4FYD

Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA and dGTP

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	DNA_pol_B_exo1_2nd	e4fydA3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: DNA_pol_B_exo1_2nd	ECOD (1.6)
A	DNA_pol_B_2nd	e4fydA6	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: DNA_pol_B_2nd	ECOD (1.6)
A	DNA_pol_B_1st_2	e4fydA4	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: DNA_pol_B_1st_2	ECOD (1.6)
A	DNA_pol_B_1st_1	e4fydA2	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_1	ECOD (1.6)
A	DNA_pol_B_exo1_1st_1	e4fydA5	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_1	ECOD (1.6)
A	DNA_pol_B_exo1_3rd	e4fydA1	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)
B	DNA_pol_B_exo1_2nd	e4fydB4	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: DNA_pol_B_exo1_2nd	ECOD (1.6)
B	DNA_pol_B_2nd	e4fydB3	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: DNA_pol_B_2nd	ECOD (1.6)
B	DNA_pol_B_1st_2	e4fydB1	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: DNA_pol_B_1st_2	ECOD (1.6)
B	DNA_pol_B_1st_1	e4fydB5	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_1	ECOD (1.6)
B	DNA_pol_B_exo1_1st_1	e4fydB2	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_1	ECOD (1.6)
B	DNA_pol_B_exo1_3rd	e4fydB6	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.50.730	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
A	3.30.70.2820	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	1.10.132.60	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	Chain A, domain 4	CATH (4.3.0)
B	2.40.50.730	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
B	3.30.70.2820	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	1.10.132.60	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	Chain A, domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00136	DNA polymerase family B (DNA_pol_B)	DNA polymerase family B	-	Family
A, 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, B	DNA polymerase alpha catalytic subunit A	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding organic cyclic compound binding nucleic acid binding DNA replication origin binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding chromatin binding iron-sulfur cluster binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding organic cyclic compound binding nucleic acid binding DNA replication origin binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding chromatin binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups H3-H4 histone complex chaperone activity protein carrier chaperone histone chaperone activity molecular carrier activity cation binding ion binding metal ion binding single-stranded DNA binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA-templated DNA replication lagging strand elongation DNA strand elongation DNA strand elongation involved in DNA replication DNA replication initiation sexual reproduction nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA-templated DNA replication lagging strand elongation DNA strand elongation DNA strand elongation involved in DNA replication DNA replication initiation sexual reproduction reproductive process meiotic cell cycle nuclear DNA replication cell cycle DNA replication meiotic cell cycle process premeiotic DNA replication cell cycle cell cycle process leading strand elongation nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA-templated DNA biosynthetic process nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process mitotic DNA replication cell cycle DNA replication initiation mitotic DNA replication initiation mitotic cell cycle nuclear cell cycle DNA replication initiation mitotic cell cycle process cellular response to stimulus double-strand break repair response to stimulus cellular response to stress DNA damage response response to stress DNA repair DNA synthesis involved in DNA repair	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membraneless organelle replication fork intracellular membraneless organelle chromosome protein-containing complex alpha DNA polymerase:primase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membraneless organelle replication fork intracellular membraneless organelle chromosome protein-containing complex alpha DNA polymerase:primase complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome transferase complex intracellular organelle lumen nuclear replisome catalytic complex protein-DNA complex nuclear replication fork DNA polymerase complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen replisome
C, D	DNA (5'-D(TPGPAPGPCPGPTPGTPGPTPAPCPCPCPCPTPGPCPCPCPGPCPCP*G)-3')	-	-	-
E, F	DNA/RNA (5'-R(CPGPGPCPGPGPGPCPAPG)-D(PGPG)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR038256	DNA polymerase alpha, zinc finger domain superfamily	Homologous Superfamily
A, B	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain	Domain
A, B	IPR045846	DNA polymerase alpha catalytic subunit, catalytic domain	Domain
A, B	IPR017964	DNA-directed DNA polymerase, family B, conserved site	Conserved Site
A, B	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B	IPR023211	DNA polymerase, palm domain superfamily	Homologous Superfamily
A, B	IPR015088	Zinc finger, DNA-directed DNA polymerase, family B, alpha	Domain
A, B	IPR006172	DNA-directed DNA polymerase, family B	Family
A, B	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
A, B	IPR042087	DNA polymerase family B, thumb domain	Homologous Superfamily
A, B	IPR024647	DNA polymerase alpha catalytic subunit, N-terminal 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.