8VAS

Structure of the E. coli clamp loader bound to the beta clamp in an Altered-Collar conformation

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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	8034535	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA polymerases epsilon N-terminal domain (Dpoe2NT)-like	8104157	3002834	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Post-AAA+ oligomerization domain-like	8034551	3000691	SCOP2B (2022-06-29)
B	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	Post-AAA+ oligomerization domain-like	8034547	3000691	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)
C	SCOP2B Superfamily	Post-AAA+ oligomerization domain-like	8034547	3000691	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)
D	SCOP2B Superfamily	Post-AAA+ oligomerization domain-like	8034547	3000691	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Post-AAA+ oligomerization domain-like	8038004	3000691	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	DNA clamp	8038076	3000780	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	DNA clamp	8038082	3000780	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	DNA clamp	8038081	3000780	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	DNA clamp	8038082	3000780	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	DNA clamp	8038081	3000780	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF06144	DNA polymerase III, delta subunit (DNA_pol3_delta)	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. This entry represents the ATPase domain [1,2]	Domain
A	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
B, C, D	PF12169	DNA polymerase III subunits gamma and tau domain III (DNA_pol3_gamma3)	DNA polymerase III subunits gamma and tau domain III	-	Family
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
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
F, G	PF02768	DNA polymerase III beta subunit, C-terminal domain (DNA_pol3_beta_3)	DNA polymerase III beta subunit, C-terminal domain	A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold.	Domain
F, G	PF02767	DNA polymerase III beta subunit, central domain (DNA_pol3_beta_2)	DNA polymerase III beta subunit, central domain	A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold.	Domain
F, G	PF00712	DNA polymerase III beta subunit, N-terminal domain (DNA_pol3_beta)	DNA polymerase III beta subunit, N-terminal domain	A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA polymerase III subunit delta	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
B, C, D	DNA polymerase III subunit tau	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-dependent activity, acting on DNA DNA clamp loader activity ATP-dependent activity ATP hydrolysis 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 cellular response to stimulus response to stimulus cellular response to stress DNA damage response response to stress 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 cellular response to stimulus response to stimulus cellular response to stress DNA damage response response to stress cellular process DNA repair 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 subunit delta'	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
F, G	Beta sliding clamp	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 identical protein binding protein binding protein homodimerization activity protein dimerization activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process DNA-templated DNA replication primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA strand elongation organic substance metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process DNA-templated DNA replication primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA strand elongation organic substance metabolic process DNA replication metabolic process DNA strand elongation involved in DNA replication macromolecule metabolic process postreplication repair cellular biosynthetic process DNA synthesis involved in DNA repair nucleic acid biosynthetic process organic substance biosynthetic process DNA repair translesion synthesis cellular metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process biosynthetic process organic cyclic compound biosynthetic process error-prone translesion synthesis DNA biosynthetic process regulation of DNA-templated DNA replication initiation negative regulation of biological process negative regulation of DNA-templated DNA replication initiation regulation of primary metabolic process negative regulation of DNA-templated DNA replication negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of biological process negative regulation of DNA replication DNA replication initiation negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process regulation of DNA-templated DNA replication negative regulation of DNA metabolic process regulation of metabolic process regulation of DNA replication regulation of DNA metabolic process bacterial-type DNA replication cell cycle DNA replication cell cycle cell cycle process	transferase complex, transferring phosphorus-containing groups DNA polymerase III complex protein-containing complex catalytic complex transferase complex DNA polymerase complex intracellular protein-containing complex intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-DNA complex chromosome replication inhibiting complex transferase complex, transferring phosphorus-containing groups DNA polymerase III complex protein-containing complex catalytic complex transferase complex DNA polymerase complex intracellular protein-containing complex intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-DNA complex chromosome replication inhibiting complex intracellular organelle organelle intracellular non-membrane-bounded organelle replication fork replisome non-membrane-bounded organelle Hda-beta clamp complex
H	DNA (5'-D(PGPCPAPGPAPCPAPCPTPAPCPGPAPGPTPAPCPAPTPA)-3')	-	-	-
I	DNA (26-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR008921	DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal	Homologous Superfamily
A	IPR010372	DNA polymerase III delta, N-terminal	Domain
A	IPR005790	DNA polymerase III, delta subunit	Family
A	IPR032780	DNA polymerase III subunit delta, C-terminal	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, C, D	IPR001270	ClpA/B family	Family
B, C, D	IPR021029	DNA polymerase III, tau subunit, domain V	Domain
B, C, D	IPR008921	DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal	Homologous Superfamily
B, C, D	IPR022754	DNA polymerase III, gamma subunit, domain III	Domain
B, C, D	IPR012763	DNA polymerase III, subunit gamma/ tau, N-terminal	Domain
B, C, D	IPR038249	DNA polymerase III, tau subunit, domain V superfamily	Homologous Superfamily
B, C, D	IPR003593	AAA+ ATPase domain	Domain
B, C, D	IPR022001	DNA polymerase III subunit tau, DnaB-binding domain IV	Domain
B, C, D	IPR045085	DNA polymerase III, subunit gamma/tau, helical lid domain	Domain
B, C, 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
F, G	IPR046938	DNA clamp superfamily	Homologous Superfamily
F, G	IPR001001	DNA polymerase III, beta sliding clamp	Family
F, G	IPR022634	DNA polymerase III, beta sliding clamp, N-terminal	Domain
F, G	IPR022635	DNA polymerase III, beta sliding clamp, C-terminal	Domain
F, G	IPR022637	DNA polymerase III, beta sliding clamp, central	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 R01GM133198.

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8VAS

Structure of the E. coli clamp loader bound to the beta clamp in an Altered-Collar conformation

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage