4FYD
Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA and dGTP
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
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) |
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) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
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) |
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) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF03104 | DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1) | DNA polymerase family B, exonuclease domain | - | Family | |
PF00136 | DNA polymerase family B (DNA_pol_B) | DNA polymerase family B | - | Family | |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR038256 | DNA polymerase alpha, zinc finger domain superfamily | Homologous Superfamily | |
IPR036397 | Ribonuclease H superfamily | Homologous Superfamily | |
IPR006134 | DNA-directed DNA polymerase, family B, multifunctional domain | Domain | |
IPR045846 | DNA polymerase alpha catalytic subunit, catalytic domain | Domain | |
IPR017964 | DNA-directed DNA polymerase, family B, conserved site | Conserved Site | |
IPR012337 | Ribonuclease H-like superfamily | Homologous Superfamily | |
IPR023211 | DNA polymerase, palm domain superfamily | Homologous Superfamily | |
IPR015088 | Zinc finger, DNA-directed DNA polymerase, family B, alpha | Domain | |
IPR006172 | DNA-directed DNA polymerase, family B | Family | |
IPR043502 | DNA/RNA polymerase superfamily | Homologous Superfamily | |
IPR006133 | DNA-directed DNA polymerase, family B, exonuclease domain | Domain | |
IPR042087 | DNA polymerase family B, thumb domain | Homologous Superfamily | |
IPR024647 | DNA polymerase alpha catalytic subunit, N-terminal domain | Domain |