5DA9 | pdb_00005da9

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

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
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)
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)
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)
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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)

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 hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on DNA 3'-5'-DNA exonuclease activity exonuclease activity catalytic activity DNA endonuclease activity 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 hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on DNA 3'-5'-DNA exonuclease activity exonuclease activity catalytic activity DNA endonuclease activity endonuclease activity single-stranded DNA endodeoxyribonuclease activity cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding	sexual reproduction reproductive process meiotic cell cycle primary metabolic process DNA metabolic process meiotic cell cycle process nucleic acid metabolic process nucleobase-containing compound metabolic process meiotic DNA double-strand break formation meiosis I cell cycle process cellular process metabolic process cell cycle macromolecule metabolic process sexual reproduction reproductive process meiotic cell cycle primary metabolic process DNA metabolic process meiotic cell cycle process nucleic acid metabolic process nucleobase-containing compound metabolic process meiotic DNA double-strand break formation meiosis I cell cycle process cellular process metabolic process cell cycle macromolecule metabolic process cell cycle process cellular response to stimulus regulation of cellular process regulation of cell cycle phase transition DNA damage checkpoint signaling response to stimulus signaling G2/M transition of mitotic cell cycle mitotic G2 DNA damage checkpoint signaling negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle mitotic G2/M transition checkpoint cell communication regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling cellular response to stress response to stress mitotic DNA damage checkpoint signaling negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction regulation of cell cycle cell cycle G2/M phase transition regulation of biological process negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process biological regulation DNA integrity checkpoint signaling regulation of cell cycle G2/M phase transition negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic cell cycle process DNA damage response negative regulation of cell cycle G2/M phase transition signal transduction in response to DNA damage negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition double-strand break repair DNA recombination recombinational repair double-strand break repair via homologous recombination DNA repair mitochondrial double-strand break repair mitochondrial double-strand break repair via homologous recombination mitotic intra-S DNA damage checkpoint signaling double-strand break repair via nonhomologous end joining 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 site of double-strand break membraneless organelle site of DNA damage intracellular membraneless organelle 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 site of double-strand break membraneless organelle site of DNA damage intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region
A, B	Putative uncharacterized protein,Putative uncharacterized protein	sequence-specific DNA binding DNA binding double-stranded telomeric DNA binding binding double-stranded DNA binding nucleic acid binding telomeric DNA binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity pyrophosphatase activity ATP hydrolysis activity sequence-specific DNA binding DNA binding double-stranded telomeric DNA binding binding double-stranded DNA binding nucleic acid binding telomeric DNA binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function 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 sequence-specific single stranded DNA binding single-stranded telomeric DNA binding single-stranded DNA binding G-quadruplex DNA binding cation binding ion binding metal ion binding small molecule binding	sexual reproduction reproductive process meiotic cell cycle chromosome organization meiotic cell cycle process cellular component organization chromosome organization involved in meiotic cell cycle organelle organization cellular process cellular component organization or biogenesis cell cycle cell cycle process telomere maintenance via telomerase telomere organization sexual reproduction reproductive process meiotic cell cycle chromosome organization meiotic cell cycle process cellular component organization chromosome organization involved in meiotic cell cycle organelle organization cellular process cellular component organization or biogenesis cell cycle cell cycle process telomere maintenance via telomerase telomere organization primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA-templated DNA biosynthetic process nucleobase-containing compound metabolic process telomere maintenance via telomere lengthening telomere maintenance nucleic acid biosynthetic process biosynthetic process metabolic process macromolecule metabolic process DNA biosynthetic process DNA recombination mitotic recombination telomere maintenance via recombination cellular response to stimulus double-strand break repair response to stimulus cellular response to stress DNA damage response response to stress DNA repair	membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle condensed chromosome nuclear lumen protein-containing complex Mre11 complex nuclear protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR038487	Mre11, capping domain	Homologous Superfamily
C, D	IPR003701	DNA double-strand break repair protein Mre11	Family
C, D	IPR004843	Calcineurin-like, phosphoesterase domain	Domain
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	IPR038729	Rad50/SbcC-type AAA domain	Domain
A, B	IPR000219	Dbl homology domain	Domain
A, B	IPR004584	DNA repair protein Rad50, eukaryotes	Family
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.