1KA8 | pdb_00001ka8

Crystal Structure of the Phage P4 Origin-Binding Domain

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)
F	d1ka8f_	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	P4 origin-binding domain-like	P4 origin-binding domain	(Enterobacteria phage P4 ) [TaxId: 10680 ],	SCOPe (2.08)
E	d1ka8e_	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	P4 origin-binding domain-like	P4 origin-binding domain	(Enterobacteria phage P4 ) [TaxId: 10680 ],	SCOPe (2.08)
D	d1ka8d_	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	P4 origin-binding domain-like	P4 origin-binding domain	(Enterobacteria phage P4 ) [TaxId: 10680 ],	SCOPe (2.08)
C	d1ka8c_	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	P4 origin-binding domain-like	P4 origin-binding domain	(Enterobacteria phage P4 ) [TaxId: 10680 ],	SCOPe (2.08)
B	d1ka8b_	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	P4 origin-binding domain-like	P4 origin-binding domain	(Enterobacteria phage P4 ) [TaxId: 10680 ],	SCOPe (2.08)
A	d1ka8a_	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	P4 origin-binding domain-like	P4 origin-binding domain	(Enterobacteria phage P4 ) [TaxId: 10680 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Winged helix DNA-binding domain	8056280	3000034	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Winged helix DNA-binding domain	8056280	3000034	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Winged helix DNA-binding domain	8056280	3000034	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8056280	3000034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8056280	3000034	SCOP2B (2022-06-29)
A	SCOP2 Family	RFX DNA-binding domain-like	8003097	4000214	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Winged helix DNA-binding domain	8056280	3000034	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	Fe_dep_repress	e1ka8F1	A: alpha bundles	X: EGF-like	H: YozE-like	T: Ribbon-helix-helix	F: Fe_dep_repress	ECOD (develop294)
E	Fe_dep_repress	e1ka8E1	A: alpha bundles	X: EGF-like	H: YozE-like	T: Ribbon-helix-helix	F: Fe_dep_repress	ECOD (develop294)
D	Fe_dep_repress	e1ka8D1	A: alpha bundles	X: EGF-like	H: YozE-like	T: Ribbon-helix-helix	F: Fe_dep_repress	ECOD (develop294)
C	Fe_dep_repress	e1ka8C1	A: alpha bundles	X: EGF-like	H: YozE-like	T: Ribbon-helix-helix	F: Fe_dep_repress	ECOD (develop294)
B	Fe_dep_repress	e1ka8B1	A: alpha bundles	X: EGF-like	H: YozE-like	T: Ribbon-helix-helix	F: Fe_dep_repress	ECOD (develop294)
A	Pox_D5	e1ka8A1	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: Pox_D5	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
E	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
D	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
C	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
B	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
A	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF03288	Poxvirus D5 protein-like (Pox_D5)	Poxvirus D5 protein-like	This family includes D5 from Poxviruses which is necessary for viral DNA replication, and is a nucleic acid independent nucleoside triphosphatase. Members of this family are also found outside of poxviruses. This domain is a DNA-binding winged HTH do ...	This family includes D5 from Poxviruses which is necessary for viral DNA replication, and is a nucleic acid independent nucleoside triphosphatase. Members of this family are also found outside of poxviruses. This domain is a DNA-binding winged HTH domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	putative P4-specific DNA primase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid 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 pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides ATP-dependent activity cation binding transition metal ion binding zinc ion binding metal ion binding ATP-dependent activity, acting on DNA nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on DNA helicase activity macromolecular conformation isomerase activity	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	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR045455	NrS-1 polymerase-like, helicase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR004968	DNA primase/nucleoside triphosphatase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR051620	ORF904-like, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR014015	Helicase, superfamily 3, DNA virus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR006171	TOPRIM domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR034154	Archaeal primase DnaG/twinkle-like, TOPRIM domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036977	DNA Primase, CHC2-type zinc finger	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR014818	Bacteriophage/plasmid primase, P4, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR013237	DNA primase/helicase Gp4, N-terminal, Bacteriophage T7-like	Domain
A, B, C, D, E A, B, C, D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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.