6I8A

The crystal structure of the Pol2 catalytic domain of DNA polymerase epsilon carrying a P301R substitution.

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	KOG1798	e6i8aA5	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: KOG1798	ECOD (1.6)
A	POLBc_epsilon_2nd	e6i8aA4	A: alpha bundles	X: thumb domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: thumb domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: thumb domain in bacteriophage RB69-like DNA polymerase I	F: POLBc_epsilon_2nd	ECOD (1.6)
A	POLBc_epsilon_1st	e6i8aA1	A: alpha bundles	X: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: fingers domain in bacteriophage RB69-like DNA polymerase I	F: POLBc_epsilon_1st	ECOD (1.6)
A	DNA_pol_B_1st	e6i8aA2	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: DNA_pol_B_1st	ECOD (1.6)
A	DNA_pol_B_exo1_1st	e6i8aA3	A: a+b two layers	X: Alpha-beta plaits	H: Family B DNA polymerase insertion domain (From Topology)	T: Family B DNA polymerase insertion domain	F: DNA_pol_B_exo1_1st	ECOD (1.6)
A	DNA_pol_B_exo1_3rd	e6i8aA6	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: DNA_pol_B_exo1_3rd	ECOD (1.6)
D [auth B]	KOG1798	e6i8aB5	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: KOG1798	ECOD (1.6)
D [auth B]	POLBc_epsilon_2nd	e6i8aB2	A: alpha bundles	X: thumb domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: thumb domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: thumb domain in bacteriophage RB69-like DNA polymerase I	F: POLBc_epsilon_2nd	ECOD (1.6)
D [auth B]	POLBc_epsilon_1st	e6i8aB6	A: alpha bundles	X: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: fingers domain in bacteriophage RB69-like DNA polymerase I	F: POLBc_epsilon_1st	ECOD (1.6)
D [auth B]	DNA_pol_B_1st	e6i8aB4	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: DNA_pol_B_1st	ECOD (1.6)
D [auth B]	DNA_pol_B_exo1_1st	e6i8aB3	A: a+b two layers	X: Alpha-beta plaits	H: Family B DNA polymerase insertion domain (From Topology)	T: Family B DNA polymerase insertion domain	F: DNA_pol_B_exo1_1st	ECOD (1.6)
D [auth B]	DNA_pol_B_exo1_3rd	e6i8aB1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: DNA_pol_B_exo1_3rd	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth B]	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, D [auth B]	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
A, D [auth B]	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 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 postreplication repair nucleobase-containing compound biosynthetic process DNA synthesis involved in DNA repair macromolecule biosynthetic process 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
B [auth P], E [auth C]	Primer DNA	-	-	-
C [auth T], F [auth D]	Template DNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth B]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, D [auth B]	IPR054475	DNA polymerase-epsilon, zinc finger domain	Domain
A, D [auth B]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, D [auth B]	IPR023211	DNA polymerase, palm domain superfamily	Homologous Superfamily
A, D [auth B]	IPR006172	DNA-directed DNA polymerase, family B	Family
A, D [auth B]	IPR029703	DNA polymerase epsilon catalytic subunit	Family
A, D [auth B]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, D [auth B]	IPR013697	DNA polymerase epsilon, catalytic subunit A, C-terminal	Domain
A, D [auth B]	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
A, D [auth B]	IPR042087	DNA polymerase family B, thumb domain	Homologous Superfamily
A, D [auth B]	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.