1JQJ

Mechanism of Processivity Clamp Opening by the Delta Subunit Wrench of the Clamp Loader Complex of E. coli DNA Polymerase III: Structure of the beta-delta complex

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1jqja1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	DNA polymerase III, beta subunit	DNA polymerase III, beta subunit	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1jqjb1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	DNA polymerase III, beta subunit	DNA polymerase III, beta subunit	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1jqjc1	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)
C	d1jqjc2	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)
D	d1jqjd1	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	d1jqjd2	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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	DNA clamp	8038082	3000780	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA clamp	8038076	3000780	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA clamp	8038081	3000780	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA clamp	8038082	3000780	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA clamp	8038076	3000780	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA clamp	8038081	3000780	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA polymerases epsilon N-terminal domain (Dpoe2NT)-like	8104157	3002834	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Post-AAA+ oligomerization domain-like	8034551	3000691	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RecA-like P-loop NTPases	8034535	3002019	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RecA-like P-loop NTPases	8034535	3002019	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DNA polymerases epsilon N-terminal domain (Dpoe2NT)-like	8104157	3002834	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Post-AAA+ oligomerization domain-like	8034551	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_beta	e1jqjA1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: DNA_pol3_beta	ECOD (1.6)
A	DNA_pol3_beta_2	e1jqjA2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: DNA_pol3_beta_2	ECOD (1.6)
A	DNA_pol3_beta_3	e1jqjA3	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: DNA_pol3_beta_3	ECOD (1.6)
B	DNA_pol3_beta	e1jqjB1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: DNA_pol3_beta	ECOD (1.6)
B	DNA_pol3_beta_2	e1jqjB2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: DNA_pol3_beta_2	ECOD (1.6)
B	DNA_pol3_beta_3	e1jqjB3	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: DNA_pol3_beta_3	ECOD (1.6)
C	DNA_pol3_delt_C	e1jqjC1	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)
C	DNA_pol3_delta_C	e1jqjC2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: DNA_pol3_delta_C	ECOD (1.6)
C	DNA_pol3_delta_N	e1jqjC3	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)
D	DNA_pol3_delt_C	e1jqjD1	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	e1jqjD2	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	e1jqjD3	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.150.10	Alpha Beta	Roll	DNA Polymerase III	Chain A, domain 2	CATH (4.3.0)
B	3.10.150.10	Alpha Beta	Roll	DNA Polymerase III	Chain A, domain 2	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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
A, B	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
A, B	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
C, D	PF06144	DNA polymerase III, delta subunit (DNA_pol3_delta)	DNA polymerase III, delta subunit	-	Family
C, 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DNA polymerase III, beta chain	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 cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound 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 cellular metabolic process cellular nitrogen compound metabolic process 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 heterocycle metabolic process nitrogen compound metabolic process metabolic process DNA strand elongation involved in DNA replication macromolecule metabolic process cellular aromatic compound 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 nucleobase-containing compound biosynthetic process heterocycle biosynthetic process macromolecule biosynthetic process biosynthetic process aromatic compound biosynthetic process organic cyclic compound biosynthetic process error-prone translesion synthesis DNA biosynthetic process regulation of DNA-templated DNA replication initiation regulation of cellular process negative regulation of biological process negative regulation of nitrogen compound metabolic process negative regulation of DNA-templated DNA replication initiation negative regulation of cellular metabolic process regulation of primary metabolic process regulation of nitrogen compound metabolic process negative regulation of DNA-templated DNA replication negative regulation of cellular process 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 cellular metabolic process 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
C, 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	cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process heterocycle metabolic process nitrogen compound metabolic process metabolic process cellular process macromolecule metabolic process cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process heterocycle metabolic process nitrogen compound metabolic process metabolic process cellular process macromolecule metabolic process cellular aromatic compound 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	IPR046938	DNA clamp superfamily	Homologous Superfamily
A, B	IPR001001	DNA polymerase III, beta sliding clamp	Family
A, B	IPR022634	DNA polymerase III, beta sliding clamp, N-terminal	Domain
A, B	IPR022635	DNA polymerase III, beta sliding clamp, C-terminal	Domain
A, B	IPR022637	DNA polymerase III, beta sliding clamp, central	Domain
C, D	IPR008921	DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal	Homologous Superfamily
C, D	IPR010372	DNA polymerase III delta, N-terminal	Domain
C, D	IPR005790	DNA polymerase III, delta subunit	Family
C, D	IPR032780	DNA polymerase III subunit delta, C-terminal	Domain
C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.