3KTQ | pdb_00003ktq

CRYSTAL STRUCTURE OF AN ACTIVE TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS

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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C [auth A]	d3ktqa1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	Exonuclease domain of prokaryotic DNA polymerase	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
C [auth A]	d3ktqa2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	DNA polymerase I	DNA polymerase I (Klenow fragment)	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037492	3001272	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Ribonuclease H-like	8044539	3000143	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037492	3001272	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)
C [auth A]	DNA_pol_A_2nd	e3ktqA1	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)
C [auth A]	DNA_pol_A_1st	e3ktqA2	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)
C [auth A]	DNA_pol_A_3rd	e3ktqA3	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)
C [auth A]	Taq-exonuc	e3ktqA4	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Taq-exonuc	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
C [auth A]	1.20.1060.10	Mainly Alpha	Up-down Bundle	Taq DNA Polymerase	Chain T, domain 4	CATH (4.3.0)
C [auth A]	3.30.70.370	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
C [auth A]	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
C [auth A]	PF09281	Taq polymerase, exonuclease (Taq-exonuc)	Taq polymerase, exonuclease	Members of this family are found in prokaryotic Taq DNA polymerase, where they assume a ribonuclease H-like motif. The domain confers 5'-3' exonuclease activity to the polymerase [1].	Domain
C [auth A]	PF00476	DNA polymerase family A (DNA_pol_A)	DNA polymerase family A		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	DNA (5'-D(GPAPCPCPAPCPGPGPCPGPCPDOC)-3')	-	-	-
B [auth C]	DNA (5'-D(APGPGPGPCPGPCPCPGPTPGPGPTPC)-3')	-	-	-
C [auth A]	PROTEIN (LARGE FRAGMENT OF 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 nucleic acid binding nucleoside binding heterocyclic compound binding carbohydrate derivative 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 DNA binding binding nucleic acid binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding hydrolase activity, acting on ester bonds nuclease activity 5'-3' exonuclease activity hydrolase activity 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
C [auth A]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
C [auth A]	IPR002421	5'-3' exonuclease	Domain
C [auth A]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
C [auth A]	IPR020045	DNA polymerase I-like, H3TH domain	Domain
C [auth A]	IPR015361	Taq polymerase, thermostable, exonuclease region	Domain
C [auth A]	IPR001098	DNA-directed DNA polymerase, family A, palm domain	Domain
C [auth A]	IPR029060	PIN-like domain superfamily	Homologous Superfamily
C [auth A]	IPR036279	5'-3' exonuclease, C-terminal domain superfamily	Homologous Superfamily
C [auth A]	IPR008918	Helix-hairpin-helix motif, class 2	Conserved Site
C [auth A]	IPR002298	DNA polymerase A	Family
C [auth A]	IPR020046	5'-3' exonuclease, alpha-helical arch, N-terminal	Domain
C [auth A]	IPR019760	DNA-directed DNA polymerase, family A, conserved site	Conserved Site
C [auth A]	IPR018320	DNA polymerase 1	Family
C [auth A]	IPR003583	Helix-hairpin-helix DNA-binding motif, class 1	Domain
C [auth A]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily

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.