-ubiquitination. Component of cullin-RING-based SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complexes such as SCF(SKP2)-like complexes. A TRIM21-containing SCF(SKP2)-like complex is shown to mediate ubiquitination of CDKN1B ('Thr-187' phosphorylated-form), thereby promoting its degradation by the proteasome. Monoubiquitinates IKBKB that will negatively regulates Tax-induced NF-kappa-B signaling. Negatively regulates IFN-beta production post-pathogen recognition by polyubiquitin-mediated degradation of IRF3. Mediates the ubiquitin-mediated proteasomal degradation of IgG1 heavy chain, which is linked to the VCP-mediated ER-associated degradation (ERAD) pathway. Promotes IRF8 ubiquitination, which enhanced the ability of IRF8 to stimulate cytokine genes transcription in macrophages. Plays a role in the regulation of the cell cycle progression. Enhances the decapping activity of DCP2. Exists as a ribonucleoprotein particle present in all mammalian cells studied and composed of a single polypeptide and one of four small RNA molecules. At least two isoforms are present in nucleated and red blood cells, and tissue specific differences in RO/SSA proteins have been identified. The common feature of these proteins is their ability to bind HY RNAs.2. Involved in the regulation of innate immunity and the inflammatory response in response to IFNG/IFN-gamma. Organizes autophagic machinery by serving as a platform for the assembly of ULK1, Beclin 1/BECN1 and ATG8 family members and recognizes specific autophagy targets, thus coordinating target recognition with assembly of the autophagic apparatus and initiation of autophagy. Acts as an autophagy receptor for the degradation of IRF3, hence attenuating type I interferon (IFN)-dependent immune responses (PubMed:26347139).<ref>PMID:16297862</ref> <ref>PMID:16316627</ref> <ref>PMID:16472766</ref> <ref>PMID:16880511</ref> <ref>PMID:18022694</ref> <ref>PMID:18361920</ref> <ref>PMID:18641315</ref> <ref>PMID:18845142</ref> <ref>PMID:19675099</ref> <ref>PMID:26347139</ref>
+[https://www.uniprot.org/uniprot/RO52_HUMAN RO52_HUMAN] E3 ubiquitin-protein ligase whose activity is dependent on E2 enzymes, UBE2D1, UBE2D2, UBE2E1 and UBE2E2. Forms a ubiquitin ligase complex in cooperation with the E2 UBE2D2 that is used not only for the ubiquitination of USP4 and IKBKB but also for its self-ubiquitination. Component of cullin-RING-based SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complexes such as SCF(SKP2)-like complexes. A TRIM21-containing SCF(SKP2)-like complex is shown to mediate ubiquitination of CDKN1B ('Thr-187' phosphorylated-form), thereby promoting its degradation by the proteasome. Monoubiquitinates IKBKB that will negatively regulates Tax-induced NF-kappa-B signaling. Negatively regulates IFN-beta production post-pathogen recognition by polyubiquitin-mediated degradation of IRF3. Mediates the ubiquitin-mediated proteasomal degradation of IgG1 heavy chain, which is linked to the VCP-mediated ER-associated degradation (ERAD) pathway. Promotes IRF8 ubiquitination, which enhanced the ability of IRF8 to stimulate cytokine genes transcription in macrophages. Plays a role in the regulation of the cell cycle progression. Enhances the decapping activity of DCP2. Exists as a ribonucleoprotein particle present in all mammalian cells studied and composed of a single polypeptide and one of four small RNA molecules. At least two isoforms are present in nucleated and red blood cells, and tissue specific differences in RO/SSA proteins have been identified. The common feature of these proteins is their ability to bind HY RNAs.2. Involved in the regulation of innate immunity and the inflammatory response in response to IFNG/IFN-gamma. Organizes autophagic machinery by serving as a platform for the assembly of ULK1, Beclin 1/BECN1 and ATG8 family members and recognizes specific autophagy targets, thus coordinating target recognition with assembly of the autophagic apparatus and initiation of autophagy. Acts as an autophagy receptor for the degradation of IRF3, hence attenuating type I interferon (IFN)-dependent immune responses (PubMed:26347139).<ref>PMID:16297862</ref> <ref>PMID:16316627</ref> <ref>PMID:16472766</ref> <ref>PMID:16880511</ref> <ref>PMID:18022694</ref> <ref>PMID:18361920</ref> <ref>PMID:18641315</ref> <ref>PMID:18845142</ref> <ref>PMID:19675099</ref> <ref>PMID:26347139</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 20: @@
 ==See Also==
-*[[Ubiquitin protein ligase|Ubiquitin protein ligase]]
+*[[Ubiquitin protein ligase 3D structures|Ubiquitin protein ligase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Anandapadamanaban, M]]
+[[Category: Anandapadamanaban M]]
-[[Category: Sunnerhagen, M]]
+[[Category: Sunnerhagen M]]
-[[Category: Wallenhammar, A]]
+[[Category: Wallenhammar A]]
-[[Category: B-box]]
-[[Category: E3 ligase]]
-[[Category: Metal binding protein]]
-[[Category: Ring-like fold]]
-[[Category: Trim protein]]
-[[Category: Ubiquitination]]
-[[Category: Zinc-binding motif]]

5jpx

From Proteopedia

Revision as of 10:11, 14 June 2023

Solution structure of the TRIM21 B-box2 (B2)

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox