5OF3 | pdb_00005of3

Crystal structure of the heterotrimeric PriSLX primase from S. solfataricus.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5of3a_	Alpha and beta proteins (a+b)	Prim-pol domain	Prim-pol domain	PriA-like	DNA primase small subunit PriA	(Saccharolobus solfataricus P2 ) [TaxId: 273057 ],	SCOPe (2.08)
C [auth D]	d5of3d_	Alpha and beta proteins (a+b)	Prim-pol domain	Prim-pol domain	PriA-like	DNA primase small subunit PriA	(Saccharolobus solfataricus P2 ) [TaxId: 273057 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Prim-pol domain-like	8036240	3001829	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Prim-pol domain-like	8036240	3001829	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PriB N-terminal domain-like	8036243	3001901	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	PriB N-terminal domain-like	8036243	3001901	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PRK00419_like	e5of3A1	A: a+b two layers	X: L9 N-domain-like	H: primase chain A, C-terminal domain (From Topology)	T: primase chain A, C-terminal domain	F: PRK00419_like	ECOD (1.6)
A	DNA_primase_S	e5of3A2	A: a+b complex topology	X: Prim-pol domain (From Topology)	H: Prim-pol domain (From Topology)	T: Prim-pol domain	F: DNA_primase_S	ECOD (1.6)
A	RNA_POL_M_15KD_like	e5of3A3	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: RNA_POL_M_15KD_like	ECOD (1.6)
C [auth D]	PRK00419_like	e5of3D2	A: a+b two layers	X: L9 N-domain-like	H: primase chain A, C-terminal domain (From Topology)	T: primase chain A, C-terminal domain	F: PRK00419_like	ECOD (1.6)
C [auth D]	DNA_primase_S	e5of3D3	A: a+b complex topology	X: Prim-pol domain (From Topology)	H: Prim-pol domain (From Topology)	T: Prim-pol domain	F: DNA_primase_S	ECOD (1.6)
C [auth D]	RNA_POL_M_15KD_like	e5of3D1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: RNA_POL_M_15KD_like	ECOD (1.6)
E [auth C]	EUF08246	e5of3C1	A: alpha complex topology	X: Cryptochrome/photolyase FAD-binding domain-related (From Homology)	H: Cryptochrome/photolyase FAD-binding domain-related	T: PriX	F: EUF08246	ECOD (1.6)
F	EUF08246	e5of3F1	A: alpha complex topology	X: Cryptochrome/photolyase FAD-binding domain-related (From Homology)	H: Cryptochrome/photolyase FAD-binding domain-related	T: PriX	F: EUF08246	ECOD (1.6)
B	DNA_primase_lrg_N	e5of3B1	A: alpha complex topology	X: PriB N-terminal domain-like (From Topology)	H: PriB N-terminal domain-like (From Topology)	T: PriB N-terminal domain-like	F: DNA_primase_lrg_N	ECOD (1.6)
D [auth E]	DNA_primase_lrg_N	e5of3E1	A: alpha complex topology	X: PriB N-terminal domain-like (From Topology)	H: PriB N-terminal domain-like (From Topology)	T: PriB N-terminal domain-like	F: DNA_primase_lrg_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.920.10	Alpha Beta	Alpha-Beta Complex	DNA primase, PRIM domain	DNA primase, PRIM domain	CATH (4.3.0)
C [auth D]	3.90.920.10	Alpha Beta	Alpha-Beta Complex	DNA primase, PRIM domain	DNA primase, PRIM domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth D]	PF20873	Primase chain A, C-terminal domain (PriS_C)	Primase chain A, C-terminal domain	This domain is found at the C-terminal end of the small subunit (PriS) of the core primase from the archaeon Sulfolobus solfataricus, an RNA polymerase that catalyzes the synthesis of the RNA primers required by the DNA polymerases. PriS is the catal ...	This domain is found at the C-terminal end of the small subunit (PriS) of the core primase from the archaeon Sulfolobus solfataricus, an RNA polymerase that catalyzes the synthesis of the RNA primers required by the DNA polymerases. PriS is the catalytic subunit, with the active site located within an exposed groove in the concave side of two divergent beta-sheets, surrounded on the outside by alpha-helices This C-terminal domain, which is not found in other homologues, shows a mixed alpha-beta fold. It seems to support and position the elongated hairpin structure leading into the zinc-binding motif (PriS-Zn) [1,2].	Domain
A, C [auth D]	PF01896	DNA primase small subunit (DNA_primase_S)	DNA primase small subunit	-	Family
E [auth C], F	PF18689	Primase X (PriX)	Primase X	This domain is found in non-catalytic subunit of the archaeal eukaryotic-type primase, PriX. Detailed sequence analysis combined with structural analysis of a truncated PriX protein from the hyperthermophilic archaeon Sulfolobus solfataricus shows th ...	This domain is found in non-catalytic subunit of the archaeal eukaryotic-type primase, PriX. Detailed sequence analysis combined with structural analysis of a truncated PriX protein from the hyperthermophilic archaeon Sulfolobus solfataricus shows that, PriX is essential for the survival of the organism and that it is homologous to the C-terminal domain of archaeal and eukaryotic large primase subunits PriL. Highly conserved PriX homologues are present in many members of the phylum Crenarchaeota [1].	Domain
B, D [auth E]	PF26466	Eukaryotic and archaeal DNA primase, large subunit N-terminal domain (DNA_primase_lrg_N)	Eukaryotic and archaeal DNA primase, large subunit N-terminal domain	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 ( ...	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].	Domain
B, D [auth E]	PF04104	Eukaryotic and archaeal DNA primase, large subunit C-terminal domain (DNA_primase_lrg)	Eukaryotic and archaeal DNA primase, large subunit C-terminal domain	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 ( ...	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth D]	DNA primase small subunit PriS	DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cation binding ion binding binding metal ion binding small molecule binding	DNA-templated DNA replication DNA replication, synthesis of primer RNA metabolic process primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA replication biosynthetic process metabolic process DNA-templated DNA replication DNA replication, synthesis of primer RNA metabolic process primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA replication biosynthetic process metabolic process cellular process macromolecule metabolic process	primosome complex protein-containing complex intracellular anatomical structure protein-DNA complex intracellular membraneless organelle chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle replication fork replisome transferase complex, transferring phosphorus-containing groups catalytic complex primosome complex protein-containing complex intracellular anatomical structure protein-DNA complex intracellular membraneless organelle chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle replication fork replisome transferase complex, transferring phosphorus-containing groups catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
E [auth C], F	Uncharacterized protein	cation binding ion binding binding metal ion binding small molecule binding	-	-
B, D [auth E]	DNA primase large subunit PriL	iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cation binding ion binding metal ion binding	DNA-templated DNA replication DNA replication, synthesis of primer RNA metabolic process primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA replication biosynthetic process metabolic process DNA-templated DNA replication DNA replication, synthesis of primer RNA metabolic process primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA replication biosynthetic process metabolic process cellular process macromolecule metabolic process	primosome complex protein-containing complex intracellular anatomical structure protein-DNA complex intracellular membraneless organelle chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle replication fork replisome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth D]	IPR002755	DNA primase, small subunit	Family
A, C [auth D]	IPR014052	DNA primase, small subunit, eukaryotic/archaeal	Family
A, C [auth D]	IPR023639	DNA primase small subunit PriS	Family
E [auth C], F	IPR040865	Primase X	Domain
B, D [auth E]	IPR023642	DNA primase large subunit PriL	Family
B, D [auth E]	IPR058560	DNA primase, large subunit C-terminal domain, eukaryotic and archaeal	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.