3SQ5 | pdb_00003sq5

Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase H432N Mutant

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)
D	d3sq5d1	Alpha and beta proteins (a+b)	Phospholipase D/nuclease	Phospholipase D/nuclease	Tyrosyl-DNA phosphodiesterase TDP1	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
C	d3sq5c1	Alpha and beta proteins (a+b)	Phospholipase D/nuclease	Phospholipase D/nuclease	Tyrosyl-DNA phosphodiesterase TDP1	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d3sq5b1	Alpha and beta proteins (a+b)	Phospholipase D/nuclease	Phospholipase D/nuclease	Tyrosyl-DNA phosphodiesterase TDP1	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d3sq5a1	Alpha and beta proteins (a+b)	Phospholipase D/nuclease	Phospholipase D/nuclease	Tyrosyl-DNA phosphodiesterase TDP1	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Phospholipase D/nuclease-like	8038464	3000664	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Phospholipase D/nuclease-like	8038467	3000664	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Phospholipase D/nuclease-like	8038464	3000664	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Phospholipase D/nuclease-like	8038467	3000664	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Phospholipase D/nuclease-like	8038467	3000664	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Phospholipase D/nuclease-like	8038464	3000664	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Phospholipase D/nuclease-like	8038464	3000664	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Phospholipase D/nuclease-like	8038467	3000664	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)
D	Tyr-DNA_phospho_1st	e3sq5D1	A: a+b three layers	X: Phospholipase D/nuclease (From Topology)	H: Phospholipase D/nuclease (From Topology)	T: Phospholipase D/nuclease	F: Tyr-DNA_phospho_1st	ECOD (1.6)
D	Tyr-DNA_phospho_2nd	e3sq5D2	A: a+b three layers	X: Phospholipase D/nuclease (From Topology)	H: Phospholipase D/nuclease (From Topology)	T: Phospholipase D/nuclease	F: Tyr-DNA_phospho_2nd	ECOD (1.6)
C	Tyr-DNA_phospho_1st	e3sq5C1	A: a+b three layers	X: Phospholipase D/nuclease (From Topology)	H: Phospholipase D/nuclease (From Topology)	T: Phospholipase D/nuclease	F: Tyr-DNA_phospho_1st	ECOD (1.6)
C	Tyr-DNA_phospho_2nd	e3sq5C2	A: a+b three layers	X: Phospholipase D/nuclease (From Topology)	H: Phospholipase D/nuclease (From Topology)	T: Phospholipase D/nuclease	F: Tyr-DNA_phospho_2nd	ECOD (1.6)
B	Tyr-DNA_phospho_1st	e3sq5B1	A: a+b three layers	X: Phospholipase D/nuclease (From Topology)	H: Phospholipase D/nuclease (From Topology)	T: Phospholipase D/nuclease	F: Tyr-DNA_phospho_1st	ECOD (1.6)
B	Tyr-DNA_phospho_2nd	e3sq5B2	A: a+b three layers	X: Phospholipase D/nuclease (From Topology)	H: Phospholipase D/nuclease (From Topology)	T: Phospholipase D/nuclease	F: Tyr-DNA_phospho_2nd	ECOD (1.6)
A	Tyr-DNA_phospho_1st	e3sq5A1	A: a+b three layers	X: Phospholipase D/nuclease (From Topology)	H: Phospholipase D/nuclease (From Topology)	T: Phospholipase D/nuclease	F: Tyr-DNA_phospho_1st	ECOD (1.6)
A	Tyr-DNA_phospho_2nd	e3sq5A2	A: a+b three layers	X: Phospholipase D/nuclease (From Topology)	H: Phospholipase D/nuclease (From Topology)	T: Phospholipase D/nuclease	F: Tyr-DNA_phospho_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.870.10	Alpha Beta	2-Layer Sandwich	Endonuclease	Chain A	CATH (4.3.0)
C	3.30.870.10	Alpha Beta	2-Layer Sandwich	Endonuclease	Chain A	CATH (4.3.0)
B	3.30.870.10	Alpha Beta	2-Layer Sandwich	Endonuclease	Chain A	CATH (4.3.0)
A	3.30.870.10	Alpha Beta	2-Layer Sandwich	Endonuclease	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF06087	Tyrosyl-DNA phosphodiesterase (Tyr-DNA_phospho)	Tyrosyl-DNA phosphodiesterase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Tyrosyl-DNA phosphodiesterase 1	hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exonuclease activity catalytic activity phosphoric ester hydrolase activity 5'-tyrosyl-DNA phosphodiesterase activity tyrosyl-DNA phosphodiesterase activity catalytic activity, acting on DNA phosphoric diester hydrolase activity 3'-tyrosyl-DNA phosphodiesterase activity DNA binding double-stranded DNA binding hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exonuclease activity catalytic activity phosphoric ester hydrolase activity 5'-tyrosyl-DNA phosphodiesterase activity tyrosyl-DNA phosphodiesterase activity catalytic activity, acting on DNA phosphoric diester hydrolase activity 3'-tyrosyl-DNA phosphodiesterase activity DNA binding double-stranded DNA binding binding nucleic acid binding single-stranded DNA binding	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR010347	Tyrosyl-DNA phosphodiesterase I	Family

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.