6xoi | pdb_00006xoi

Structure of SUMO1-ML00752641 adduct bound to SAE

Structural highlights

6xoi is a 3 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	SO4, VBA, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SAE1_HUMAN The heterodimer acts as a E1 ligase for SUMO1, SUMO2, SUMO3, and probably SUMO4. It mediates ATP-dependent activation of SUMO proteins followed by formation of a thioester bond between a SUMO protein and a conserved active site cysteine residue on UBA2/SAE2.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

Publication Abstract from PubMed

SUMOylation is a reversible post-translational modification that regulates protein function through covalent attachment of small ubiquitin-like modifier (SUMO) proteins. The process of SUMOylating proteins involves an enzymatic cascade, the first step of which entails the activation of a SUMO protein through an ATP-dependent process catalyzed by SUMO-activating enzyme (SAE). Here, we describe the identification of TAK-981, a mechanism-based inhibitor of SAE which forms a SUMO-TAK-981 adduct as the inhibitory species within the enzyme catalytic site. Optimization of selectivity against related enzymes as well as enhancement of mean residence time of the adduct were critical to the identification of compounds with potent cellular pathway inhibition and ultimately a prolonged pharmacodynamic effect and efficacy in preclinical tumor models, culminating in the identification of the clinical molecule TAK-981.

Discovery of TAK-981, a First-in-Class Inhibitor of SUMO-Activating Enzyme for the Treatment of Cancer.,Langston SP, Grossman S, England D, Afroze R, Bence N, Bowman D, Bump N, Chau R, Chuang BC, Claiborne C, Cohen L, Connolly K, Duffey M, Durvasula N, Freeze S, Gallery M, Galvin K, Gaulin J, Gershman R, Greenspan P, Grieves J, Guo J, Gulavita N, Hailu S, He X, Hoar K, Hu Y, Hu Z, Ito M, Kim MS, Lane SW, Lok D, Lublinsky A, Mallender W, McIntyre C, Minissale J, Mizutani H, Mizutani M, Molchinova N, Ono K, Patil A, Qian M, Riceberg J, Shindi V, Sintchak MD, Song K, Soucy T, Wang Y, Xu H, Yang X, Zawadzka A, Zhang J, Pulukuri SM J Med Chem. 2021 Mar 11;64(5):2501-2520. doi: 10.1021/acs.jmedchem.0c01491. Epub , 2021 Feb 25. PMID:33631934^[8]

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

References

↑ Okuma T, Honda R, Ichikawa G, Tsumagari N, Yasuda H. In vitro SUMO-1 modification requires two enzymatic steps, E1 and E2. Biochem Biophys Res Commun. 1999 Jan 27;254(3):693-8. PMID:9920803 doi:10.1006/bbrc.1998.9995
↑ Gong L, Li B, Millas S, Yeh ET. Molecular cloning and characterization of human AOS1 and UBA2, components of the sentrin-activating enzyme complex. FEBS Lett. 1999 Apr 1;448(1):185-9. PMID:10217437
↑ Desterro JM, Rodriguez MS, Kemp GD, Hay RT. Identification of the enzyme required for activation of the small ubiquitin-like protein SUMO-1. J Biol Chem. 1999 Apr 9;274(15):10618-24. PMID:10187858
↑ Azuma Y, Tan SH, Cavenagh MM, Ainsztein AM, Saitoh H, Dasso M. Expression and regulation of the mammalian SUMO-1 E1 enzyme. FASEB J. 2001 Aug;15(10):1825-7. PMID:11481243
↑ Tatham MH, Jaffray E, Vaughan OA, Desterro JM, Botting CH, Naismith JH, Hay RT. Polymeric chains of SUMO-2 and SUMO-3 are conjugated to protein substrates by SAE1/SAE2 and Ubc9. J Biol Chem. 2001 Sep 21;276(38):35368-74. Epub 2001 Jul 12. PMID:11451954 doi:10.1074/jbc.M104214200
↑ Lois LM, Lima CD. Structures of the SUMO E1 provide mechanistic insights into SUMO activation and E2 recruitment to E1. EMBO J. 2005 Feb 9;24(3):439-51. Epub 2005 Jan 20. PMID:15660128
↑ Olsen SK, Capili AD, Lu X, Tan DS, Lima CD. Active site remodelling accompanies thioester bond formation in the SUMO E1. Nature. 2010 Feb 18;463(7283):906-12. PMID:20164921 doi:10.1038/nature08765
↑ Langston SP, Grossman S, England D, Afroze R, Bence N, Bowman D, Bump N, Chau R, Chuang BC, Claiborne C, Cohen L, Connolly K, Duffey M, Durvasula N, Freeze S, Gallery M, Galvin K, Gaulin J, Gershman R, Greenspan P, Grieves J, Guo J, Gulavita N, Hailu S, He X, Hoar K, Hu Y, Hu Z, Ito M, Kim MS, Lane SW, Lok D, Lublinsky A, Mallender W, McIntyre C, Minissale J, Mizutani H, Mizutani M, Molchinova N, Ono K, Patil A, Qian M, Riceberg J, Shindi V, Sintchak MD, Song K, Soucy T, Wang Y, Xu H, Yang X, Zawadzka A, Zhang J, Pulukuri SM. Discovery of TAK-981, a First-in-Class Inhibitor of SUMO-Activating Enzyme for the Treatment of Cancer. J Med Chem. 2021 Mar 11;64(5):2501-2520. PMID:33631934 doi:10.1021/acs.jmedchem.0c01491

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OCA

[1] Okuma T, Honda R, Ichikawa G, Tsumagari N, Yasuda H. In vitro SUMO-1 modification requires two enzymatic steps, E1 and E2. Biochem Biophys Res Commun. 1999 Jan 27;254(3):693-8. PMID:9920803 doi:10.1006/bbrc.1998.9995

[2] Gong L, Li B, Millas S, Yeh ET. Molecular cloning and characterization of human AOS1 and UBA2, components of the sentrin-activating enzyme complex. FEBS Lett. 1999 Apr 1;448(1):185-9. PMID:10217437

[3] Desterro JM, Rodriguez MS, Kemp GD, Hay RT. Identification of the enzyme required for activation of the small ubiquitin-like protein SUMO-1. J Biol Chem. 1999 Apr 9;274(15):10618-24. PMID:10187858

[4] Azuma Y, Tan SH, Cavenagh MM, Ainsztein AM, Saitoh H, Dasso M. Expression and regulation of the mammalian SUMO-1 E1 enzyme. FASEB J. 2001 Aug;15(10):1825-7. PMID:11481243

[5] Tatham MH, Jaffray E, Vaughan OA, Desterro JM, Botting CH, Naismith JH, Hay RT. Polymeric chains of SUMO-2 and SUMO-3 are conjugated to protein substrates by SAE1/SAE2 and Ubc9. J Biol Chem. 2001 Sep 21;276(38):35368-74. Epub 2001 Jul 12. PMID:11451954 doi:10.1074/jbc.M104214200

[6] Lois LM, Lima CD. Structures of the SUMO E1 provide mechanistic insights into SUMO activation and E2 recruitment to E1. EMBO J. 2005 Feb 9;24(3):439-51. Epub 2005 Jan 20. PMID:15660128

[7] Olsen SK, Capili AD, Lu X, Tan DS, Lima CD. Active site remodelling accompanies thioester bond formation in the SUMO E1. Nature. 2010 Feb 18;463(7283):906-12. PMID:20164921 doi:10.1038/nature08765

[8] Langston SP, Grossman S, England D, Afroze R, Bence N, Bowman D, Bump N, Chau R, Chuang BC, Claiborne C, Cohen L, Connolly K, Duffey M, Durvasula N, Freeze S, Gallery M, Galvin K, Gaulin J, Gershman R, Greenspan P, Grieves J, Guo J, Gulavita N, Hailu S, He X, Hoar K, Hu Y, Hu Z, Ito M, Kim MS, Lane SW, Lok D, Lublinsky A, Mallender W, McIntyre C, Minissale J, Mizutani H, Mizutani M, Molchinova N, Ono K, Patil A, Qian M, Riceberg J, Shindi V, Sintchak MD, Song K, Soucy T, Wang Y, Xu H, Yang X, Zawadzka A, Zhang J, Pulukuri SM. Discovery of TAK-981, a First-in-Class Inhibitor of SUMO-Activating Enzyme for the Treatment of Cancer. J Med Chem. 2021 Mar 11;64(5):2501-2520. PMID:33631934 doi:10.1021/acs.jmedchem.0c01491

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6xoi | pdb_00006xoi

Structure of SUMO1-ML00752641 adduct bound to SAE

Structural highlights

Function

Publication Abstract from PubMed

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References

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