3DSD

Crystal structure of P. furiosus Mre11-H85S bound to a branched DNA and manganese

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)
A	d3dsda_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	DNA double-strand break repair nuclease	Mre11	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
B	d3dsdb_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	DNA double-strand break repair nuclease	Mre11	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Metallo-dependent phosphatases	8033969	3001067	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Mre11 C-terminal domain-like	8090758	3002453	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metallo-dependent phosphatases	8033969	3001067	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Mre11 C-terminal domain-like	8090758	3002453	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	Metallophos_2_1	e3dsdA1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: Metallophos_2_1	ECOD (1.6)
A	EUF08527	e3dsdA2	A: a+b four layers	X: Mre11 nuclease C-terminal domain (From Topology)	H: Mre11 nuclease C-terminal domain (From Topology)	T: Mre11 nuclease C-terminal domain	F: EUF08527	ECOD (1.6)
B	Metallophos_2_1	e3dsdB1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: Metallophos_2_1	ECOD (1.6)
B	EUF08527	e3dsdB2	A: a+b four layers	X: Mre11 nuclease C-terminal domain (From Topology)	H: Mre11 nuclease C-terminal domain (From Topology)	T: Mre11 nuclease C-terminal domain	F: EUF08527	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
A	3.30.110.80	Alpha Beta	2-Layer Sandwich	Translation Initiation Factor IF3	DNA double-strand break repair nuclease	CATH (4.3.0)
B	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
B	3.30.110.80	Alpha Beta	2-Layer Sandwich	Translation Initiation Factor IF3	DNA double-strand break repair nuclease	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00149	Calcineurin-like phosphoesterase (Metallophos)	Calcineurin-like phosphoesterase	This family includes a diverse range of phosphoesterases [1], including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD Swiss:P13457 or ...	This family includes a diverse range of phosphoesterases [1], including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD Swiss:P13457 or yeast MRE11 Swiss:P32829. The most conserved regions in this superfamily centre around the metal chelating residues.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DNA double-strand break repair protein mre11	DNA secondary structure binding DNA binding binding organic cyclic compound binding Y-form DNA binding nucleic acid binding cation binding manganese ion binding transition metal ion binding ion binding metal ion binding small molecule binding nuclease activity hydrolase activity, acting on ester bonds DNA secondary structure binding DNA binding binding organic cyclic compound binding Y-form DNA binding nucleic acid binding cation binding manganese ion binding transition metal ion binding ion binding metal ion binding small molecule binding nuclease activity hydrolase activity, acting on ester bonds 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity endonuclease activity DNA end binding identical protein binding protein binding	cellular response to stimulus double-strand break repair 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 cellular response to stimulus double-strand break repair 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	-
C	DNA (5'-D(DCPDGPDCPDGPDCPDAPDCPDAPDAPDGPDCPDTPDTPDTPDTPDGPDCPDTPDTPDGPDTPDGPDGPDAPDTPDA)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR004843	Calcineurin-like phosphoesterase domain, ApaH type	Domain
A, B	IPR032885	DNA double-strand break repair protein Mre11, archaea-type	Family
A, B	IPR041796	Mre11 nuclease, N-terminal metallophosphatase domain	Domain
A, B	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.