8FOJ | pdb_00008foj

Cryo-EM structure of S. cerevisiae DNA polymerase alpha-primase complex in the post RNA handoff 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
A [auth 1]PF00136DNA polymerase family B (DNA_pol_B)DNA polymerase family B- Family
A [auth 1]PF03104DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1)DNA polymerase family B, exonuclease domain- Family
B [auth A]PF01896DNA primase small subunit (DNA_primase_S)DNA primase small subunit- Family
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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

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

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
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
B [auth A]IPR002755DNA primase, small subunitFamily
B [auth A]IPR014052DNA primase, small subunit, eukaryotic/archaealFamily
C [auth B]IPR016558DNA primase, large subunit, eukaryoticFamily
C [auth B]IPR007238DNA primase large subunit, eukaryotic/archaealFamily
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