5FKU

cryo-EM structure of the E. coli replicative DNA polymerase complex in DNA free state (DNA polymerase III alpha, beta, epsilon, tau complex)

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	8038081	3000780	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA clamp	8038082	3000780	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA clamp	8038082	3000780	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA clamp	8038076	3000780	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA clamp	8038081	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	PF01336	e5fkuA5	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF01336	ECOD (1.6)
A	PF14579	e5fkuA6	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF14579	ECOD (1.6)
A	PF17657	e5fkuA2	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: PF17657	ECOD (1.6)
A	PF20914	e5fkuA4	A: a+b two layers	X: DNA polymerase III C-terminal domain (From Topology)	H: DNA polymerase III C-terminal domain (From Topology)	T: DNA polymerase III C-terminal domain	F: PF20914	ECOD (1.6)
A	PF07733	e5fkuA3	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: PF07733	ECOD (1.6)
A	PF02811	e5fkuA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF02811	ECOD (1.6)
B	PF00712	e5fkuB3	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PF00712	ECOD (1.6)
B	PF02767	e5fkuB1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PF02767	ECOD (1.6)
B	PF02768	e5fkuB2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PF02768	ECOD (1.6)
C	PF00712	e5fkuC1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PF00712	ECOD (1.6)
C	PF02767	e5fkuC3	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PF02767	ECOD (1.6)
C	PF02768	e5fkuC2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PF02768	ECOD (1.6)
D	PF00929	e5fkuD1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00929	ECOD (1.6)
E	PF12170	e5fkuE1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: C-terminal domain of DNA Polymerase III subunit tau (From Topology)	T: C-terminal domain of DNA Polymerase III subunit tau	F: PF12170	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02811	PHP domain (PHP)	PHP domain	-	Family
A	PF20914	DNA polymerase III subunit alpha, C-terminal domain (DNA_pol_IIIA_C)	DNA polymerase III subunit alpha, C-terminal domain	This domain is found at the C-terminal end of DNA polymerase III subunit alpha and similar proteins from Proteobacteria and Actinobacteria. This protein, which is the replicative DNA polymerase, consists of six domains that form an irregular pyramid ...	This domain is found at the C-terminal end of DNA polymerase III subunit alpha and similar proteins from Proteobacteria and Actinobacteria. This protein, which is the replicative DNA polymerase, consists of six domains that form an irregular pyramid around a central cavity. The C-terminal domain lies on top of this structure [1].	Domain
A	PF07733	Bacterial DNA polymerase III alpha NTPase domain (DNA_pol3_alpha)	Bacterial DNA polymerase III alpha NTPase 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
A	PF01336	OB-fold nucleic acid binding domain (tRNA_anti-codon)	OB-fold nucleic acid binding domain	This family contains OB-fold domains that bind to nucleic acids [4]. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See Pfam:PF00152). Aminoacyl-tRNA synthetases catalyse the addition of an a ...	This family contains OB-fold domains that bind to nucleic acids [4]. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See Pfam:PF00152). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family [2,3]. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.	Domain
A	PF17657	Bacterial DNA polymerase III alpha subunit finger domain (DNA_pol3_finger)	Bacterial DNA polymerase III alpha subunit finger domain	-	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
E	PF12170	DNA polymerase III tau subunit V interacting with alpha (DNA_pol3_tau_5)	DNA polymerase III tau subunit V interacting with alpha	-	Family

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	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 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

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
E	IPR001270	ClpA/B family	Family
E	IPR021029	DNA polymerase III, tau subunit, domain V	Domain
E	IPR008921	DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal	Homologous Superfamily
E	IPR022754	DNA polymerase III, gamma subunit, domain III	Domain
E	IPR012763	DNA polymerase III, subunit gamma/ tau, N-terminal	Domain
E	IPR038249	DNA polymerase III, tau subunit, domain V superfamily	Homologous Superfamily
E	IPR003593	AAA+ ATPase domain	Domain
E	IPR022001	DNA polymerase III subunit tau, DnaB-binding domain IV	Domain
E	IPR045085	DNA polymerase III, subunit gamma/tau, helical lid domain	Domain
E	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily