1LV5

Crystal Structure of the Closed Conformation of Bacillus DNA Polymerase I Fragment Bound to DNA and dCTP

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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
E [auth A]	d1lv5a1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	Exonuclease domain of prokaryotic DNA polymerase	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
E [auth A]	d1lv5a2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	DNA polymerase I	DNA polymerase I (Klenow fragment)	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
F [auth B]	d1lv5b1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	Exonuclease domain of prokaryotic DNA polymerase	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
F [auth B]	d1lv5b2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	DNA polymerase I	DNA polymerase I (Klenow fragment)	(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)
E [auth A]	DNA_pol_A_2nd	e1lv5A1	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)
E [auth A]	DNA_pol_A_1st	e1lv5A2	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)
E [auth A]	DNA_pol_A_3rd	e1lv5A3	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)
E [auth A]	DNA_pol_A_exo1_1	e1lv5A4	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)
F [auth B]	DNA_pol_A_2nd	e1lv5B1	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)
F [auth B]	DNA_pol_A_1st	e1lv5B2	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)
F [auth B]	DNA_pol_A_3rd	e1lv5B3	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)
F [auth B]	DNA_pol_A_exo1_1	e1lv5B4	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)
E [auth A]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
E [auth A]	1.20.1060.10	Mainly Alpha	Up-down Bundle	Taq DNA Polymerase	Chain T, domain 4	CATH (4.3.0)
E [auth A]	3.30.70.370	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
E [auth A]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
F [auth B]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
F [auth B]	1.20.1060.10	Mainly Alpha	Up-down Bundle	Taq DNA Polymerase	Chain T, domain 4	CATH (4.3.0)
F [auth B]	3.30.70.370	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
F [auth B]	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
E [auth A], F [auth B]	PF22619	DNA polymerase I, ribonuclease H-like domain (DNA_polI_exo1)	DNA polymerase I, ribonuclease H-like domain	This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other related enzymes. It is one of the constituent domains of Klenow fragment.	Domain
E [auth A], F [auth B]	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 [auth C], C [auth E]	5'-D(GPGPAPTPCPAPGPCPGPA)-3'	-	-	-
B [auth D], D [auth F]	5'-D(APCPGPTPCPGPCPTPGPAPTPCPCPG)-3'	-	-	-
E [auth A], F [auth B]	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 5'-3' exonuclease activity	nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus double-strand break repair response to stimulus cellular response to stress DNA damage response nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus double-strand break repair response to stimulus cellular response to stress DNA damage response response to stress DNA repair	-

InterPro: Protein Family Classification InterPro Database Homepage

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.