Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	The proofreading mechanism of the human leading-strand DNA polymerase ε holoenzyme.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 122, Issue 22, Page e2507232122, Year 2025
Publish date	Jun 3, 2025
Authors	Feng Wang / Qing He / Michael E O'Donnell / Huilin Li /
PubMed Abstract	The eukaryotic leading-strand DNA polymerase ε (Polε) is a dual-function enzyme with a proofreading 3'-5' exonuclease () site located 40 Å from the DNA synthesizing site. Errors in Polε ...The eukaryotic leading-strand DNA polymerase ε (Polε) is a dual-function enzyme with a proofreading 3'-5' exonuclease () site located 40 Å from the DNA synthesizing site. Errors in Polε proofreading can cause various mutations, including C-to-G transversions, the most prevalent mutation in cancers and genetic diseases. Polε interacts with all three subunits of the PCNA ring to assemble a functional holoenzyme. Despite previous studies on proofreading of several Pol's, how Polε-or any Pol complexed with its sliding clamp-proofreads a mismatch generated in situ has been unknown. We show here by cryo-EM that a template/primer DNA substrate with a preexisting mismatch cannot enter the site of Polε-PCNA holoenzyme, but a mismatch generated in situ in the site yields three bona fide proofreading intermediates of Polε-PCNA holoenzyme. These intermediates reveal how the mismatch is dislodged from the site, how the DNA unwinds six base pairs, and how the unpaired primer 3'-end is inserted into the site for cleavage. These results unexpectedly demonstrate that PCNA imposes strong steric constraints that extend unwinding and direct the trajectory of mismatched DNA and that this trajectory is dramatically different than for Polε in the absence of PCNA. These findings suggest a physiologically relevant proofreading mechanism for the human Polε holoenzyme.
External links	Proc Natl Acad Sci U S A / PubMed:40440070
Methods	EM (single particle)
Resolution	3.11 - 3.88 Å
Structure data	49299 9ne6 EMDB-49299, PDB-9ne6: Human polymerase epsilon bound to PCNA and DNA with an in-situ-generated mismatch in the mismatch-editing state Method: EM (single particle) / Resolution: 3.11 Å 49300 9ne7 EMDB-49300, PDB-9ne7: Human polymerase epsilon bound to PCNA and DNA with an in-situ-generated mismatch in the Pol-backtracking state Method: EM (single particle) / Resolution: 3.53 Å 49301 9ne8 EMDB-49301, PDB-9ne8: Human polymerase epsilon bound to PCNA and DNA with an in-situ-generated mismatch in the mismatch-locking state Method: EM (single particle) / Resolution: 3.6 Å 49302 9ne9 EMDB-49302, PDB-9ne9: Human polymerase epsilon bound to PCNA and DNA with a pre-existing mismatch in the blocked conformation I Method: EM (single particle) / Resolution: 3.88 Å 49303 9nea EMDB-49303, PDB-9nea: Human polymerase epsilon bound to PCNA and DNA with a pre-existing mismatch in the blocked conformation II Method: EM (single particle) / Resolution: 3.81 Å
Chemicals	ChemComp-SF4: IRON/SULFUR CLUSTER ChemComp-MG: Unknown entry
Source	homo sapiens (human) synthetic construct (others)
Keywords	REPLICATION / DNA polymerase / exo / holoenzyme / DNA