5W6Q

Structural basis for recognition of artificial DNA by an evolved KlenTaq variant

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037492	3001272	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037492	3001272	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8044539	3000143	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037492	3001272	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037492	3001272	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	Ribonuclease H-like	8044539	3000143	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037492	3001272	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ribonuclease H-like	8044539	3000143	SCOP2B (2022-06-29)
G	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)
A	PF00476	e5w6qA3	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: PF00476	ECOD (1.6)
A	PF00476	e5w6qA4	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: PF00476	ECOD (1.6)
A	PF00476	e5w6qA1	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: PF00476	ECOD (1.6)
A	PF09281	e5w6qA2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF09281	ECOD (1.6)
D [auth C]	PF00476	e5w6qC2	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: PF00476	ECOD (1.6)
D [auth C]	PF00476	e5w6qC3	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: PF00476	ECOD (1.6)
D [auth C]	PF00476	e5w6qC4	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: PF00476	ECOD (1.6)
D [auth C]	PF09281	e5w6qC1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF09281	ECOD (1.6)
G	PF00476	e5w6qG4	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: PF00476	ECOD (1.6)
G	PF00476	e5w6qG2	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: PF00476	ECOD (1.6)
G	PF00476	e5w6qG3	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: PF00476	ECOD (1.6)
G	PF09281	e5w6qG1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF09281	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)
D [auth C]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
D [auth C]	1.20.1060.10	Mainly Alpha	Up-down Bundle	Taq DNA Polymerase	Chain T, domain 4	CATH (4.3.0)
D [auth C]	3.30.70.370	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
G	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
G	1.20.1060.10	Mainly Alpha	Up-down Bundle	Taq DNA Polymerase	Chain T, domain 4	CATH (4.3.0)
G	3.30.70.370	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth C], G	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
A, D [auth C], G	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, D [auth C], G	DNA polymerase I, thermostable	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 nucleoside binding heterocyclic compound 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 organic cyclic compound binding nucleic acid binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding hydrolase activity, acting on ester bonds hydrolase activity	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair DNA-templated DNA replication DNA replication	-
B, E, H	DNA (5'-D(GPAPCPCPAPCPGPGPCPGPCP(1W5))-3')	-	-	-
C [auth D], F, I	DNA (5'-D(PGP(1WA)PGPCPGPCPCPGPTPGPGPTP*C)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth C], G	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, D [auth C], G	IPR002421	5'-3' exonuclease	Domain
A, D [auth C], G	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, D [auth C], G	IPR020045	DNA polymerase I-like, H3TH domain	Domain
A, D [auth C], G	IPR015361	Taq polymerase, thermostable, exonuclease region	Domain
A, D [auth C], G	IPR001098	DNA-directed DNA polymerase, family A, palm domain	Domain
A, D [auth C], G	IPR029060	PIN-like domain superfamily	Homologous Superfamily
A, D [auth C], G	IPR036279	5'-3' exonuclease, C-terminal domain superfamily	Homologous Superfamily
A, D [auth C], G	IPR008918	Helix-hairpin-helix motif, class 2	Conserved Site
A, D [auth C], G	IPR002298	DNA polymerase A	Family
A, D [auth C], G	IPR020046	5'-3' exonuclease, alpha-helical arch, N-terminal	Domain
A, D [auth C], G	IPR019760	DNA-directed DNA polymerase, family A, conserved site	Conserved Site
A, D [auth C], G	IPR018320	DNA polymerase 1	Family
A, D [auth C], G	IPR003583	Helix-hairpin-helix DNA-binding motif, class 1	Domain
A, D [auth C], G	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 R01GM133198.