8vf2: Difference between revisions

Latest revision as of 08:00, 11 December 2025

CryoEM structure of Ku homodimer super-complex with linear DNA

Structural highlights

8vf2 is a 10 chain structure with sequence from Mycobacterium tuberculosis H37Rv and Saltans group. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.7Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KU_MYCTU With LigD forms a non-homologous end joining (NHEJ) repair enzyme. Binds linear dsDNA with 5'- and 3'-overhangs but not closed circular dsDNA nor ssDNA. One dimer binds for every 30 bp. Recruits and stimulates the ligase activity of LigD but not of T4 ligase or a human ligase complex (LIG4/XRCC4). Attenuates the 3'- to 5'-exonuclease activity of LigD. Stimulates the template-directed addition of dNTPs by LigD on 5'-overhangs and nuclease activity on 3'-overhangs.^[1] ^[2] ^[3] ^[4]

References

↑ Weller GR, Kysela B, Roy R, Tonkin LM, Scanlan E, Della M, Devine SK, Day JP, Wilkinson A, d'Adda di Fagagna F, Devine KM, Bowater RP, Jeggo PA, Jackson SP, Doherty AJ. Identification of a DNA nonhomologous end-joining complex in bacteria. Science. 2002 Sep 6;297(5587):1686-9. PMID:12215643 doi:10.1126/science.1074584
↑ Della M, Palmbos PL, Tseng HM, Tonkin LM, Daley JM, Topper LM, Pitcher RS, Tomkinson AE, Wilson TE, Doherty AJ. Mycobacterial Ku and ligase proteins constitute a two-component NHEJ repair machine. Science. 2004 Oct 22;306(5696):683-5. doi: 10.1126/science.1099824. PMID:15499016 doi:https://dx.doi.org/10.1126/science.1099824
↑ Gong C, Bongiorno P, Martins A, Stephanou NC, Zhu H, Shuman S, Glickman MS. Mechanism of nonhomologous end-joining in mycobacteria: a low-fidelity repair system driven by Ku, ligase D and ligase C. Nat Struct Mol Biol. 2005 Apr;12(4):304-12. PMID:15778718 doi:10.1038/nsmb915
↑ Pitcher RS, Tonkin LM, Green AJ, Doherty AJ. Domain structure of a NHEJ DNA repair ligase from Mycobacterium tuberculosis. J Mol Biol. 2005 Aug 19;351(3):531-44. PMID:16023671 doi:10.1016/j.jmb.2005.06.038

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OCA

[1] Weller GR, Kysela B, Roy R, Tonkin LM, Scanlan E, Della M, Devine SK, Day JP, Wilkinson A, d'Adda di Fagagna F, Devine KM, Bowater RP, Jeggo PA, Jackson SP, Doherty AJ. Identification of a DNA nonhomologous end-joining complex in bacteria. Science. 2002 Sep 6;297(5587):1686-9. PMID:12215643 doi:10.1126/science.1074584

[2] Della M, Palmbos PL, Tseng HM, Tonkin LM, Daley JM, Topper LM, Pitcher RS, Tomkinson AE, Wilson TE, Doherty AJ. Mycobacterial Ku and ligase proteins constitute a two-component NHEJ repair machine. Science. 2004 Oct 22;306(5696):683-5. doi: 10.1126/science.1099824. PMID:15499016 doi:https://dx.doi.org/10.1126/science.1099824

[3] Gong C, Bongiorno P, Martins A, Stephanou NC, Zhu H, Shuman S, Glickman MS. Mechanism of nonhomologous end-joining in mycobacteria: a low-fidelity repair system driven by Ku, ligase D and ligase C. Nat Struct Mol Biol. 2005 Apr;12(4):304-12. PMID:15778718 doi:10.1038/nsmb915

[4] Pitcher RS, Tonkin LM, Green AJ, Doherty AJ. Domain structure of a NHEJ DNA repair ligase from Mycobacterium tuberculosis. J Mol Biol. 2005 Aug 19;351(3):531-44. PMID:16023671 doi:10.1016/j.jmb.2005.06.038

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8vf2 is ON HOLD  until Paper Publication
+==CryoEM structure of Ku homodimer super-complex with linear DNA==
+<StructureSection load='8vf2' size='340' side='right'caption='[[8vf2]], [[Resolution|resolution]] 3.70&Aring;' scene=''>
-Authors:
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8vf2]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv] and [https://en.wikipedia.org/wiki/Saltans_group Saltans group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8VF2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8VF2 FirstGlance]. <br>
-Description:
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.7&#8491;</td></tr>
-[[Category: Unreleased Structures]]
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8vf2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8vf2 OCA], [https://pdbe.org/8vf2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8vf2 RCSB], [https://www.ebi.ac.uk/pdbsum/8vf2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8vf2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/KU_MYCTU KU_MYCTU] With LigD forms a non-homologous end joining (NHEJ) repair enzyme. Binds linear dsDNA with 5'- and 3'-overhangs but not closed circular dsDNA nor ssDNA. One dimer binds for every 30 bp. Recruits and stimulates the ligase activity of LigD but not of T4 ligase or a human ligase complex (LIG4/XRCC4). Attenuates the 3'- to 5'-exonuclease activity of LigD. Stimulates the template-directed addition of dNTPs by LigD on 5'-overhangs and nuclease activity on 3'-overhangs.<ref>PMID:12215643</ref> <ref>PMID:15499016</ref> <ref>PMID:15778718</ref> <ref>PMID:16023671</ref>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Mycobacterium tuberculosis H37Rv]]
+[[Category: Saltans group]]
+[[Category: Baral J]]
+[[Category: Das AK]]
+[[Category: Rouiller I]]

8vf2: Difference between revisions

Latest revision as of 08:00, 11 December 2025

CryoEM structure of Ku homodimer super-complex with linear DNA

Structural highlights

Function

References

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