6WJV | pdb_00006wjv

Structure of the Saccharomyces cerevisiae polymerase epsilon holoenzyme

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth 4]	SCOP2 Family	TBP-associated factors, TAFs	8099093	4000797	SCOP2 (2022-06-29)
D [auth 4]	SCOP2 Superfamily	Core histone-like	8099094	3001387	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth 3]	CBFD_NFYB_HMF	e6wjv31	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: CBFD_NFYB_HMF	ECOD (1.6)
D [auth 4]	CBFD_NFYB_HMF	e6wjv41	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: CBFD_NFYB_HMF	ECOD (1.6)
B [auth 2]	UNK_F_TYPE	e6wjv21	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: UNK_F_TYPE	ECOD (1.6)
B [auth 2]	DNA_pol_E_B	e6wjv22	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: DNA_pol_E_B	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth 2]	PF04042	DNA polymerase alpha/epsilon subunit B (DNA_pol_E_B)	DNA polymerase alpha/epsilon subunit B	-	Family
A	PF08490	Domain of unknown function (DUF1744) (DUF1744)	Domain of unknown function (DUF1744)	This domain is found at the C-terminal of the epsilon catalytic subunit of DNA polymerase. It is found C terminal to Pfam:PF03104 and Pfam:PF00136.	Domain
A	PF22912	Zinc finger domain of DNA polymerase-epsilon (zf-DPOE)	Zinc finger domain of DNA polymerase-epsilon	This zinc finger domain is found in the epsilon subunit of DNA polymerase.	Domain
A	PF22634	DNA polymerase epsilon catalytic subunit A, thumb domain (POL2_thumb)	DNA polymerase epsilon catalytic subunit A, thumb domain	This entry represents the thumb domain of DNA polymerase epsilon catalytic subunit A from Saccharomyces cerevisiae (POL2), the catalytic component of this complex involved in chromosomal DNA replication. This domain, which makes contacts in the DNA m ...	This entry represents the thumb domain of DNA polymerase epsilon catalytic subunit A from Saccharomyces cerevisiae (POL2), the catalytic component of this complex involved in chromosomal DNA replication. This domain, which makes contacts in the DNA minor groove, shows a mainly alpha-helical structure [2].	Domain
A	PF03104	DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1)	DNA polymerase family B, exonuclease domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth 3]	DNA polymerase epsilon subunit C	protein heterodimerization activity protein binding binding protein dimerization activity	DNA-templated DNA replication primary metabolic process DNA metabolic process leading strand elongation nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process cellular process DNA strand elongation involved in DNA replication macromolecule metabolic process translesion synthesis cellular response to stimulus DNA-templated DNA replication primary metabolic process DNA metabolic process leading strand elongation nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process cellular process DNA strand elongation involved in DNA replication macromolecule metabolic process translesion synthesis cellular response to stimulus response to stimulus nucleobase-containing compound biosynthetic process DNA damage tolerance macromolecule biosynthetic process DNA synthesis involved in DNA replication nucleic acid biosynthetic process biosynthetic process cellular response to stress DNA damage response response to stress error-prone translesion synthesis DNA biosynthetic process	membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membraneless organelle chromatin chromosome intracellular membrane-bounded organelle intracellular organelle ISWI-type complex cellular anatomical structure membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membraneless organelle chromatin chromosome intracellular membrane-bounded organelle intracellular organelle ISWI-type complex cellular anatomical structure organelle membraneless organelle SWI/SNF superfamily-type complex CHRAC membrane-enclosed lumen nuclear replication fork nuclear chromosome intracellular organelle lumen organelle lumen replication fork nuclear lumen transferase complex epsilon DNA polymerase complex DNA polymerase complex transferase complex, transferring phosphorus-containing groups intracellular protein-containing complex
D [auth 4]	DNA polymerase epsilon subunit D	DNA binding binding chromatin binding nucleic acid binding chromatin DNA binding protein-containing complex binding nucleosome binding nucleosomal DNA binding protein heterodimerization activity protein binding protein dimerization activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process DNA double-strand break processing regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process DNA repair double-strand break repair regulation of biological process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process DNA double-strand break processing regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process DNA repair double-strand break repair regulation of biological process biological regulation regulation of DNA double-strand break processing primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process DNA-templated DNA replication leading strand elongation DNA strand elongation DNA replication DNA strand elongation involved in DNA replication RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription translesion synthesis DNA damage tolerance DNA synthesis involved in DNA replication error-prone translesion synthesis DNA biosynthetic process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process heterochromatin organization negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex intracellular membraneless organelle intracellular membrane-bounded organelle epsilon DNA polymerase complex DNA polymerase complex transferase complex, transferring phosphorus-containing groups organelle lumen organelle intracellular protein-containing complex nuclear lumen ATPase complex chromatin ISWI-type complex SWI/SNF superfamily-type complex CHRAC nuclear replication fork replication fork
B [auth 2]	DNA polymerase epsilon subunit B	DNA binding binding nucleic acid binding	translesion synthesis cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process DNA damage tolerance macromolecule biosynthetic process nucleic acid metabolic process DNA synthesis involved in DNA replication nucleobase-containing compound metabolic process nucleic acid biosynthetic process DNA replication biosynthetic process cellular response to stress translesion synthesis cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process DNA damage tolerance macromolecule biosynthetic process nucleic acid metabolic process DNA synthesis involved in DNA replication nucleobase-containing compound metabolic process nucleic acid biosynthetic process DNA replication biosynthetic process cellular response to stress DNA damage response response to stress metabolic process cellular process error-prone translesion synthesis macromolecule metabolic process DNA biosynthetic process DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen nuclear replication fork intracellular membraneless organelle nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen nuclear replication fork intracellular membraneless organelle nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen organelle membraneless organelle replication fork nuclear lumen protein-containing complex nuclear protein-containing complex transferase complex catalytic complex epsilon DNA polymerase complex DNA polymerase complex transferase complex, transferring phosphorus-containing groups intracellular protein-containing complex
A	DNA polymerase epsilon catalytic subunit A	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding DNA exonuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity single-stranded DNA exodeoxyribonuclease activity catalytic activity, acting on DNA nuclease activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding DNA exonuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity single-stranded DNA exodeoxyribonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds 3'-5'-DNA exonuclease activity catalytic activity exonuclease activity single-stranded DNA 3'-5' DNA exonuclease activity iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups DNA binding nucleic acid binding RNA binding mRNA binding double-stranded DNA binding SUMO binding protein binding ubiquitin-like protein binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding single-stranded DNA binding	cellular process cell cycle mitotic cell cycle cellular response to stimulus regulation of cellular process regulation of cell cycle phase transition response to stimulus signaling G2/M transition of mitotic cell cycle negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction negative regulation of mitotic cell cycle cellular process cell cycle mitotic cell cycle cellular response to stimulus regulation of cellular process regulation of cell cycle phase transition response to stimulus signaling G2/M transition of mitotic cell cycle negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction negative regulation of mitotic cell cycle cell communication mitotic G2/M transition checkpoint regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction DNA replication checkpoint signaling regulation of cell cycle cell cycle process cell cycle G2/M phase transition regulation of biological process mitotic DNA replication checkpoint signaling negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process biological regulation DNA integrity checkpoint signaling regulation of cell cycle G2/M phase transition negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic cell cycle process negative regulation of cell cycle G2/M phase transition negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition DNA-templated DNA replication primary metabolic process DNA metabolic process leading strand elongation nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process DNA strand elongation involved in DNA replication macromolecule metabolic process DNA-templated DNA replication maintenance of fidelity DNA replication proofreading cellular response to stress DNA damage response response to stress DNA repair translesion synthesis nucleobase-containing compound biosynthetic process DNA damage tolerance macromolecule biosynthetic process DNA synthesis involved in DNA replication nucleic acid biosynthetic process biosynthetic process error-prone translesion synthesis DNA biosynthetic process base-excision repair cellular component organization organelle organization mitotic sister chromatid cohesion chromosome organization sister chromatid cohesion cellular component organization or biogenesis nucleotide-excision repair, DNA gap filling nucleotide-excision repair base-excision repair, gap-filling double-strand break repair homologous recombination DNA recombination gene conversion DNA damage checkpoint signaling mitotic DNA damage checkpoint signaling mitotic intra-S DNA damage checkpoint signaling signal transduction in response to DNA damage double-strand break repair via nonhomologous end joining	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex intracellular membraneless organelle intracellular membrane-bounded organelle epsilon DNA polymerase complex DNA polymerase complex transferase complex, transferring phosphorus-containing groups organelle lumen organelle intracellular protein-containing complex nuclear lumen replication fork nuclear replication fork

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth 3]	IPR009072	Histone-fold	Homologous Superfamily
C [auth 3]	IPR050568	Transcription/DNA replication regulator	Family
D [auth 4]	IPR009072	Histone-fold	Homologous Superfamily
D [auth 4]	IPR051377	DNA Polymerase Epsilon Subunit	Family
B [auth 2]	IPR016266	DNA polymerase epsilon, subunit B	Family
B [auth 2]	IPR007185	DNA polymerase alpha/delta/epsilon, subunit B	Domain
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR054475	DNA polymerase-epsilon, zinc finger domain	Domain
A	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A	IPR023211	DNA polymerase, palm domain superfamily	Homologous Superfamily
A	IPR006172	DNA-directed DNA polymerase, family B	Family
A	IPR029703	DNA polymerase epsilon catalytic subunit	Family
A	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A	IPR013697	DNA polymerase epsilon, catalytic subunit A, C-terminal	Domain
A	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
A	IPR042087	DNA polymerase family B, thumb domain	Homologous Superfamily
A	IPR055191	DNA polymerase epsilon ,catalytic subunit A, thumb domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.