4zdt: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4zdt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe_972h- Schizosaccharomyces pombe 972h-]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZDT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZDT FirstGlance]. <br>
<table><tr><td colspan='2'>[[4zdt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe_972h- Schizosaccharomyces pombe 972h-]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZDT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZDT FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <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&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <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=4zdt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zdt OCA], [https://pdbe.org/4zdt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zdt RCSB], [https://www.ebi.ac.uk/pdbsum/4zdt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zdt ProSAT]</span></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=4zdt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zdt OCA], [https://pdbe.org/4zdt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zdt RCSB], [https://www.ebi.ac.uk/pdbsum/4zdt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zdt ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[https://www.uniprot.org/uniprot/SLX1_SCHPO SLX1_SCHPO] Catalytic subunit of the slx1-slx4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. Has a preference for stem-loop (SL) and splayed arm Y structures. Introduces a single-strand cut in duplex DNA on the 3' side of a double-strand/single-strand junction with respect to the single-strand moving 3' to 5' away from the junction. Plays a critical role in maintaining the integrity of the ribosomal DNA (rDNA) loci, where it has a role in re-starting stalled replication forks. The complex initiates homologous recombination (HR) events, used to maintain rDNA copy number, in the rDNA repeats that are processed by a mechanism that requires rad22, but not rhp51. It is also required for suppression of methyl methanesulfonate (MMS) and UV-C irradiation hypersensitivity of the structural maintenance of chromosome (SMC) protein mutant, smc6-74, by overexpression of brc1. Has Holliday junction resolvase activity in vitro.[HAMAP-Rule:MF_03100]<ref>PMID:14528010</ref> <ref>PMID:15972456</ref> <ref>PMID:16467377</ref> <ref>PMID:17277362</ref> <ref>PMID:19596236</ref>  
[https://www.uniprot.org/uniprot/SLX1_SCHPO SLX1_SCHPO] Catalytic subunit of the slx1-slx4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. Has a preference for stem-loop (SL) and splayed arm Y structures. Introduces a single-strand cut in duplex DNA on the 3' side of a double-strand/single-strand junction with respect to the single-strand moving 3' to 5' away from the junction. Plays a critical role in maintaining the integrity of the ribosomal DNA (rDNA) loci, where it has a role in re-starting stalled replication forks. The complex initiates homologous recombination (HR) events, used to maintain rDNA copy number, in the rDNA repeats that are processed by a mechanism that requires rad22, but not rhp51. It is also required for suppression of methyl methanesulfonate (MMS) and UV-C irradiation hypersensitivity of the structural maintenance of chromosome (SMC) protein mutant, smc6-74, by overexpression of brc1. Has Holliday junction resolvase activity in vitro.[HAMAP-Rule:MF_03100]<ref>PMID:14528010</ref> <ref>PMID:15972456</ref> <ref>PMID:16467377</ref> <ref>PMID:17277362</ref> <ref>PMID:19596236</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The SLX1-SLX4 complex is a structure-specific endonuclease that cleaves branched DNA structures and plays significant roles in DNA recombination and repair in eukaryotic cells. The heterodimeric interaction between SLX1 and SLX4 is essential for the endonuclease activity of SLX1. Here, we present the crystal structure of Slx1 C-terminal zinc finger domain in complex with the C-terminal helix-turn-helix domain of Slx4 from Schizosaccharomyces pombe at 2.0 A resolution. The structure reveals a conserved binding mechanism underling the Slx1-Slx4 interaction. Structural and sequence analyses indicate Slx1 C-terminal domain is actually an atypical C4HC3-type RING finger which normally possesses E3 ubiquitin ligase activity, but here is absolutely required for Slx1 interaction with Slx4. Furthermore, we found the C-terminal tail of S. pombe Slx1 contains a SUMO-interacting motif and can recognize Pmt3 (S. pombe SUMO), suggesting that Slx1-Slx4 complex could be recruited by SUMOylated protein targets to take part in replication associated DNA repair processes.
Crystal structure and SUMO binding of Slx1-Slx4 complex.,Lian FM, Xie S, Qian C Sci Rep. 2016 Jan 20;6:19331. doi: 10.1038/srep19331. PMID:26787556<ref>PMID:26787556</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4zdt" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==

Latest revision as of 12:04, 20 March 2024

Crystal structure of the RING finger domain of Slx1 in complex with the C-terminal domain of Slx4Crystal structure of the RING finger domain of Slx1 in complex with the C-terminal domain of Slx4

Structural highlights

4zdt is a 4 chain structure with sequence from Schizosaccharomyces pombe 972h-. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SLX1_SCHPO Catalytic subunit of the slx1-slx4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. Has a preference for stem-loop (SL) and splayed arm Y structures. Introduces a single-strand cut in duplex DNA on the 3' side of a double-strand/single-strand junction with respect to the single-strand moving 3' to 5' away from the junction. Plays a critical role in maintaining the integrity of the ribosomal DNA (rDNA) loci, where it has a role in re-starting stalled replication forks. The complex initiates homologous recombination (HR) events, used to maintain rDNA copy number, in the rDNA repeats that are processed by a mechanism that requires rad22, but not rhp51. It is also required for suppression of methyl methanesulfonate (MMS) and UV-C irradiation hypersensitivity of the structural maintenance of chromosome (SMC) protein mutant, smc6-74, by overexpression of brc1. Has Holliday junction resolvase activity in vitro.[HAMAP-Rule:MF_03100][1] [2] [3] [4] [5]

See Also

References

  1. ↑ Coulon S, Gaillard PH, Chahwan C, McDonald WH, Yates JR 3rd, Russell P. Slx1-Slx4 are subunits of a structure-specific endonuclease that maintains ribosomal DNA in fission yeast. Mol Biol Cell. 2004 Jan;15(1):71-80. Epub 2003 Oct 3. PMID:14528010 doi:http://dx.doi.org/10.1091/mbc.E03-08-0586
  2. ↑ Sheedy DM, Dimitrova D, Rankin JK, Bass KL, Lee KM, Tapia-Alveal C, Harvey SH, Murray JM, O'Connell MJ. Brc1-mediated DNA repair and damage tolerance. Genetics. 2005 Oct;171(2):457-68. Epub 2005 Jun 21. PMID:15972456 doi:http://dx.doi.org/10.1534/genetics.105.044966
  3. ↑ Coulon S, Noguchi E, Noguchi C, Du LL, Nakamura TM, Russell P. Rad22Rad52-dependent repair of ribosomal DNA repeats cleaved by Slx1-Slx4 endonuclease. Mol Biol Cell. 2006 Apr;17(4):2081-90. Epub 2006 Feb 8. PMID:16467377 doi:http://dx.doi.org/E05-11-1006
  4. ↑ Lee KM, Nizza S, Hayes T, Bass KL, Irmisch A, Murray JM, O'Connell MJ. Brc1-mediated rescue of Smc5/6 deficiency: requirement for multiple nucleases and a novel Rad18 function. Genetics. 2007 Apr;175(4):1585-95. Epub 2007 Feb 4. PMID:17277362 doi:http://dx.doi.org/10.1534/genetics.106.067801
  5. ↑ Fekairi S, Scaglione S, Chahwan C, Taylor ER, Tissier A, Coulon S, Dong MQ, Ruse C, Yates JR 3rd, Russell P, Fuchs RP, McGowan CH, Gaillard PH. Human SLX4 is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases. Cell. 2009 Jul 10;138(1):78-89. PMID:19596236 doi:S0092-8674(09)00776-4

4zdt, resolution 2.00Å

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