8bd9 | pdb_00008bd9

Crystal structure of TRIM33 alpha PHD-Bromo domain in complex with 10

Structural highlights

8bd9 is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	CA, QCU, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

TRI33_HUMAN Papillary or follicular thyroid carcinoma. The disease is caused by mutations affecting the gene represented in this entry. A chromosomal aberration involving TRIM33 is found in thyroid papillary carcinomas. Translocation t(1;10)(p13;q11) with RET. The translocation generates the TRIM33/RET (PTC7) oncogene.

Function

TRI33_HUMAN Acts as an E3 ubiquitin-protein ligase. Promotes SMAD4 ubiquitination, nuclear exclusion and degradation via the ubiquitin proteasome pathway. According to PubMed:16751102, does not promote a decrease in the level of endogenous SMAD4. May act as a transcriptional repressor. Inhibits the transcriptional response to TGF-beta/BMP signaling cascade. Plays a role in the control of cell proliferation. Its association with SMAD2 and SMAD3 stimulates erythroid differentiation of hematopoietic stem/progenitor (By similarity). Monoubiquitinates SMAD4 and acts as an inhibitor of SMAD4-dependent TGF-beta/BMP signaling cascade (Monoubiquitination of SMAD4 hampers its ability to form a stable complex with activated SMAD2/3 resulting in inhibition of TGF-beta/BMP signaling cascade).^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

The field of targeted protein degradation, through the control of the ubiquitin-proteasome system (UPS), is progressing considerably; to exploit this new therapeutic modality, the proteolysis targeting chimera (PROTAC) technology was born. The opportunity to use PROTACs engaging of new E3 ligases that can hijack and control the UPS system could greatly extend the applicability of degrading molecules. To this end, here we show a potential application of the ELIOT (E3 LIgase pocketOme navigaTor) platform, previously published by this group, for a scaffold-repurposing strategy to identify new ligands for a novel E3 ligase, such as TRIM33. Starting from ELIOT, a case study of the cross-relationship using GRID Molecular Interaction Field (MIF) similarities between TRIM24 and TRIM33 binding sites was selected. Based on the assumption that similar pockets could bind similar ligands and considering that TRIM24 has 12 known co-crystalised ligands, we applied a scaffold-repurposing strategy for the identification of TRIM33 ligands exploiting the scaffold of TRIM24 ligands. We performed a deeper computational analysis to identify pocket similarities and differences, followed by docking and water analysis; selected ligands were synthesised and subsequently tested against TRIM33 via HTRF binding assay, and we obtained the first-ever X-ray crystallographic complexes of TRIM33alpha with three of the selected compounds.

Exploiting ELIOT for Scaffold-Repurposing Opportunities: TRIM33 a Possible Novel E3 Ligase to Expand the Toolbox for PROTAC Design.,Palomba T, Tassone G, Vacca C, Bartalucci M, Valeri A, Pozzi C, Cross S, Siragusa L, Desantis J Int J Mol Sci. 2022 Nov 17;23(22):14218. doi: 10.3390/ijms232214218. PMID:36430693^[5]

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

References

↑ Venturini L, You J, Stadler M, Galien R, Lallemand V, Koken MH, Mattei MG, Ganser A, Chambon P, Losson R, de The H. TIF1gamma, a novel member of the transcriptional intermediary factor 1 family. Oncogene. 1999 Feb 4;18(5):1209-17. PMID:10022127 doi:https://dx.doi.org/10.1038/sj.onc.1202655
↑ Dupont S, Zacchigna L, Cordenonsi M, Soligo S, Adorno M, Rugge M, Piccolo S. Germ-layer specification and control of cell growth by Ectodermin, a Smad4 ubiquitin ligase. Cell. 2005 Apr 8;121(1):87-99. PMID:15820681 doi:https://dx.doi.org/S0092-8674(05)00107-8
↑ He W, Dorn DC, Erdjument-Bromage H, Tempst P, Moore MA, Massague J. Hematopoiesis controlled by distinct TIF1gamma and Smad4 branches of the TGFbeta pathway. Cell. 2006 Jun 2;125(5):929-41. PMID:16751102 doi:https://dx.doi.org/10.1016/j.cell.2006.03.045
↑ Dupont S, Mamidi A, Cordenonsi M, Montagner M, Zacchigna L, Adorno M, Martello G, Stinchfield MJ, Soligo S, Morsut L, Inui M, Moro S, Modena N, Argenton F, Newfeld SJ, Piccolo S. FAM/USP9x, a deubiquitinating enzyme essential for TGFbeta signaling, controls Smad4 monoubiquitination. Cell. 2009 Jan 9;136(1):123-35. doi: 10.1016/j.cell.2008.10.051. PMID:19135894 doi:https://dx.doi.org/10.1016/j.cell.2008.10.051
↑ Palomba T, Tassone G, Vacca C, Bartalucci M, Valeri A, Pozzi C, Cross S, Siragusa L, Desantis J. Exploiting ELIOT for Scaffold-Repurposing Opportunities: TRIM33 a Possible Novel E3 Ligase to Expand the Toolbox for PROTAC Design. Int J Mol Sci. 2022 Nov 17;23(22):14218. doi: 10.3390/ijms232214218. PMID:36430693 doi:https://dx.doi.org/10.3390/ijms232214218

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Venturini L, You J, Stadler M, Galien R, Lallemand V, Koken MH, Mattei MG, Ganser A, Chambon P, Losson R, de The H. TIF1gamma, a novel member of the transcriptional intermediary factor 1 family. Oncogene. 1999 Feb 4;18(5):1209-17. PMID:10022127 doi:https://dx.doi.org/10.1038/sj.onc.1202655

[2] Dupont S, Zacchigna L, Cordenonsi M, Soligo S, Adorno M, Rugge M, Piccolo S. Germ-layer specification and control of cell growth by Ectodermin, a Smad4 ubiquitin ligase. Cell. 2005 Apr 8;121(1):87-99. PMID:15820681 doi:https://dx.doi.org/S0092-8674(05)00107-8

[3] He W, Dorn DC, Erdjument-Bromage H, Tempst P, Moore MA, Massague J. Hematopoiesis controlled by distinct TIF1gamma and Smad4 branches of the TGFbeta pathway. Cell. 2006 Jun 2;125(5):929-41. PMID:16751102 doi:https://dx.doi.org/10.1016/j.cell.2006.03.045

[4] Dupont S, Mamidi A, Cordenonsi M, Montagner M, Zacchigna L, Adorno M, Martello G, Stinchfield MJ, Soligo S, Morsut L, Inui M, Moro S, Modena N, Argenton F, Newfeld SJ, Piccolo S. FAM/USP9x, a deubiquitinating enzyme essential for TGFbeta signaling, controls Smad4 monoubiquitination. Cell. 2009 Jan 9;136(1):123-35. doi: 10.1016/j.cell.2008.10.051. PMID:19135894 doi:https://dx.doi.org/10.1016/j.cell.2008.10.051

[5] Palomba T, Tassone G, Vacca C, Bartalucci M, Valeri A, Pozzi C, Cross S, Siragusa L, Desantis J. Exploiting ELIOT for Scaffold-Repurposing Opportunities: TRIM33 a Possible Novel E3 Ligase to Expand the Toolbox for PROTAC Design. Int J Mol Sci. 2022 Nov 17;23(22):14218. doi: 10.3390/ijms232214218. PMID:36430693 doi:https://dx.doi.org/10.3390/ijms232214218

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8bd9 | pdb_00008bd9

Crystal structure of TRIM33 alpha PHD-Bromo domain in complex with 10

Structural highlights

Disease

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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