3DSD | pdb_00003dsd

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	Mlh1_C	e3dsdA1	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: Mlh1_C	ECOD (v294.1)
B	Mlh1_C	e3dsdB1	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: Mlh1_C	ECOD (v294.1)

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
A, B	PF22411	Mre11 nuclease, second domain (Mre11_2nd)	Mre11 nuclease, second domain	This entry represents the second calcineurin-like nuclease domain of DNA double-strand break repair protein Mre11 from Pyrococcus furiosus and similar archaeal proteins. Mre11, also known as Mre11 nuclease, is part of the Rad50/Mre11 complex, which i ...	This entry represents the second calcineurin-like nuclease domain of DNA double-strand break repair protein Mre11 from Pyrococcus furiosus and similar archaeal proteins. Mre11, also known as Mre11 nuclease, is part of the Rad50/Mre11 complex, which is involved in the early steps of DNA double-strand break (DSB) repair. This domain shows a beta-sheet and two alpha-helices [1-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR054745	DNA double-strand break repair protein Mre11, thermococcales	Family
A, B	IPR054741	DNA double-strand break repair protein Mre11, second domain	Domain
A, B	IPR004843	Calcineurin-like, phosphoesterase domain	Domain
A, B	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily
A, B	IPR032885	DNA double-strand break repair protein Mre11, archaea-type	Family
A, B	IPR050535	DNA Repair and Maintenance Complex Component	Family
A, B	IPR041796	DNA double-strand break repair protein Mre11, N-terminal metallophosphatase domain	Domain

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.