2IDO

Structure of the E. coli Pol III epsilon-Hot proofreading 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	d2idoa_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2idoc_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2idob_	All alpha proteins	DNA polymerase III theta subunit-like	DNA polymerase III theta subunit-like	DNA polymerase III theta subunit-like	Homolog of theta (HOT)	(Punavirus P1 ) [TaxId: 10678 ],	SCOPe (2.08)
D	d2idod_	All alpha proteins	DNA polymerase III theta subunit-like	DNA polymerase III theta subunit-like	DNA polymerase III theta subunit-like	Homolog of theta (HOT)	(Punavirus P1 ) [TaxId: 10678 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ribonuclease H-like	8042074	3000143	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribonuclease H-like	8042074	3000143	SCOP2B (2022-06-29)
B	SCOP2 Family	DNA polymerase III theta subunit-like	8030323	4000612	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	DNA polymerase III theta subunit-like	8042702	3000744	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	DNA polymerase III theta subunit-like	8042702	3000744	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	RNase_T	e2idoA1	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)
C	RNase_T	e2idoC1	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)
B	DNA_pol3_theta	e2idoB1	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)
D	DNA_pol3_theta	e2idoD1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
C	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	1.20.58.250	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
D	1.20.58.250	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF00929	Exonuclease (RNase_T)	Exonuclease	-	Family
B, D	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, C	DNA polymerase III epsilon 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 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 cellular metabolic process lagging strand elongation 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 DNA-templated DNA replication cellular metabolic process lagging strand elongation 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 cellular process DNA strand elongation involved in DNA replication macromolecule metabolic process cellular aromatic compound metabolic process leading strand elongation cellular response to stimulus response to stimulus DNA-templated DNA replication maintenance of fidelity cellular response to stress response to stress DNA repair DNA replication proofreading DNA damage response	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, D	Hot protein	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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, C	IPR006054	DNA polymerase III epsilon subunit, exonuclease domain	Domain
A, C	IPR006309	DNA polymerase 3, epsilon subunit	Family
A, C	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, C	IPR013520	Exonuclease, RNase T/DNA polymerase III	Domain
B, D	IPR036745	DNA polymerase III-theta superfamily	Homologous Superfamily
B, D	IPR009052	DNA polymerase III-theta, bacterial	Family

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.