5M1S

Cryo-EM structure of the E. coli replicative DNA polymerase-clamp-exonuclase-theta complex bound to DNA in the editing mode

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD 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)
B	SCOP2B Superfamily	DNA clamp	8038076	3000780	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA clamp	8038082	3000780	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA clamp	8038081	3000780	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA clamp	8038082	3000780	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA clamp	8038081	3000780	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA clamp	8038076	3000780	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribonuclease H-like	8042074	3000143	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	HHH_6	e5m1sA4	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_6	ECOD (1.6)
A	DNA_pol3_alpha_C	e5m1sA2	A: alpha arrays	X: DNA polymerase III finger domain (From Topology)	H: DNA polymerase III finger domain (From Topology)	T: DNA polymerase III finger domain	F: DNA_pol3_alpha_C	ECOD (1.6)
A	DNA_pol3_alpha_N	e5m1sA1	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: DNA_pol3_alpha_N	ECOD (1.6)
A	PHP	e5m1sA3	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PHP	ECOD (1.6)
B	DNA_pol3_beta	e5m1sB2	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	e5m1sB1	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	e5m1sB3	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_beta	e5m1sC3	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)
C	DNA_pol3_beta_2	e5m1sC1	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)
C	DNA_pol3_beta_3	e5m1sC2	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)
D	RNase_T	e5m1sD1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_T	ECOD (1.6)
G [auth F]	DNA_pol3_theta	e5m1sF1	A: alpha arrays	X: DNA polymerase III theta subunit-like	H: DNA polymerase III theta subunit-like (From Topology)	T: DNA polymerase III theta subunit-like	F: DNA_pol3_theta	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02811	PHP domain (PHP)	PHP domain	-	Family
A	PF07733	Bacterial DNA polymerase III alpha NTPase domain (DNA_pol3_alpha)	Bacterial DNA polymerase III alpha NTPase domain	-	Domain
A	PF17657	Bacterial DNA polymerase III alpha subunit finger domain (DNA_pol3_finger)	Bacterial DNA polymerase III alpha subunit finger domain	-	Domain
A	PF14579	Helix-hairpin-helix motif (HHH_6)	Helix-hairpin-helix motif	The HHH domain is a short DNA-binding domain [1].	Domain
B, C	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
B, C	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
B, C	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
D	PF00929	Exonuclease (RNase_T)	Exonuclease	-	Family
G [auth F]	PF06440	DNA polymerase III, theta subunit (DNA_pol3_theta)	DNA polymerase III, theta subunit	DNA polymerase III (EC 2.7.7.7) is comprised of three tightly associated subunits, alpha, epsilon and theta. This family contains the theta subunit. The structure of the theta subunit shows that the N-terminal two thirds is comprised of three helic ...	DNA polymerase III (EC 2.7.7.7) is comprised of three tightly associated subunits, alpha, epsilon and theta. This family contains the theta subunit. The structure of the theta subunit shows that the N-terminal two thirds is comprised of three helices while the C-terminal third is disordered [1]. The function of the theta subunit is poorly understood, but the interaction of the theta subunit with the epsilon subunit is thought to enhance the 3' to 5' exonucleolytic proofreading activity of epsilon [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA polymerase III subunit alpha	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	DNA-templated DNA replication lagging strand elongation 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 leading strand elongation	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 membrane-bounded organelle nucleus nuclear protein-containing 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 membrane-bounded organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle DNA polymerase III, core complex organelle protein-DNA complex chromosome intracellular non-membrane-bounded organelle replication fork replisome non-membrane-bounded organelle
B, C	DNA polymerase III subunit beta	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
D	DNA polymerase III subunit epsilon	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 nuclease activity hydrolase activity, acting on ester bonds hydrolase activity exonuclease activity DNA binding 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 nuclease activity hydrolase activity, acting on ester bonds hydrolase activity exonuclease activity DNA binding binding organic cyclic compound binding nucleic acid binding 3'-5' exonuclease activity cation binding ion binding metal ion binding small molecule binding	DNA-templated DNA replication lagging strand elongation 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 leading strand elongation DNA-templated DNA replication lagging strand elongation 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 leading strand elongation cellular response to stimulus response to stimulus DNA-templated DNA replication maintenance of fidelity DNA replication proofreading cellular response to stress DNA damage response response to stress cellular process DNA repair	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 membrane-bounded organelle nucleus nuclear protein-containing 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 membrane-bounded organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle DNA polymerase III, core complex organelle protein-DNA complex chromosome intracellular non-membrane-bounded organelle replication fork replisome non-membrane-bounded organelle
E [auth P]	DNA Primer Strand	-	-	-
F [auth T]	DNA Template Strand	-	-	-
G [auth F]	DNA polymerase III subunit theta	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	DNA-templated DNA replication lagging strand elongation 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 leading strand elongation	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle protein-containing complex catalytic complex nucleus nuclear protein-containing complex transferase complex intracellular membrane-bounded organelle DNA polymerase complex transferase complex, transferring phosphorus-containing groups intracellular organelle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle protein-containing complex 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, core complex DNA polymerase III complex organelle 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	IPR040982	DNA polymerase III alpha subunit finger domain	Domain
A	IPR004013	PHP domain	Domain
A	IPR049821	DnaE1-like, PHP domain	Domain
A	IPR016195	Polymerase/histidinol phosphatase-like	Homologous Superfamily
A	IPR004365	OB-fold nucleic acid binding domain, AA-tRNA synthetase-type	Domain
A	IPR041931	Bacterial DNA polymerase III alpha subunit, thumb domain	Homologous Superfamily
A	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A	IPR003141	Polymerase/histidinol phosphatase, N-terminal	Domain
A	IPR048472	DNA polymerase III subunit alpha, C-terminal domain	Domain
A	IPR011708	Bacterial DNA polymerase III, alpha subunit, NTPase domain	Domain
A	IPR029460	DNA polymerase, helix-hairpin-helix motif	Domain
A	IPR004805	Error-prone DNA polymerase/DNA polymerase III subunit alpha DnaE/PolC	Family
B, C	IPR046938	DNA clamp superfamily	Homologous Superfamily
B, C	IPR001001	DNA polymerase III, beta sliding clamp	Family
B, C	IPR022634	DNA polymerase III, beta sliding clamp, N-terminal	Domain
B, C	IPR022635	DNA polymerase III, beta sliding clamp, C-terminal	Domain
B, C	IPR022637	DNA polymerase III, beta sliding clamp, central	Domain
D	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
D	IPR006054	DNA polymerase III epsilon subunit, exonuclease domain	Domain
D	IPR006309	DNA polymerase 3, epsilon subunit	Family
D	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
D	IPR013520	Exonuclease, RNase T/DNA polymerase III	Domain
G [auth F]	IPR036745	DNA polymerase III-theta superfamily	Homologous Superfamily
G [auth F]	IPR009052	DNA polymerase III-theta, bacterial	Family