6p1h

From Proteopedia

(Difference between revisions)

Revision as of 04:17, 11 April 2020

Cryo-EM Structure of DNA Polymerase Delta Holoenzyme

6p1h, resolution 3.20Å

Structural highlights

6p1h is a 5 chain structure with sequence from Baker's yeast. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	POL3, CDC2, TEX1, YDL102W, D2366 (Baker's yeast), POL31, HUS2, HYS2, SDP5, YJR006W, J1427, YJR83.7 (Baker's yeast), POL32, YJR043C, J1626 (Baker's yeast)
Activity:	DNA-directed DNA polymerase, with EC number 2.7.7.7
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DPOD_YEAST] DNA polymerase delta (DNA polymerase III) participates in chromosomal DNA replication. It is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair. POL3 contains the polymerase active site and most likely the active site for the 3'-5' exonuclease activity.^[1] [DPOD3_YEAST] DNA polymerase delta (DNA polymerase III) participates in chromosomal DNA replication. It is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair. [DPOD2_YEAST] DNA polymerase delta (DNA polymerase III) participates in chromosomal DNA replication. It is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair.^[2]

Publication Abstract from PubMed

DNA polymerase delta (Poldelta) plays pivotal roles in eukaryotic DNA replication and repair. Poldelta is conserved from yeast to humans, and mutations in human Poldelta have been implicated in various cancers. Saccharomyces cerevisiae Poldelta consists of catalytic Pol3 and the regulatory Pol31 and Pol32 subunits. Here, we present the near atomic resolution (3.2 A) cryo-EM structure of yeast Poldelta holoenzyme in the act of DNA synthesis. The structure reveals an unexpected arrangement in which the regulatory subunits (Pol31 and Pol32) lie next to the exonuclease domain of Pol3 but do not engage the DNA. The Pol3 C-terminal domain contains a 4Fe-4S cluster and emerges as the keystone of Poldelta assembly. We also show that the catalytic and regulatory subunits rotate relative to each other and that this is an intrinsic feature of the Poldelta architecture. Collectively, the structure provides a framework for understanding DNA transactions at the replication fork.

Cryo-EM structure and dynamics of eukaryotic DNA polymerase delta holoenzyme.,Jain R, Rice WJ, Malik R, Johnson RE, Prakash L, Prakash S, Ubarretxena-Belandia I, Aggarwal AK Nat Struct Mol Biol. 2019 Oct;26(10):955-962. doi: 10.1038/s41594-019-0305-z., Epub 2019 Oct 3. PMID:31582849^[3]

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

References

↑ Simon M, Giot L, Faye G. The 3' to 5' exonuclease activity located in the DNA polymerase delta subunit of Saccharomyces cerevisiae is required for accurate replication. EMBO J. 1991 Aug;10(8):2165-70. PMID:1648480
↑ Sugimoto K, Sakamoto Y, Takahashi O, Matsumoto K. HYS2, an essential gene required for DNA replication in Saccharomyces cerevisiae. Nucleic Acids Res. 1995 Sep 11;23(17):3493-500. doi: 10.1093/nar/23.17.3493. PMID:7567461 doi:http://dx.doi.org/10.1093/nar/23.17.3493
↑ Jain R, Rice WJ, Malik R, Johnson RE, Prakash L, Prakash S, Ubarretxena-Belandia I, Aggarwal AK. Cryo-EM structure and dynamics of eukaryotic DNA polymerase delta holoenzyme. Nat Struct Mol Biol. 2019 Oct;26(10):955-962. doi: 10.1038/s41594-019-0305-z., Epub 2019 Oct 3. PMID:31582849 doi:http://dx.doi.org/10.1038/s41594-019-0305-z

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6p1h"

@@ Line 3: / Line 3: @@
 <SX load='6p1h' size='340' side='right' viewer='molstar' caption='[[6p1h]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6p1h]] is a 5 chain structure with sequence from [http://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=6P1H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P1H FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6p1h]] is a 5 chain structure with sequence from [http://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=6P1H OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6P1H FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">POL3, CDC2, TEX1, YDL102W, D2366 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), POL31, HUS2, HYS2, SDP5, YJR006W, J1427, YJR83.7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), POL32, YJR043C, J1626 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=6p1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p1h OCA], [http://pdbe.org/6p1h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p1h RCSB], [http://www.ebi.ac.uk/pdbsum/6p1h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p1h ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6p1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p1h OCA], [http://pdbe.org/6p1h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p1h RCSB], [http://www.ebi.ac.uk/pdbsum/6p1h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p1h ProSAT]</span></td></tr>
 </table>
 == Function ==

6p1h

From Proteopedia

Revision as of 04:17, 11 April 2020

Cryo-EM Structure of DNA Polymerase Delta Holoenzyme

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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