5DA9

ATP-gamma-S bound Rad50 from Chaetomium thermophilum in complex with the Rad50-binding domain of Mre11

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	Mre11_DNA_bind_C	e5da9C1	A: alpha bundles	X: Rad50-binding domain of Mre11 (From Topology)	H: Rad50-binding domain of Mre11 (From Topology)	T: Rad50-binding domain of Mre11	F: Mre11_DNA_bind_C	ECOD (1.6)
D	Mre11_DNA_bind_C	e5da9D1	A: alpha bundles	X: Rad50-binding domain of Mre11 (From Topology)	H: Rad50-binding domain of Mre11 (From Topology)	T: Rad50-binding domain of Mre11	F: Mre11_DNA_bind_C	ECOD (1.6)
A	SMC_N_1	e5da9A1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: SMC_N_1	ECOD (1.6)
B	SMC_N_1	e5da9B1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: SMC_N_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF13558	SbcC/RAD50-like, Walker B motif (SbcC_Walker_B)	SbcC/RAD50-like, Walker B motif	This entry represents the Walker B domain of RAD50 from eukaryotes and the prokaryotic homologue SbcCD complex subunit C. RAD50-ATPase forms a complex with Mre11-nuclease that detects and processes diverse and obstructed DNA ends. This domain is sepa ...	This entry represents the Walker B domain of RAD50 from eukaryotes and the prokaryotic homologue SbcCD complex subunit C. RAD50-ATPase forms a complex with Mre11-nuclease that detects and processes diverse and obstructed DNA ends. This domain is separated of the Walker A domain by a long coiled-coil domain and forms the nucleotide-binding domain (NBD) when the coiled coils fold back on themselves and bring together Walker A and B domains [1,2,3,4]. Two RAD50-NBDs forms heterotetramers with a Mre11 nuclease dimer that assemble as catalytic head module that binds and cleaves DNA in an ATP-dependent reaction. Through secondary structural analysis, it has been suggested that there is a wide structural conservation in the Rad50/SMC protein family as seen in structural similarities between RAD50's hook and ABC-ATPase MukB's elbow region [4].	Domain
A, B	PF13476	AAA domain (AAA_23)	AAA domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Putative double-strand break protein	DNA exonuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA 3'-5'-DNA exonuclease activity exonuclease activity catalytic activity DNA endonuclease activity DNA exonuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA 3'-5'-DNA exonuclease activity exonuclease activity catalytic activity DNA endonuclease activity endonuclease activity cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule 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 cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair 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 cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair sexual reproduction reproductive process meiotic cell cycle cell cycle	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure Mre11 complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure Mre11 complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region
A, B	Putative uncharacterized protein,Putative uncharacterized protein	pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity DNA binding double-stranded DNA binding binding organic cyclic compound binding nucleic acid binding GTPase regulator activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity DNA binding double-stranded DNA binding binding organic cyclic compound binding nucleic acid binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity cation binding ion binding metal ion binding small molecule 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 cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair 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 cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair telomere organization chromosome organization telomere maintenance cellular component organization organelle organization cellular component organization or biogenesis	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure Mre11 complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle membraneless organelle intracellular membraneless organelle chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR004843	Calcineurin-like phosphoesterase domain, ApaH type	Domain
C, D	IPR038487	Mre11, capping domain	Homologous Superfamily
C, D	IPR003701	DNA double-strand break repair protein Mre11	Family
C, D	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily
C, D	IPR007281	Mre11, DNA-binding	Domain
C, D	IPR041796	DNA double-strand break repair protein Mre11, N-terminal metallophosphatase domain	Domain
A, B	IPR004584	DNA repair protein Rad50, eukaryotes	Family
A, B	IPR038729	Rad50/SbcC-type AAA domain	Domain
A, B	IPR000219	Dbl homology (DH) domain	Domain
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	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 R01GM157729.