2HCB | pdb_00002hcb

Structure of AMPPCP-bound DnaA from Aquifex aeolicus

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	d2hcba1	All alpha proteins	DNA/RNA-binding 3-helical bundle	TrpR-like	Chromosomal replication initiation factor DnaA C-terminal domain IV	Chromosomal replication initiation factor DnaA C-terminal domain IV	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
A	d2hcba2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	Chromosomal replication initiation factor DnaA	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
B	d2hcbb1	All alpha proteins	DNA/RNA-binding 3-helical bundle	TrpR-like	Chromosomal replication initiation factor DnaA C-terminal domain IV	Chromosomal replication initiation factor DnaA C-terminal domain IV	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
B	d2hcbb2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	Chromosomal replication initiation factor DnaA	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
C	d2hcbc1	All alpha proteins	DNA/RNA-binding 3-helical bundle	TrpR-like	Chromosomal replication initiation factor DnaA C-terminal domain IV	Chromosomal replication initiation factor DnaA C-terminal domain IV	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
C	d2hcbc2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	Chromosomal replication initiation factor DnaA	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
D	d2hcbd1	All alpha proteins	DNA/RNA-binding 3-helical bundle	TrpR-like	Chromosomal replication initiation factor DnaA C-terminal domain IV	Chromosomal replication initiation factor DnaA C-terminal domain IV	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
D	d2hcbd2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	Chromosomal replication initiation factor DnaA	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	TrpR-like	8042930	3001097	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8042931	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TrpR-like	8042930	3001097	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8042931	3002019	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RecA-like P-loop NTPases	8042931	3002019	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TrpR-like	8042930	3001097	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RecA-like P-loop NTPases	8042931	3002019	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	TrpR-like	8042930	3001097	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	Bac_DnaA_C	e2hcbA1	A: alpha arrays	X: HTH	H: HTH	T: TrpR	F: Bac_DnaA_C	ECOD (1.6)
A	DnaA	e2hcbA2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: DnaA	ECOD (1.6)
A	Bac_DnaA_N	e2hcbA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Bac_DnaA_N	ECOD (1.6)
B	Bac_DnaA_C	e2hcbB1	A: alpha arrays	X: HTH	H: HTH	T: TrpR	F: Bac_DnaA_C	ECOD (1.6)
B	DnaA	e2hcbB2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: DnaA	ECOD (1.6)
B	Bac_DnaA_N	e2hcbB3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Bac_DnaA_N	ECOD (1.6)
C	Bac_DnaA_C	e2hcbC1	A: alpha arrays	X: HTH	H: HTH	T: TrpR	F: Bac_DnaA_C	ECOD (1.6)
C	DnaA	e2hcbC2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: DnaA	ECOD (1.6)
C	Bac_DnaA_N	e2hcbC3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Bac_DnaA_N	ECOD (1.6)
D	Bac_DnaA_C	e2hcbD1	A: alpha arrays	X: HTH	H: HTH	T: TrpR	F: Bac_DnaA_C	ECOD (1.6)
D	DnaA	e2hcbD2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: DnaA	ECOD (1.6)
D	Bac_DnaA_N	e2hcbD3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Bac_DnaA_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	1.10.1750.10	Mainly Alpha	Orthogonal Bundle	Chromosomal Replication Initiator Protein Dnaa	Chain: A	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B	1.10.1750.10	Mainly Alpha	Orthogonal Bundle	Chromosomal Replication Initiator Protein Dnaa	Chain: A	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
C	1.10.1750.10	Mainly Alpha	Orthogonal Bundle	Chromosomal Replication Initiator Protein Dnaa	Chain: A	CATH (4.3.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
D	1.10.1750.10	Mainly Alpha	Orthogonal Bundle	Chromosomal Replication Initiator Protein Dnaa	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF08299	Bacterial dnaA protein helix-turn-helix (Bac_DnaA_C)	Bacterial dnaA protein helix-turn-helix		Domain
A, B, C, D	PF00308	Bacterial DnaA ATPAse domain (Bac_DnaA)	Bacterial DnaA ATPAse domain	This entry represents the ATPAse domain of DnaA and similar proteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Chromosomal replication initiator protein dnaA	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 sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding nucleic acid binding DNA replication origin binding 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 catalytic activity ATP-dependent activity identical protein binding protein binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA-templated DNA replication DNA replication initiation regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA-templated DNA replication DNA replication initiation regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process regulation of primary metabolic process regulation of nucleobase-containing compound metabolic process regulation of metabolic process regulation of DNA replication regulation of DNA metabolic process	cell periphery cellular anatomical structure plasma membrane membrane intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR018312	Chromosomal replication control, initiator DnaA, conserved site	Conserved Site
A, B, C, D	IPR013159	Chromosomal replication initiator, DnaA C-terminal	Domain
A, B, C, D	IPR001957	Chromosomal replication control, initiator DnaA	Family
A, B, C, D	IPR013317	Chromosomal replication initiator protein DnaA, ATPAse domain	Domain
A, B, C, D	IPR003593	AAA+ ATPase domain	Domain
A, B, C, D	IPR020591	Chromosomal replication control, initiator DnaA-like	Family
A, B, C, D	IPR010921	Trp repressor/replication initiator	Homologous Superfamily
A, B, C, D	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.