3EZ5

Cocrystal structure of Bacillus fragment DNA polymerase I with duplex DNA , dCTP, and zinc (closed form).

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d3ez5a1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	Exonuclease domain of prokaryotic DNA polymerase	( ) [TaxId: ], (Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
A	d3ez5a2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	DNA polymerase I	DNA polymerase I (Klenow fragment)	( ) [TaxId: ], (Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
A	d3ez5a3	Artifacts	Tags	Tags	Tags	N-terminal Tags	( ) [TaxId: ], (Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
B [auth D]	d3ez5d1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	Exonuclease domain of prokaryotic DNA polymerase	( ) [TaxId: ], (Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
B [auth D]	d3ez5d2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	DNA polymerase I	DNA polymerase I (Klenow fragment)	( ) [TaxId: ], (Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	DNA_pol_A_2nd	e3ez5A1	A: alpha arrays	X: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology)	H: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology)	T: helical bundle in Bacillus stearothermophilus-like DNA polymerase I	F: DNA_pol_A_2nd	ECOD (1.6)
A	DNA_pol_A_1st	e3ez5A2	A: alpha bundles	X: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: fingers domain in bacteriophage RB69-like DNA polymerase I	F: DNA_pol_A_1st	ECOD (1.6)
A	DNA_pol_A_3rd	e3ez5A3	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: DNA_pol_A_3rd	ECOD (1.6)
A	DNA_pol_A_exo1_1	e3ez5A4	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: DNA_pol_A_exo1_1	ECOD (1.6)
B [auth D]	DNA_pol_A_2nd	e3ez5D1	A: alpha arrays	X: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology)	H: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology)	T: helical bundle in Bacillus stearothermophilus-like DNA polymerase I	F: DNA_pol_A_2nd	ECOD (1.6)
B [auth D]	DNA_pol_A_1st	e3ez5D2	A: alpha bundles	X: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: fingers domain in bacteriophage RB69-like DNA polymerase I	F: DNA_pol_A_1st	ECOD (1.6)
B [auth D]	DNA_pol_A_3rd	e3ez5D3	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: DNA_pol_A_3rd	ECOD (1.6)
B [auth D]	DNA_pol_A_exo1_1	e3ez5D4	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: DNA_pol_A_exo1_1	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)
A	1.20.1060.10	Mainly Alpha	Up-down Bundle	Taq DNA Polymerase	Chain T, domain 4	CATH (4.3.0)
A	3.30.70.370	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
B [auth D]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B [auth D]	1.20.1060.10	Mainly Alpha	Up-down Bundle	Taq DNA Polymerase	Chain T, domain 4	CATH (4.3.0)
B [auth D]	3.30.70.370	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B [auth D]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth D]	PF00476	DNA polymerase family A (DNA_pol_A)	DNA polymerase family A	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth D]	DNA polymerase I	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	cellular response to stimulus response to stimulus 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 organic substance metabolic process heterocycle metabolic process cellular response to stress DNA damage response response to stress cellular response to stimulus response to stimulus 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 organic substance metabolic process heterocycle metabolic process cellular response to stress DNA damage response response to stress nitrogen compound metabolic process metabolic process cellular process macromolecule metabolic process cellular aromatic compound metabolic process DNA repair DNA-templated DNA replication DNA replication	-
C [auth B], E	5'-D(DCPDCPDTPDGPDAPDCPDTPDCP*DG)-3'	-	-	-
D [auth C], F	5'-D(DAPDTPDTPDCPDGPDAPDGPDTPDCPDAPDGPDG)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth D]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B [auth D]	IPR002421	5'-3' exonuclease	Domain
A, B [auth D]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B [auth D]	IPR020045	DNA polymerase I-like, H3TH domain	Domain
A, B [auth D]	IPR001098	DNA-directed DNA polymerase, family A, palm domain	Domain
A, B [auth D]	IPR029060	PIN-like domain superfamily	Homologous Superfamily
A, B [auth D]	IPR036279	5'-3' exonuclease, C-terminal domain superfamily	Homologous Superfamily
A, B [auth D]	IPR008918	Helix-hairpin-helix motif, class 2	Conserved Site
A, B [auth D]	IPR002298	DNA polymerase A	Family
A, B [auth D]	IPR020046	5'-3' exonuclease, alpha-helical arch, N-terminal	Domain
A, B [auth D]	IPR019760	DNA-directed DNA polymerase, family A, conserved site	Conserved Site
A, B [auth D]	IPR018320	DNA polymerase 1	Family
A, B [auth D]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B [auth D]	IPR002562	3'-5' exonuclease domain	Domain

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.