8FOK | pdb_00008fok

Cryo-EM structure of S. cerevisiae DNA polymerase alpha-primase complex in the DNA elongation state


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
D [auth C]SCOP2B SuperfamilyNucleic acid-binding proteins 8053388 3000135 SCOP2B (2022-06-29)
D [auth C]SCOP2B SuperfamilyMetallo-dependent phosphatases 8053387 3001067 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
D [auth C]PF04042DNA polymerase alpha/epsilon subunit B (DNA_pol_E_B)DNA polymerase alpha/epsilon subunit B- Family
D [auth C]PF22062DNA polymerase alpha subunit B, OB domain (OB_DPOA2)DNA polymerase alpha subunit B, OB domainThis entry represents the OB domain of DNA polymerase alpha subunit B [1-4]. B subunits of DNA polymerases stabilize the catalytic subunit, play a role in regulation of the DNA synthesis in a cell cycle-dependent manner and act as scaffolds mediating ...This entry represents the OB domain of DNA polymerase alpha subunit B [1-4]. B subunits of DNA polymerases stabilize the catalytic subunit, play a role in regulation of the DNA synthesis in a cell cycle-dependent manner and act as scaffolds mediating interactions with other components of the replication machinery [1-4].
Domain
C [auth B]PF04104Eukaryotic and archaeal DNA primase, large subunit C-terminal domain (DNA_primase_lrg)Eukaryotic and archaeal DNA primase, large subunit C-terminal domainDNA primase is the polymerase that synthesises small RNA primers for the Okazaki fragments made during discontinuous DNA replication. DNA primase is a heterodimer of two subunits, the small subunit Pri1 (48 kDa in yeast), and the large subunit Pri2 ( ...DNA primase is the polymerase that synthesises small RNA primers for the Okazaki fragments made during discontinuous DNA replication. DNA primase is a heterodimer of two subunits, the small subunit Pri1 (48 kDa in yeast), and the large subunit Pri2 (58 kDa in the yeast S. cerevisiae) [1]. The large subunit of DNA primase forms interactions with the small subunit and the structure implicates that it is not directly involved in catalysis, but plays roles in correctly positioning the primase/DNA complex, and in the transfer of RNA to DNA polymerase [4]. This entry represents the C-terminal alpha helical domain.
Domain
B [auth A]PF01896DNA primase small subunit (DNA_primase_S)DNA primase small subunit- Family
A [auth 1]PF08996DNA Polymerase alpha zinc finger (zf-DNA_Pol)DNA Polymerase alpha zinc fingerThe DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parall ...The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. Function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain [1].
Domain
A [auth 1]PF03104DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1)DNA polymerase family B, exonuclease domain- Family
A [auth 1]PF00136DNA polymerase family B (DNA_pol_B)DNA polymerase family B- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
F [auth P]RNA-DNA chimeric primer---
E [auth T]template DNA---
D [auth C]DNA polymerase alpha subunit B
C [auth B]DNA primase large subunit
B [auth A]DNA primase
A [auth 1]DNA polymerase

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
D [auth C]IPR007185DNA polymerase alpha/delta/epsilon, subunit BDomain
D [auth C]IPR054300DNA polymerase alpha subunit B, OB domainDomain
D [auth C]IPR016722DNA polymerase alpha, subunit BFamily
C [auth B]IPR016558DNA primase, large subunit, eukaryoticFamily
C [auth B]IPR007238DNA primase large subunit, eukaryotic/archaealFamily
B [auth A]IPR002755DNA primase, small subunitFamily
B [auth A]IPR014052DNA primase, small subunit, eukaryotic/archaealFamily
A [auth 1]IPR038256DNA polymerase alpha, zinc finger domain superfamilyHomologous Superfamily
A [auth 1]IPR036397Ribonuclease H superfamilyHomologous Superfamily
A [auth 1]IPR006134DNA-directed DNA polymerase, family B, multifunctional domainDomain
A [auth 1]IPR045846DNA polymerase alpha catalytic subunit, catalytic domainDomain
A [auth 1]IPR017964DNA-directed DNA polymerase, family B, conserved siteConserved Site
A [auth 1]IPR012337Ribonuclease H-like superfamilyHomologous Superfamily
A [auth 1]IPR023211DNA polymerase, palm domain superfamilyHomologous Superfamily
A [auth 1]IPR015088Zinc finger, DNA-directed DNA polymerase, family B, alphaDomain
A [auth 1]IPR006172DNA-directed DNA polymerase, family BFamily
A [auth 1]IPR043502DNA/RNA polymerase superfamilyHomologous Superfamily
A [auth 1]IPR006133DNA-directed DNA polymerase, family B, exonuclease domainDomain
A [auth 1]IPR042087DNA polymerase family B, thumb domainHomologous Superfamily
A [auth 1]IPR024647DNA polymerase alpha catalytic subunit, N-terminal domainDomain