4y1l: Difference between revisions

Revision as of 18:03, 26 April 2023

Ubc9 Homodimer The Missing Link in Poly-SUMO Chain Formation

Structural highlights

4y1l 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.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

UBC9_HUMAN Accepts the ubiquitin-like proteins SUMO1, SUMO2, SUMO3 and SUMO4 from the UBLE1A-UBLE1B E1 complex and catalyzes their covalent attachment to other proteins with the help of an E3 ligase such as RANBP2 or CBX4. Can catalyze the formation of poly-SUMO chains. Necessary for sumoylation of FOXL2 and KAT5. Essential for nuclear architecture and chromosome segregation.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

Publication Abstract from PubMed

An RWD domain is a well-conserved domain found through bioinformatic analysis of the human proteome sequence; however its function has been unknown. Ubiquitin-like modifications require the catalysis of three enzymes generally known as E1, E2 and E3. We solved the crystal structure of the E2 for the small ubiquitin-like modifiers (SUMO) in complex with an RWD domain, and confirmed the structure using solution NMR analysis. RWD's binding surface on Ubc9 is located near the N-terminus of Ubc9 that is known to be involved in non-covalent binding of the proteins in the conjugation machinery, including a domain of E1, SUMO, and an E3 ligase. NMR data indicates that the RWD domain does not bind to SUMO and E1. The interaction between RWD and Ubc9 has a Kd of 32.30+/-3.86 microM. Consistent with the structure and binding affinity and in contrast to a previous report, the RWD domain and RWDD3 have minimal effects on global SUMOylation. The structural and biochemical information presented here forms the basis for further investigation of the functions of RWD containing proteins.

RWD Domain as an E2 (Ubc9)-Interaction Module.,Alontaga AY, Ambaye ND, Li YJ, Vega R, Chen CH, Bzymek KP, Williams JC, Hu W, Chen Y J Biol Chem. 2015 Apr 27. pii: jbc.M115.644047. PMID:25918163^[8]

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

References

↑ Yasugi T, Howley PM. Identification of the structural and functional human homolog of the yeast ubiquitin conjugating enzyme UBC9. Nucleic Acids Res. 1996 Jun 1;24(11):2005-10. PMID:8668529
↑ 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
↑ Kim YE, Kim DY, Lee JM, Kim ST, Han TH, Ahn JH. Requirement of the coiled-coil domain of PML-RARalpha oncoprotein for localization, sumoylation, and inhibition of monocyte differentiation. Biochem Biophys Res Commun. 2005 May 13;330(3):746-54. PMID:15809060 doi:10.1016/j.bbrc.2005.03.052
↑ Kuo FT, Bentsi-Barnes IK, Barlow GM, Bae J, Pisarska MD. Sumoylation of forkhead L2 by Ubc9 is required for its activity as a transcriptional repressor of the Steroidogenic Acute Regulatory gene. Cell Signal. 2009 Dec;21(12):1935-44. doi: 10.1016/j.cellsig.2009.09.001. Epub, 2009 Sep 8. PMID:19744555 doi:10.1016/j.cellsig.2009.09.001
↑ Figueroa-Romero C, Iniguez-Lluhi JA, Stadler J, Chang CR, Arnoult D, Keller PJ, Hong Y, Blackstone C, Feldman EL. SUMOylation of the mitochondrial fission protein Drp1 occurs at multiple nonconsensus sites within the B domain and is linked to its activity cycle. FASEB J. 2009 Nov;23(11):3917-27. doi: 10.1096/fj.09-136630. Epub 2009 Jul 28. PMID:19638400 doi:10.1096/fj.09-136630
↑ Capili AD, Lima CD. Structure and analysis of a complex between SUMO and Ubc9 illustrates features of a conserved E2-Ubl interaction. J Mol Biol. 2007 Jun 8;369(3):608-18. Epub 2007 Apr 6. PMID:17466333 doi:10.1016/j.jmb.2007.04.006
↑ Sekiyama N, Arita K, Ikeda Y, Hashiguchi K, Ariyoshi M, Tochio H, Saitoh H, Shirakawa M. Structural basis for regulation of poly-SUMO chain by a SUMO-like domain of Nip45. Proteins. 2009 Dec 4. PMID:20077568 doi:10.1002/prot.22667
↑ Alontaga AY, Ambaye ND, Li YJ, Vega R, Chen CH, Bzymek KP, Williams JC, Hu W, Chen Y. RWD Domain as an E2 (Ubc9)-Interaction Module. J Biol Chem. 2015 Apr 27. pii: jbc.M115.644047. PMID:25918163 doi:https://dx.doi.org/10.1074/jbc.M115.644047

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Yasugi T, Howley PM. Identification of the structural and functional human homolog of the yeast ubiquitin conjugating enzyme UBC9. Nucleic Acids Res. 1996 Jun 1;24(11):2005-10. PMID:8668529

[2] 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

[3] Kim YE, Kim DY, Lee JM, Kim ST, Han TH, Ahn JH. Requirement of the coiled-coil domain of PML-RARalpha oncoprotein for localization, sumoylation, and inhibition of monocyte differentiation. Biochem Biophys Res Commun. 2005 May 13;330(3):746-54. PMID:15809060 doi:10.1016/j.bbrc.2005.03.052

[4] Kuo FT, Bentsi-Barnes IK, Barlow GM, Bae J, Pisarska MD. Sumoylation of forkhead L2 by Ubc9 is required for its activity as a transcriptional repressor of the Steroidogenic Acute Regulatory gene. Cell Signal. 2009 Dec;21(12):1935-44. doi: 10.1016/j.cellsig.2009.09.001. Epub, 2009 Sep 8. PMID:19744555 doi:10.1016/j.cellsig.2009.09.001

[5] Figueroa-Romero C, Iniguez-Lluhi JA, Stadler J, Chang CR, Arnoult D, Keller PJ, Hong Y, Blackstone C, Feldman EL. SUMOylation of the mitochondrial fission protein Drp1 occurs at multiple nonconsensus sites within the B domain and is linked to its activity cycle. FASEB J. 2009 Nov;23(11):3917-27. doi: 10.1096/fj.09-136630. Epub 2009 Jul 28. PMID:19638400 doi:10.1096/fj.09-136630

[6] Capili AD, Lima CD. Structure and analysis of a complex between SUMO and Ubc9 illustrates features of a conserved E2-Ubl interaction. J Mol Biol. 2007 Jun 8;369(3):608-18. Epub 2007 Apr 6. PMID:17466333 doi:10.1016/j.jmb.2007.04.006

[7] Sekiyama N, Arita K, Ikeda Y, Hashiguchi K, Ariyoshi M, Tochio H, Saitoh H, Shirakawa M. Structural basis for regulation of poly-SUMO chain by a SUMO-like domain of Nip45. Proteins. 2009 Dec 4. PMID:20077568 doi:10.1002/prot.22667

[8] Alontaga AY, Ambaye ND, Li YJ, Vega R, Chen CH, Bzymek KP, Williams JC, Hu W, Chen Y. RWD Domain as an E2 (Ubc9)-Interaction Module. J Biol Chem. 2015 Apr 27. pii: jbc.M115.644047. PMID:25918163 doi:https://dx.doi.org/10.1074/jbc.M115.644047

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[3]

[4]

[5]

[6]

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[8]

@@ Line 3: / Line 3: @@
 <StructureSection load='4y1l' size='340' side='right'caption='[[4y1l]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4y1l]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y1L FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4y1l]] is a 3 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=4Y1L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y1L FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UBE2I, UBC9, UBCE9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RWDD3, RSUME ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+</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=4y1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y1l OCA], [https://pdbe.org/4y1l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y1l RCSB], [https://www.ebi.ac.uk/pdbsum/4y1l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y1l 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=4y1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y1l OCA], [http://pdbe.org/4y1l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y1l RCSB], [http://www.ebi.ac.uk/pdbsum/4y1l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4y1l ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/UBC9_HUMAN UBC9_HUMAN]] Accepts the ubiquitin-like proteins SUMO1, SUMO2, SUMO3 and SUMO4 from the UBLE1A-UBLE1B E1 complex and catalyzes their covalent attachment to other proteins with the help of an E3 ligase such as RANBP2 or CBX4. Can catalyze the formation of poly-SUMO chains. Necessary for sumoylation of FOXL2 and KAT5. Essential for nuclear architecture and chromosome segregation.<ref>PMID:8668529</ref> <ref>PMID:11451954</ref> <ref>PMID:15809060</ref> <ref>PMID:19744555</ref> <ref>PMID:19638400</ref> <ref>PMID:17466333</ref> <ref>PMID:20077568</ref>  [[http://www.uniprot.org/uniprot/RWDD3_HUMAN RWDD3_HUMAN]] Enhances the sumoylation of a number of proteins including HIF1A, PIAS and I-kappa-B, through direct interaction with UBC9. Has no effect on ubiquitination.<ref>PMID:17956732</ref>
+[https://www.uniprot.org/uniprot/UBC9_HUMAN UBC9_HUMAN] Accepts the ubiquitin-like proteins SUMO1, SUMO2, SUMO3 and SUMO4 from the UBLE1A-UBLE1B E1 complex and catalyzes their covalent attachment to other proteins with the help of an E3 ligase such as RANBP2 or CBX4. Can catalyze the formation of poly-SUMO chains. Necessary for sumoylation of FOXL2 and KAT5. Essential for nuclear architecture and chromosome segregation.<ref>PMID:8668529</ref> <ref>PMID:11451954</ref> <ref>PMID:15809060</ref> <ref>PMID:19744555</ref> <ref>PMID:19638400</ref> <ref>PMID:17466333</ref> <ref>PMID:20077568</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 24: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Aileen, Y A]]
+[[Category: Aileen YA]]
-[[Category: Ambaye, N D]]
+[[Category: Ambaye ND]]
-[[Category: Bzymek, K]]
+[[Category: Bzymek K]]
-[[Category: Chen, Y]]
+[[Category: Chen Y]]
-[[Category: Hu, W]]
+[[Category: Hu W]]
-[[Category: Li, Y J]]
+[[Category: Li YJ]]
-[[Category: Vega, R]]
+[[Category: Vega R]]
-[[Category: Williams, J C]]
+[[Category: Williams JC]]
-[[Category: Homodimer]]
-[[Category: Ligase-nuclear protein complex]]
-[[Category: Rwd]]
-[[Category: Sumo]]
-[[Category: Sumoylation]]
-[[Category: Ubc9]]

4y1l: Difference between revisions

Revision as of 18:03, 26 April 2023

Ubc9 Homodimer The Missing Link in Poly-SUMO Chain Formation

Structural highlights

Function

Publication Abstract from PubMed

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References

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