9ekb: Difference between revisions

Latest revision as of 06:27, 5 February 2025

Cryo-EM structure of apo-form human DNA polymerase delta

Structural highlights

9ekb is a 4 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:	Electron Microscopy, Resolution 3.65Å
Ligands:	ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

DPOD1_HUMAN Mandibular hypoplasia-deafness-progeroid features-lipodystrophy syndrome;Polymerase proofreading-related adenomatous polyposis. Disease susceptibility is associated with variations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.

Function

DPOD1_HUMAN As the catalytic component of the trimeric (Pol-delta3 complex) and tetrameric DNA polymerase delta complexes (Pol-delta4 complex), plays a crucial role in high fidelity genome replication, including in lagging strand synthesis, and repair. Exhibits both DNA polymerase and 3'- to 5'-exonuclease activities (PubMed:16510448, PubMed:19074196, PubMed:20334433, PubMed:24035200, PubMed:24022480). Requires the presence of accessory proteins POLD2, POLD3 and POLD4 for full activity. Depending upon the absence (Pol-delta3) or the presence of POLD4 (Pol-delta4), displays differences in catalytic activity. Most notably, expresses higher proofreading activity in the context of Pol-delta3 compared with that of Pol-delta4 (PubMed:19074196, PubMed:20334433). Although both Pol-delta3 and Pol-delta4 process Okazaki fragments in vitro, Pol-delta3 may be better suited to fulfill this task, exhibiting near-absence of strand displacement activity compared to Pol-delta4 and stalling on encounter with the 5'-blocking oligonucleotides. Pol-delta3 idling process may avoid the formation of a gap, while maintaining a nick that can be readily ligated (PubMed:24035200). Along with DNA polymerase kappa, DNA polymerase delta carries out approximately half of nucleotide excision repair (NER) synthesis following UV irradiation (PubMed:20227374). Under conditions of DNA replication stress, in the presence of POLD3 and POLD4, may catalyze the repair of broken replication forks through break-induced replication (BIR) (PubMed:24310611). Involved in the translesion synthesis (TLS) of templates carrying O6-methylguanine or abasic sites (PubMed:19074196).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

References

↑ Li H, Xie B, Zhou Y, Rahmeh A, Trusa S, Zhang S, Gao Y, Lee EY, Lee MY. Functional roles of p12, the fourth subunit of human DNA polymerase delta. J Biol Chem. 2006 May 26;281(21):14748-55. Epub 2006 Feb 28. PMID:16510448 doi:https://dx.doi.org/10.1074/jbc.M600322200
↑ Meng X, Zhou Y, Zhang S, Lee EY, Frick DN, Lee MY. DNA damage alters DNA polymerase delta to a form that exhibits increased discrimination against modified template bases and mismatched primers. Nucleic Acids Res. 2009 Feb;37(2):647-57. doi: 10.1093/nar/gkn1000. Epub 2008 Dec, 11. PMID:19074196 doi:https://dx.doi.org/10.1093/nar/gkn1000
↑ Ogi T, Limsirichaikul S, Overmeer RM, Volker M, Takenaka K, Cloney R, Nakazawa Y, Niimi A, Miki Y, Jaspers NG, Mullenders LH, Yamashita S, Fousteri MI, Lehmann AR. Three DNA polymerases, recruited by different mechanisms, carry out NER repair synthesis in human cells. Mol Cell. 2010 Mar 12;37(5):714-27. doi: 10.1016/j.molcel.2010.02.009. PMID:20227374 doi:https://dx.doi.org/10.1016/j.molcel.2010.02.009
↑ Meng X, Zhou Y, Lee EY, Lee MY, Frick DN. The p12 subunit of human polymerase delta modulates the rate and fidelity of DNA synthesis. Biochemistry. 2010 May 4;49(17):3545-54. doi: 10.1021/bi100042b. PMID:20334433 doi:https://dx.doi.org/10.1021/bi100042b
↑ Terai K, Shibata E, Abbas T, Dutta A. Degradation of p12 subunit by CRL4Cdt2 E3 ligase inhibits fork progression after DNA damage. J Biol Chem. 2013 Oct 18;288(42):30509-14. doi: 10.1074/jbc.C113.505586. Epub, 2013 Sep 10. PMID:24022480 doi:https://dx.doi.org/10.1074/jbc.C113.505586
↑ Lin SH, Wang X, Zhang S, Zhang Z, Lee EY, Lee MY. Dynamics of enzymatic interactions during short flap human Okazaki fragment processing by two forms of human DNA polymerase delta. DNA Repair (Amst). 2013 Nov;12(11):922-35. doi: 10.1016/j.dnarep.2013.08.008., Epub 2013 Sep 10. PMID:24035200 doi:https://dx.doi.org/10.1016/j.dnarep.2013.08.008
↑ Costantino L, Sotiriou SK, Rantala JK, Magin S, Mladenov E, Helleday T, Haber JE, Iliakis G, Kallioniemi OP, Halazonetis TD. Break-induced replication repair of damaged forks induces genomic duplications in human cells. Science. 2014 Jan 3;343(6166):88-91. doi: 10.1126/science.1243211. Epub 2013 Dec , 5. PMID:24310611 doi:https://dx.doi.org/10.1126/science.1243211

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Li H, Xie B, Zhou Y, Rahmeh A, Trusa S, Zhang S, Gao Y, Lee EY, Lee MY. Functional roles of p12, the fourth subunit of human DNA polymerase delta. J Biol Chem. 2006 May 26;281(21):14748-55. Epub 2006 Feb 28. PMID:16510448 doi:https://dx.doi.org/10.1074/jbc.M600322200

[2] Meng X, Zhou Y, Zhang S, Lee EY, Frick DN, Lee MY. DNA damage alters DNA polymerase delta to a form that exhibits increased discrimination against modified template bases and mismatched primers. Nucleic Acids Res. 2009 Feb;37(2):647-57. doi: 10.1093/nar/gkn1000. Epub 2008 Dec, 11. PMID:19074196 doi:https://dx.doi.org/10.1093/nar/gkn1000

[3] Ogi T, Limsirichaikul S, Overmeer RM, Volker M, Takenaka K, Cloney R, Nakazawa Y, Niimi A, Miki Y, Jaspers NG, Mullenders LH, Yamashita S, Fousteri MI, Lehmann AR. Three DNA polymerases, recruited by different mechanisms, carry out NER repair synthesis in human cells. Mol Cell. 2010 Mar 12;37(5):714-27. doi: 10.1016/j.molcel.2010.02.009. PMID:20227374 doi:https://dx.doi.org/10.1016/j.molcel.2010.02.009

[4] Meng X, Zhou Y, Lee EY, Lee MY, Frick DN. The p12 subunit of human polymerase delta modulates the rate and fidelity of DNA synthesis. Biochemistry. 2010 May 4;49(17):3545-54. doi: 10.1021/bi100042b. PMID:20334433 doi:https://dx.doi.org/10.1021/bi100042b

[5] Terai K, Shibata E, Abbas T, Dutta A. Degradation of p12 subunit by CRL4Cdt2 E3 ligase inhibits fork progression after DNA damage. J Biol Chem. 2013 Oct 18;288(42):30509-14. doi: 10.1074/jbc.C113.505586. Epub, 2013 Sep 10. PMID:24022480 doi:https://dx.doi.org/10.1074/jbc.C113.505586

[6] Lin SH, Wang X, Zhang S, Zhang Z, Lee EY, Lee MY. Dynamics of enzymatic interactions during short flap human Okazaki fragment processing by two forms of human DNA polymerase delta. DNA Repair (Amst). 2013 Nov;12(11):922-35. doi: 10.1016/j.dnarep.2013.08.008., Epub 2013 Sep 10. PMID:24035200 doi:https://dx.doi.org/10.1016/j.dnarep.2013.08.008

[7] Costantino L, Sotiriou SK, Rantala JK, Magin S, Mladenov E, Helleday T, Haber JE, Iliakis G, Kallioniemi OP, Halazonetis TD. Break-induced replication repair of damaged forks induces genomic duplications in human cells. Science. 2014 Jan 3;343(6166):88-91. doi: 10.1126/science.1243211. Epub 2013 Dec , 5. PMID:24310611 doi:https://dx.doi.org/10.1126/science.1243211

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9ekb is ON HOLD
+==Cryo-EM structure of apo-form human DNA polymerase delta==
+<StructureSection load='9ekb' size='340' side='right'caption='[[9ekb]], [[Resolution|resolution]] 3.65&Aring;' scene=''>
-Authors: Murakami, K.S., Shin, Y.
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9ekb]] is a 4 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=9EKB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9EKB FirstGlance]. <br>
-Description: Cryo-EM structure of apo-form human DNA polymerase delta
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.65&#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=ZN:ZINC+ION'>ZN</scene></td></tr>
-[[Category: Shin, Y]]
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9ekb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9ekb OCA], [https://pdbe.org/9ekb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9ekb RCSB], [https://www.ebi.ac.uk/pdbsum/9ekb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9ekb ProSAT]</span></td></tr>
-[[Category: Murakami, K.S]]
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/DPOD1_HUMAN DPOD1_HUMAN] Mandibular hypoplasia-deafness-progeroid features-lipodystrophy syndrome;Polymerase proofreading-related adenomatous polyposis. Disease susceptibility is associated with variations affecting the gene represented in this entry.  The disease is caused by mutations affecting the gene represented in this entry.
+== Function ==
+[https://www.uniprot.org/uniprot/DPOD1_HUMAN DPOD1_HUMAN] As the catalytic component of the trimeric (Pol-delta3 complex) and tetrameric DNA polymerase delta complexes (Pol-delta4 complex), plays a crucial role in high fidelity genome replication, including in lagging strand synthesis, and repair. Exhibits both DNA polymerase and 3'- to 5'-exonuclease activities (PubMed:16510448, PubMed:19074196, PubMed:20334433, PubMed:24035200, PubMed:24022480). Requires the presence of accessory proteins POLD2, POLD3 and POLD4 for full activity. Depending upon the absence (Pol-delta3) or the presence of POLD4 (Pol-delta4), displays differences in catalytic activity. Most notably, expresses higher proofreading activity in the context of Pol-delta3 compared with that of Pol-delta4 (PubMed:19074196, PubMed:20334433). Although both Pol-delta3 and Pol-delta4 process Okazaki fragments in vitro, Pol-delta3 may be better suited to fulfill this task, exhibiting near-absence of strand displacement activity compared to Pol-delta4 and stalling on encounter with the 5'-blocking oligonucleotides. Pol-delta3 idling process may avoid the formation of a gap, while maintaining a nick that can be readily ligated (PubMed:24035200). Along with DNA polymerase kappa, DNA polymerase delta carries out approximately half of nucleotide excision repair (NER) synthesis following UV irradiation (PubMed:20227374). Under conditions of DNA replication stress, in the presence of POLD3 and POLD4, may catalyze the repair of broken replication forks through break-induced replication (BIR) (PubMed:24310611). Involved in the translesion synthesis (TLS) of templates carrying O6-methylguanine or abasic sites (PubMed:19074196).<ref>PMID:16510448</ref> <ref>PMID:19074196</ref> <ref>PMID:20227374</ref> <ref>PMID:20334433</ref> <ref>PMID:24022480</ref> <ref>PMID:24035200</ref> <ref>PMID:24310611</ref>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Murakami KS]]
+[[Category: Shin Y]]

9ekb: Difference between revisions

Latest revision as of 06:27, 5 February 2025

Cryo-EM structure of apo-form human DNA polymerase delta

Structural highlights

Disease

Function

References

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