3SQ8 | pdb_00003sq8

Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase 1 H432R Mutant (SCAN1 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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d3sq8d1	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)
D	d3sq8d3	Artifacts	Tags	Tags	Tags	C-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
C	d3sq8c1	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	d3sq8c3	Artifacts	Tags	Tags	Tags	C-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d3sq8b1	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	d3sq8b3	Artifacts	Tags	Tags	Tags	C-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d3sq8a1	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	8038467	3000664	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Phospholipase D/nuclease-like	8038464	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	Pkinase, PK_Tyr_Ser-Thr	e3sq8D1	A: alpha bundles	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: Pkinase, PK_Tyr_Ser-Thr	ECOD (develop294)
C	Pkinase, PK_Tyr_Ser-Thr	e3sq8C1	A: alpha bundles	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: Pkinase, PK_Tyr_Ser-Thr	ECOD (develop294)
B	Pkinase, PK_Tyr_Ser-Thr	e3sq8B1	A: alpha bundles	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: Pkinase, PK_Tyr_Ser-Thr	ECOD (develop294)
A	Pkinase, PK_Tyr_Ser-Thr	e3sq8A1	A: alpha bundles	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: Pkinase, PK_Tyr_Ser-Thr	ECOD (develop294)

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D	NEP	Parent Component: HIS RESID: AA0035 PSI-MOD : 1'-phospho-L-histidine MOD:00044

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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