1NJF | pdb_00001njf

Nucleotide bound form of an isolated E. coli clamp loader gamma subunit

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	d1njfa_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	delta prime subunit of DNA polymerase III, N-domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1njfb_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	delta prime subunit of DNA polymerase III, N-domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1njfc_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	delta prime subunit of DNA polymerase III, N-domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1njfd_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	delta prime subunit of DNA polymerase III, N-domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8034548	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104152	3002834	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8034548	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104152	3002834	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104152	3002834	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RecA-like P-loop NTPases	8034548	3002019	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RecA-like P-loop NTPases	8034548	3002019	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104152	3002834	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	DNAX_ATPase_lid	e1njfA3	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: DNAX_ATPase_lid	ECOD (develop294)
A	ClpB_D2-small	e1njfA4	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: ClpB_D2-small	ECOD (develop294)
B	Cobalamin_bind	e1njfB4	A: alpha bundles	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Cobalamin_bind	ECOD (develop294)
B	Thaumatin	e1njfB1	A: alpha bundles	X: Ntn/PP2C	H: Ntn	T: Penicillin acylase, catalytic domain	F: Thaumatin	ECOD (develop294)
C	Cobalamin_bind	e1njfC4	A: alpha bundles	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Cobalamin_bind	ECOD (develop294)
C	Thaumatin	e1njfC1	A: alpha bundles	X: Ntn/PP2C	H: Ntn	T: Penicillin acylase, catalytic domain	F: Thaumatin	ECOD (develop294)
D	Cobalamin_bind	e1njfD4	A: alpha bundles	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Cobalamin_bind	ECOD (develop294)
D	Thaumatin	e1njfD3	A: alpha bundles	X: Ntn/PP2C	H: Ntn	T: Penicillin acylase, catalytic domain	F: Thaumatin	ECOD (develop294)

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)
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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF22608	DNA polymerase III clamp loader subunit, ATPase lid domain (DNAX_ATPase_lid)	DNA polymerase III clamp loader subunit, ATPase lid domain	This entry represents the AAA+ ATPase lid domain of DNA polymerase III clamp loader subunit [1-4].	Domain
A, B, C, D	PF13177	DNA polymerase III, delta subunit (DNA_pol3_delta2)	DNA polymerase III, delta subunit	DNA polymerase III, delta subunit (EC 2.7.7.7) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalysed reaction [1]. The delta subunit is also known as ...	DNA polymerase III, delta subunit (EC 2.7.7.7) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalysed reaction [1]. The delta subunit is also known as HolA.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	DNA polymerase III subunit gamma	ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid DNA clamp loader activity catalytic activity ATP-dependent activity DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid DNA clamp loader activity catalytic activity ATP-dependent activity DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups 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 pyrophosphatase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides ATP hydrolysis activity enzyme regulator activity DNA polymerase processivity factor activity enzyme activator activity molecular function activator activity molecular function regulator activity cation binding metal ion binding 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 viral gene expression viral process viral translational frameshifting viral translation	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex transferase complex intracellular membrane-bounded organelle DNA polymerase complex transferase complex, transferring phosphorus-containing groups intracellular organelle DNA polymerase III complex cellular anatomical structure organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex transferase complex intracellular membrane-bounded organelle DNA polymerase complex transferase complex, transferring phosphorus-containing groups intracellular organelle DNA polymerase III complex cellular anatomical structure organelle DNA polymerase III, clamp loader complex intracellular protein-containing complex protein-DNA complex intracellular membraneless organelle chromosome membraneless organelle replication fork replisome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR050238	DNA Replication and Repair Clamp Loader Complex	Family
A, B, C, D	IPR021029	DNA polymerase III, tau subunit, domain V	Domain
A, B, C, D	IPR008921	DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal	Homologous Superfamily
A, B, C, D	IPR038249	DNA polymerase III, tau subunit, domain V superfamily	Homologous Superfamily
A, B, C, D	IPR003593	AAA+ ATPase domain	Domain
A, B, C, D	IPR045085	DNA polymerase III, subunit gamma/tau, helical lid domain	Domain
A, B, C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D	IPR001270	ClpA/B family	Family
A, B, C, D	IPR022754	DNA polymerase III, gamma subunit, domain III	Domain
A, B, C, D	IPR012763	DNA polymerase III, subunit gamma/ tau, N-terminal	Domain
A, B, C, D	IPR022001	DNA polymerase III subunit tau, DnaB-binding domain IV	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.