9me8: Difference between revisions

Latest revision as of 05:45, 6 August 2025

Co-crystal structure of maltose binding protein (MBP)-human SENP3 fusion protein in complex with PELP1 peptide

Structural highlights

9me8 is a 2 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 2.93Å
Ligands:	GLC, NA, PRD_900010
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SENP3_HUMAN Protease that releases SUMO2 and SUMO3 monomers from sumoylated substrates, but has only weak activity against SUMO1 conjugates (PubMed:16608850, PubMed:32832608, PubMed:36050397). Deconjugates SUMO2 from MEF2D, which increases its transcriptional activation capability (PubMed:15743823). Deconjugates SUMO2 and SUMO3 from CDCA8 (PubMed:18946085). Redox sensor that, when redistributed into nucleoplasm, can act as an effector to enhance HIF1A transcriptional activity by desumoylating EP300 (PubMed:19680224). Required for rRNA processing through deconjugation of SUMO2 and SUMO3 from nucleophosmin, NPM1 (PubMed:19015314). Plays a role in the regulation of sumoylation status of ZNF148 (PubMed:18259216). Functions as a component of the Five Friends of Methylated CHTOP (5FMC) complex; the 5FMC complex is recruited to ZNF148 by methylated CHTOP, leading to desumoylation of ZNF148 and subsequent transactivation of ZNF148 target genes (PubMed:22872859). Deconjugates SUMO2 from KAT5 (PubMed:32832608). Catalyzes desumoylation of MRE11 (PubMed:36050397).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] MALE_ECO57 Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides (By similarity).

References

↑ Grégoire S, Yang XJ. Association with class IIa histone deacetylases upregulates the sumoylation of MEF2 transcription factors. Mol Cell Biol. 2005 Mar;25(6):2273-87. PMID:15743823 doi:10.1128/MCB.25.6.2273-2287.2005
↑ Gong L, Yeh ET. Characterization of a family of nucleolar SUMO-specific proteases with preference for SUMO-2 or SUMO-3. J Biol Chem. 2006 Jun 9;281(23):15869-77. PMID:16608850 doi:10.1074/jbc.M511658200
↑ Haindl M, Harasim T, Eick D, Muller S. The nucleolar SUMO-specific protease SENP3 reverses SUMO modification of nucleophosmin and is required for rRNA processing. EMBO Rep. 2008 Mar;9(3):273-9. PMID:18259216 doi:10.1038/embor.2008.3
↑ Klein UR, Haindl M, Nigg EA, Muller S. RanBP2 and SENP3 function in a mitotic SUMO2/3 conjugation-deconjugation cycle on Borealin. Mol Biol Cell. 2009 Jan;20(1):410-8. PMID:18946085 doi:10.1091/mbc.e08-05-0511
↑ Yun C, Wang Y, Mukhopadhyay D, Backlund P, Kolli N, Yergey A, Wilkinson KD, Dasso M. Nucleolar protein B23/nucleophosmin regulates the vertebrate SUMO pathway through SENP3 and SENP5 proteases. J Cell Biol. 2008 Nov 17;183(4):589-95. PMID:19015314 doi:10.1083/jcb.200807185
↑ Huang C, Han Y, Wang Y, Sun X, Yan S, Yeh ET, Chen Y, Cang H, Li H, Shi G, Cheng J, Tang X, Yi J. SENP3 is responsible for HIF-1 transactivation under mild oxidative stress via p300 de-SUMOylation. EMBO J. 2009 Sep 16;28(18):2748-62. PMID:19680224 doi:10.1038/emboj.2009.210
↑ Fanis P, Gillemans N, Aghajanirefah A, Pourfarzad F, Demmers J, Esteghamat F, Vadlamudi RK, Grosveld F, Philipsen S, van Dijk TB. Five friends of methylated chromatin target of protein-arginine-methyltransferase[prmt]-1 (chtop), a complex linking arginine methylation to desumoylation. Mol Cell Proteomics. 2012 Nov;11(11):1263-73. doi: 10.1074/mcp.M112.017194. Epub , 2012 Aug 7. PMID:22872859 doi:https://dx.doi.org/10.1074/mcp.M112.017194
↑ Gao SS, Guan H, Yan S, Hu S, Song M, Guo ZP, Xie DF, Liu Y, Liu X, Zhang S, Zhou PK. TIP60 K430 SUMOylation attenuates its interaction with DNA-PKcs in S-phase cells: Facilitating homologous recombination and emerging target for cancer therapy. Sci Adv. 2020 Jul 10;6(28):eaba7822. PMID:32832608 doi:10.1126/sciadv.aba7822
↑ Zhang T, Yang H, Zhou Z, Bai Y, Wang J, Wang W. Crosstalk between SUMOylation and ubiquitylation controls DNA end resection by maintaining MRE11 homeostasis on chromatin. Nat Commun. 2022 Sep 1;13(1):5133. PMID:36050397 doi:10.1038/s41467-022-32920-x

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OCA

[1] Grégoire S, Yang XJ. Association with class IIa histone deacetylases upregulates the sumoylation of MEF2 transcription factors. Mol Cell Biol. 2005 Mar;25(6):2273-87. PMID:15743823 doi:10.1128/MCB.25.6.2273-2287.2005

[2] Gong L, Yeh ET. Characterization of a family of nucleolar SUMO-specific proteases with preference for SUMO-2 or SUMO-3. J Biol Chem. 2006 Jun 9;281(23):15869-77. PMID:16608850 doi:10.1074/jbc.M511658200

[3] Haindl M, Harasim T, Eick D, Muller S. The nucleolar SUMO-specific protease SENP3 reverses SUMO modification of nucleophosmin and is required for rRNA processing. EMBO Rep. 2008 Mar;9(3):273-9. PMID:18259216 doi:10.1038/embor.2008.3

[4] Klein UR, Haindl M, Nigg EA, Muller S. RanBP2 and SENP3 function in a mitotic SUMO2/3 conjugation-deconjugation cycle on Borealin. Mol Biol Cell. 2009 Jan;20(1):410-8. PMID:18946085 doi:10.1091/mbc.e08-05-0511

[5] Yun C, Wang Y, Mukhopadhyay D, Backlund P, Kolli N, Yergey A, Wilkinson KD, Dasso M. Nucleolar protein B23/nucleophosmin regulates the vertebrate SUMO pathway through SENP3 and SENP5 proteases. J Cell Biol. 2008 Nov 17;183(4):589-95. PMID:19015314 doi:10.1083/jcb.200807185

[6] Huang C, Han Y, Wang Y, Sun X, Yan S, Yeh ET, Chen Y, Cang H, Li H, Shi G, Cheng J, Tang X, Yi J. SENP3 is responsible for HIF-1 transactivation under mild oxidative stress via p300 de-SUMOylation. EMBO J. 2009 Sep 16;28(18):2748-62. PMID:19680224 doi:10.1038/emboj.2009.210

[7] Fanis P, Gillemans N, Aghajanirefah A, Pourfarzad F, Demmers J, Esteghamat F, Vadlamudi RK, Grosveld F, Philipsen S, van Dijk TB. Five friends of methylated chromatin target of protein-arginine-methyltransferase[prmt]-1 (chtop), a complex linking arginine methylation to desumoylation. Mol Cell Proteomics. 2012 Nov;11(11):1263-73. doi: 10.1074/mcp.M112.017194. Epub , 2012 Aug 7. PMID:22872859 doi:https://dx.doi.org/10.1074/mcp.M112.017194

[8] Gao SS, Guan H, Yan S, Hu S, Song M, Guo ZP, Xie DF, Liu Y, Liu X, Zhang S, Zhou PK. TIP60 K430 SUMOylation attenuates its interaction with DNA-PKcs in S-phase cells: Facilitating homologous recombination and emerging target for cancer therapy. Sci Adv. 2020 Jul 10;6(28):eaba7822. PMID:32832608 doi:10.1126/sciadv.aba7822

[9] Zhang T, Yang H, Zhou Z, Bai Y, Wang J, Wang W. Crosstalk between SUMOylation and ubiquitylation controls DNA end resection by maintaining MRE11 homeostasis on chromatin. Nat Commun. 2022 Sep 1;13(1):5133. PMID:36050397 doi:10.1038/s41467-022-32920-x

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9me8 is ON HOLD  until Paper Publication
+==Co-crystal structure of maltose binding protein (MBP)-human SENP3 fusion protein in complex with PELP1 peptide==
+<StructureSection load='9me8' size='340' side='right'caption='[[9me8]], [[Resolution|resolution]] 2.93&Aring;' scene=''>
-Authors:
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9me8]] 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=9ME8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9ME8 FirstGlance]. <br>
-Description:
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.93&#8491;</td></tr>
-[[Category: Unreleased Structures]]
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PRD_900010:alpha-maltotetraose'>PRD_900010</scene></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=9me8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9me8 OCA], [https://pdbe.org/9me8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9me8 RCSB], [https://www.ebi.ac.uk/pdbsum/9me8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9me8 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SENP3_HUMAN SENP3_HUMAN] Protease that releases SUMO2 and SUMO3 monomers from sumoylated substrates, but has only weak activity against SUMO1 conjugates (PubMed:16608850, PubMed:32832608, PubMed:36050397). Deconjugates SUMO2 from MEF2D, which increases its transcriptional activation capability (PubMed:15743823). Deconjugates SUMO2 and SUMO3 from CDCA8 (PubMed:18946085). Redox sensor that, when redistributed into nucleoplasm, can act as an effector to enhance HIF1A transcriptional activity by desumoylating EP300 (PubMed:19680224). Required for rRNA processing through deconjugation of SUMO2 and SUMO3 from nucleophosmin, NPM1 (PubMed:19015314). Plays a role in the regulation of sumoylation status of ZNF148 (PubMed:18259216). Functions as a component of the Five Friends of Methylated CHTOP (5FMC) complex; the 5FMC complex is recruited to ZNF148 by methylated CHTOP, leading to desumoylation of ZNF148 and subsequent transactivation of ZNF148 target genes (PubMed:22872859). Deconjugates SUMO2 from KAT5 (PubMed:32832608). Catalyzes desumoylation of MRE11 (PubMed:36050397).<ref>PMID:15743823</ref> <ref>PMID:16608850</ref> <ref>PMID:18259216</ref> <ref>PMID:18946085</ref> <ref>PMID:19015314</ref> <ref>PMID:19680224</ref> <ref>PMID:22872859</ref> <ref>PMID:32832608</ref> <ref>PMID:36050397</ref> [https://www.uniprot.org/uniprot/MALE_ECO57 MALE_ECO57] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides (By similarity).
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Gordon J]]
+[[Category: Kaminski AM]]
+[[Category: Pedersen LC]]
+[[Category: Stanley RE]]

9me8: Difference between revisions

Latest revision as of 05:45, 6 August 2025

Co-crystal structure of maltose binding protein (MBP)-human SENP3 fusion protein in complex with PELP1 peptide

Structural highlights

Function

References

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