6HV8

Cryo-EM structure of S. cerevisiae Polymerase epsilon deltacat mutant

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth B]	F_UNCLASSIFIED	e6hv8B1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: F_UNCLASSIFIED	ECOD (1.6)
A [auth B]	PF04042	e6hv8B2	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: PF04042	ECOD (1.6)
B [auth A]	PF08490	e6hv8A3	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: PF08490	ECOD (1.6)
B [auth A]	F_UNCLASSIFIED	e6hv8A2	A: few secondary structure elements	X: Rubredoxin-like	H: Zinc finger domain of DNA polymerase-alpha (From Topology)	T: Zinc finger domain of DNA polymerase-alpha	F: F_UNCLASSIFIED	ECOD (1.6)
B [auth A]	PF22912	e6hv8A1	A: few secondary structure elements	X: Rubredoxin-like	H: Zinc finger domain of DNA polymerase-alpha (From Topology)	T: Zinc finger domain of DNA polymerase-alpha	F: PF22912	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B]	PF04042	DNA polymerase alpha/epsilon subunit B (DNA_pol_E_B)	DNA polymerase alpha/epsilon subunit B	-	Family
B [auth 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	DNA polymerase epsilon subunit B	DNA binding binding organic cyclic compound binding nucleic acid binding	cellular process cell cycle cellular response to stimulus postreplication repair response to stimulus cellular biosynthetic process DNA synthesis involved in DNA repair nucleobase-containing compound metabolic process nucleic acid biosynthetic process organic substance metabolic process cellular response to stress response to stress organic substance biosynthetic process DNA repair cellular process cell cycle cellular response to stimulus postreplication repair response to stimulus cellular biosynthetic process DNA synthesis involved in DNA repair nucleobase-containing compound metabolic process nucleic acid biosynthetic process organic substance metabolic process cellular response to stress response to stress organic substance biosynthetic process DNA repair translesion synthesis cellular metabolic process primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process DNA damage response organic cyclic compound biosynthetic process metabolic process error-prone translesion synthesis macromolecule metabolic process DNA biosynthetic process DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity DNA replication	intracellular anatomical structure cytoplasm cellular anatomical entity membrane-bounded organelle nucleus membrane-enclosed lumen nuclear replication fork nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular anatomical structure cytoplasm cellular anatomical entity membrane-bounded organelle nucleus membrane-enclosed lumen nuclear replication fork nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle replication fork non-membrane-bounded organelle 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
B [auth A]	DNA polymerase epsilon catalytic subunit A	binding nucleoside phosphate binding organic cyclic compound 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 exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters single-stranded DNA exodeoxyribonuclease activity binding nucleoside phosphate binding organic cyclic compound 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 exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters 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 organic cyclic compound metabolic process DNA strand elongation organic substance metabolic process 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 postreplication repair cellular biosynthetic process DNA synthesis involved in DNA repair nucleic acid biosynthetic process organic substance biosynthetic process translesion synthesis cellular metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process biosynthetic process organic cyclic compound 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 non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle 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 non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle cellular anatomical entity epsilon DNA polymerase complex DNA polymerase complex transferase complex, transferring phosphorus-containing groups organelle lumen organelle intracellular non-membrane-bounded organelle intracellular protein-containing complex nuclear lumen replication fork nuclear replication fork

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B]	IPR016266	DNA polymerase epsilon, subunit B	Family
A [auth B]	IPR007185	DNA polymerase alpha/delta/epsilon, subunit B	Domain
B [auth A]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
B [auth A]	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain	Domain
B [auth A]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
B [auth A]	IPR023211	DNA polymerase, palm domain superfamily	Homologous Superfamily
B [auth A]	IPR006172	DNA-directed DNA polymerase, family B	Family
B [auth A]	IPR029703	DNA polymerase epsilon catalytic subunit	Family
B [auth A]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
B [auth A]	IPR013697	DNA polymerase epsilon, catalytic subunit A, C-terminal	Domain
B [auth A]	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
B [auth A]	IPR042087	DNA polymerase family B, thumb domain	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.