6u75: Difference between revisions

Latest revision as of 07:45, 11 October 2023

Crystal Structure of S. Cerevisiae SUMO E3 Ligase SIZ2

Structural highlights

6u75 is a 2 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.63Å
Ligands:	ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SIZ2_YEAST May act as an E3 ligase mediating SUMO/Smt3 attachment to septins. May be involved in chromosome maintenance.^[1] ^[2]

Publication Abstract from PubMed

Repair of DNA double-stranded breaks by homologous recombination (HR) is dependent on DNA end resection and on post-translational modification of repair factors. In budding yeast, single-stranded DNA is coated by replication protein A (RPA) following DNA end resection, and DNA-RPA complexes are then SUMO-modified by the E3 ligase Siz2 to promote repair. Here, we show using enzymatic assays that DNA duplexes containing 3' single-stranded DNA overhangs increase the rate of RPA SUMO modification by Siz2. The SAP domain of Siz2 binds DNA duplexes and makes a key contribution to this process as highlighted by models and a crystal structure of Siz2 and by assays performed using protein mutants. Enzymatic assays performed using DNA that can accommodate multiple RPA proteins suggest a model in which the SUMO-RPA signal is amplified by successive rounds of Siz2-dependent SUMO modification of RPA and dissociation of SUMO-RPA at the junction between single- and double-stranded DNA. Our results provide insights on how DNA architecture scaffolds a substrate and E3 ligase to promote SUMO modification in the context of DNA repair.

DNA asymmetry promotes SUMO modification of the single-stranded DNA-binding protein RPA.,Cappadocia L, Kochanczyk T, Lima CD EMBO J. 2021 Nov 15;40(22):e103787. doi: 10.15252/embj.2019103787. Epub 2021 Sep , 29. PMID:34585421^[3]

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

References

↑ Strunnikov AV, Aravind L, Koonin EV. Saccharomyces cerevisiae SMT4 encodes an evolutionarily conserved protease with a role in chromosome condensation regulation. Genetics. 2001 May;158(1):95-107. PMID:11333221
↑ Takahashi Y, Toh-E A, Kikuchi Y. Comparative analysis of yeast PIAS-type SUMO ligases in vivo and in vitro. J Biochem. 2003 Apr;133(4):415-22. PMID:12761287
↑ Cappadocia L, Kochanczyk T, Lima CD. DNA asymmetry promotes SUMO modification of the single-stranded DNA-binding protein RPA. EMBO J. 2021 Nov 15;40(22):e103787. doi: 10.15252/embj.2019103787. Epub 2021 Sep , 29. PMID:34585421 doi:https://dx.doi.org/10.15252/embj.2019103787

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Strunnikov AV, Aravind L, Koonin EV. Saccharomyces cerevisiae SMT4 encodes an evolutionarily conserved protease with a role in chromosome condensation regulation. Genetics. 2001 May;158(1):95-107. PMID:11333221

[2] Takahashi Y, Toh-E A, Kikuchi Y. Comparative analysis of yeast PIAS-type SUMO ligases in vivo and in vitro. J Biochem. 2003 Apr;133(4):415-22. PMID:12761287

[3] Cappadocia L, Kochanczyk T, Lima CD. DNA asymmetry promotes SUMO modification of the single-stranded DNA-binding protein RPA. EMBO J. 2021 Nov 15;40(22):e103787. doi: 10.15252/embj.2019103787. Epub 2021 Sep , 29. PMID:34585421 doi:https://dx.doi.org/10.15252/embj.2019103787

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[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='6u75' size='340' side='right'caption='[[6u75]], [[Resolution|resolution]] 2.63&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6u75]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U75 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6U75 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6u75]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U75 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6U75 FirstGlance]. <br>
-</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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.63&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NFI1, SIZ2, YOR156C ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6u75 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u75 OCA], [https://pdbe.org/6u75 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6u75 RCSB], [https://www.ebi.ac.uk/pdbsum/6u75 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6u75 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/SIZ2_YEAST SIZ2_YEAST]] May act as an E3 ligase mediating SUMO/Smt3 attachment to septins. May be involved in chromosome maintenance.<ref>PMID:11333221</ref> <ref>PMID:12761287</ref>
+[https://www.uniprot.org/uniprot/SIZ2_YEAST SIZ2_YEAST] May act as an E3 ligase mediating SUMO/Smt3 attachment to septins. May be involved in chromosome maintenance.<ref>PMID:11333221</ref> <ref>PMID:12761287</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Baker's yeast]]
 [[Category: Large Structures]]
-[[Category: Cappadocia, L]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Lima, C D]]
+[[Category: Cappadocia L]]
-[[Category: Ligase]]
+[[Category: Lima CD]]
-[[Category: Metal-binding]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Pia]]
-[[Category: Replication]]
-[[Category: Ring e3]]
-[[Category: Signal transduction]]
-[[Category: Siz]]
-[[Category: Sumo]]
-[[Category: Ubc9]]
-[[Category: Ubiquitin]]
-[[Category: Ubl conjugation pathway]]
-[[Category: Zinc-finger]]

6u75: Difference between revisions

Latest revision as of 07:45, 11 October 2023

Crystal Structure of S. Cerevisiae SUMO E3 Ligase SIZ2

Structural highlights

Function

Publication Abstract from PubMed

References

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