1JR3

Crystal Structure of the Processivity Clamp Loader Gamma Complex of E. coli DNA Polymerase III

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	d1jr3a1	All alpha proteins	post-AAA+ oligomerization domain-like	post-AAA+ oligomerization domain-like	DNA polymerase III clamp loader subunits, C-terminal domain	gamma subunit	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1jr3a2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	gamma subunit of DNA polymerase III, N-domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1jr3b1	All alpha proteins	post-AAA+ oligomerization domain-like	post-AAA+ oligomerization domain-like	DNA polymerase III clamp loader subunits, C-terminal domain	gamma subunit	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1jr3b2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	gamma subunit of DNA polymerase III, N-domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1jr3c1	All alpha proteins	post-AAA+ oligomerization domain-like	post-AAA+ oligomerization domain-like	DNA polymerase III clamp loader subunits, C-terminal domain	gamma subunit	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1jr3c2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	gamma subunit of DNA polymerase III, N-domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1jr3d1	All alpha proteins	post-AAA+ oligomerization domain-like	post-AAA+ oligomerization domain-like	DNA polymerase III clamp loader subunits, C-terminal domain	delta subunit	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1jr3d2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	delta subunit of DNA polymerase III, N-domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d1jr3e1	All alpha proteins	post-AAA+ oligomerization domain-like	post-AAA+ oligomerization domain-like	DNA polymerase III clamp loader subunits, C-terminal domain	delta prime subunit	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d1jr3e2	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	SCOP2 Family	Extended AAA-ATPase domain	8022168	4000283	SCOP2 (2022-06-29)
A	SCOP2 Family	DNA polymerase III clamp loader subunits C-terminal domain	8022167	4001080	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DNA polymerases epsilon N-terminal domain (Dpoe2NT)-like	8104152	3002834	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RecA-like P-loop NTPases	8034548	3002019	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Post-AAA+ oligomerization domain-like	8034547	3000691	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8034548	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Post-AAA+ oligomerization domain-like	8034547	3000691	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	Post-AAA+ oligomerization domain-like	8034547	3000691	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RecA-like P-loop NTPases	8034548	3002019	SCOP2B (2022-06-29)
D	SCOP2 Family	Extended AAA-ATPase domain	8022155	4000283	SCOP2 (2022-06-29)
D	SCOP2 Family	DNA polymerase III clamp loader subunits C-terminal domain	8022171	4001080	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	DNA polymerases epsilon N-terminal domain (Dpoe2NT)-like	8104157	3002834	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	RecA-like P-loop NTPases	8034535	3002019	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Post-AAA+ oligomerization domain-like	8034551	3000691	SCOP2 (2022-06-29)
E	SCOP2B Superfamily	Post-AAA+ oligomerization domain-like	8038004	3000691	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	DNA_pol3_gamma3	e1jr3A1	A: alpha arrays	X: DNA polymerase III clamp loader subunits, C-terminal domain (From Topology)	H: DNA polymerase III clamp loader subunits, C-terminal domain (From Topology)	T: DNA polymerase III clamp loader subunits, C-terminal domain	F: DNA_pol3_gamma3	ECOD (1.6)
A	AAA_assoc_2_3	e1jr3A3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: AAA_assoc_2_3	ECOD (1.6)
A	Sigma54_activat	e1jr3A2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
B	DNA_pol3_gamma3	e1jr3B1	A: alpha arrays	X: DNA polymerase III clamp loader subunits, C-terminal domain (From Topology)	H: DNA polymerase III clamp loader subunits, C-terminal domain (From Topology)	T: DNA polymerase III clamp loader subunits, C-terminal domain	F: DNA_pol3_gamma3	ECOD (1.6)
B	AAA_assoc_2_3	e1jr3B3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: AAA_assoc_2_3	ECOD (1.6)
B	Sigma54_activat	e1jr3B2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
C	DNA_pol3_gamma3	e1jr3C1	A: alpha arrays	X: DNA polymerase III clamp loader subunits, C-terminal domain (From Topology)	H: DNA polymerase III clamp loader subunits, C-terminal domain (From Topology)	T: DNA polymerase III clamp loader subunits, C-terminal domain	F: DNA_pol3_gamma3	ECOD (1.6)
C	AAA_assoc_2_3	e1jr3C3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: AAA_assoc_2_3	ECOD (1.6)
C	Sigma54_activat	e1jr3C2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
D	DNA_pol3_delt_C	e1jr3D1	A: alpha arrays	X: DNA polymerase III clamp loader subunits, C-terminal domain (From Topology)	H: DNA polymerase III clamp loader subunits, C-terminal domain (From Topology)	T: DNA polymerase III clamp loader subunits, C-terminal domain	F: DNA_pol3_delt_C	ECOD (1.6)
D	DNA_pol3_delta_C	e1jr3D2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: DNA_pol3_delta_C	ECOD (1.6)
D	DNA_pol3_delta_N	e1jr3D3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DNA_pol3_delta_N	ECOD (1.6)
E	DNApol3-delta_C	e1jr3E2	A: alpha arrays	X: DNA polymerase III clamp loader subunits, C-terminal domain (From Topology)	H: DNA polymerase III clamp loader subunits, C-terminal domain (From Topology)	T: DNA polymerase III clamp loader subunits, C-terminal domain	F: DNApol3-delta_C	ECOD (1.6)
E	PRK07993_2nd	e1jr3E3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PRK07993_2nd	ECOD (1.6)
E	PRK07993_1st	e1jr3E4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PRK07993_1st	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	1.20.272.10	Mainly Alpha	Up-down Bundle	Zinc Finger, Delta Prime	domain 3	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	1.20.272.10	Mainly Alpha	Up-down Bundle	Zinc Finger, Delta Prime	domain 3	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	1.20.272.10	Mainly Alpha	Up-down Bundle	Zinc Finger, Delta Prime	domain 3	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	1.20.272.10	Mainly Alpha	Up-down Bundle	Zinc Finger, Delta Prime	domain 3	CATH (4.3.0)
D	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E	1.10.8.10	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
E	1.20.272.10	Mainly Alpha	Up-down Bundle	Zinc Finger, Delta Prime	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF12169	DNA polymerase III subunits gamma and tau domain III (DNA_pol3_gamma3)	DNA polymerase III subunits gamma and tau domain III	-	Family
A, B, C	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
D	PF06144	DNA polymerase III, delta subunit (DNA_pol3_delta)	DNA polymerase III, delta subunit	-	Family
D	PF14840	Processivity clamp loader gamma complex DNA pol III C-term (DNA_pol3_delt_C)	Processivity clamp loader gamma complex DNA pol III C-term	-	Family
E	PF09115	DNA polymerase III, delta subunit, C terminal (DNApol3-delta_C)	DNA polymerase III, delta subunit, C terminal	Members of this family, which are predominantly found in prokaryotic DNA polymerase III, assume an alpha helical structure, with a core of five alpha helices, and an additional small helix. They are essential for the formation of the polymerase clamp ...	Members of this family, which are predominantly found in prokaryotic DNA polymerase III, assume an alpha helical structure, with a core of five alpha helices, and an additional small helix. They are essential for the formation of the polymerase clamp loader [1].	Domain
E	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
E	PF21500	DNA polymerase III subunit delta', AAA+ ATPase lid domain (HolB_lid)	DNA polymerase III subunit delta', AAA+ ATPase lid domain	DNA polymerase III subunit delta' is part of the beta sliding clamp loading complex, which hydrolyses ATP to load the beta clamp onto primed DNA to form the DNA replication pre-initiation complex [1,2]. It consists of three domains, of which the N-te ...	DNA polymerase III subunit delta' is part of the beta sliding clamp loading complex, which hydrolyses ATP to load the beta clamp onto primed DNA to form the DNA replication pre-initiation complex [1,2]. It consists of three domains, of which the N-terminal domain contains a nonfunctional nucleotide binding site. This entry represents the lid domain (or domain 2 in [1]).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	DNA polymerase III subunit gamma	catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic 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 organic cyclic compound 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 ATP-dependent activity enzyme regulator activity DNA polymerase processivity factor activity enzyme activator activity molecular function activator activity molecular function regulator activity identical protein binding protein binding	nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA-templated DNA replication	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex transferase complex intracellular membrane-bounded organelle cellular anatomical entity DNA polymerase complex transferase complex, transferring phosphorus-containing groups intracellular organelle DNA polymerase III complex organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex transferase complex intracellular membrane-bounded organelle cellular anatomical entity DNA polymerase complex transferase complex, transferring phosphorus-containing groups intracellular organelle DNA polymerase III complex organelle DNA polymerase III, clamp loader complex intracellular protein-containing complex protein-DNA complex chromosome intracellular non-membrane-bounded organelle replication fork replisome non-membrane-bounded organelle
D	DNA polymerase III, delta subunit	catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding	nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA-templated DNA replication	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex transferase complex intracellular membrane-bounded organelle cellular anatomical entity DNA polymerase complex transferase complex, transferring phosphorus-containing groups intracellular organelle DNA polymerase III complex organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex transferase complex intracellular membrane-bounded organelle cellular anatomical entity DNA polymerase complex transferase complex, transferring phosphorus-containing groups intracellular organelle DNA polymerase III complex organelle DNA polymerase III, clamp loader complex intracellular protein-containing complex protein-DNA complex chromosome intracellular non-membrane-bounded organelle replication fork replisome non-membrane-bounded organelle
E	DNA polymerase III, delta' subunit	catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding nuclease activity hydrolase activity, acting on ester bonds 3'-5' exonuclease activity hydrolase activity exonuclease activity	nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA-templated DNA replication	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex transferase complex intracellular membrane-bounded organelle cellular anatomical entity DNA polymerase complex transferase complex, transferring phosphorus-containing groups intracellular organelle DNA polymerase III complex organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex transferase complex intracellular membrane-bounded organelle cellular anatomical entity DNA polymerase complex transferase complex, transferring phosphorus-containing groups intracellular organelle DNA polymerase III complex organelle DNA polymerase III, clamp loader complex intracellular protein-containing complex protein-DNA complex chromosome intracellular non-membrane-bounded organelle replication fork replisome non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR001270	ClpA/B family	Family
A, B, C	IPR021029	DNA polymerase III, tau subunit, domain V	Domain
A, B, C	IPR008921	DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal	Homologous Superfamily
A, B, C	IPR022754	DNA polymerase III, gamma subunit, domain III	Domain
A, B, C	IPR012763	DNA polymerase III, subunit gamma/ tau, N-terminal	Domain
A, B, C	IPR038249	DNA polymerase III, tau subunit, domain V superfamily	Homologous Superfamily
A, B, C	IPR003593	AAA+ ATPase domain	Domain
A, B, C	IPR022001	DNA polymerase III subunit tau, DnaB-binding domain IV	Domain
A, B, C	IPR045085	DNA polymerase III, subunit gamma/tau, helical lid domain	Domain
A, B, C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
D	IPR008921	DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal	Homologous Superfamily
D	IPR010372	DNA polymerase III delta, N-terminal	Domain
D	IPR005790	DNA polymerase III, delta subunit	Family
D	IPR032780	DNA polymerase III subunit delta, C-terminal	Domain
D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
E	IPR048731	DNA polymerase III subunit delta', AAA+ ATPase lid domain, gammaproteobacteria	Domain
E	IPR004622	DNA polymerase III, delta prime subunit	Domain
E	IPR008921	DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal	Homologous Superfamily
E	IPR015199	DNA polymerase III, delta subunit, C-terminal	Domain
E	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily