Annotations: 9Q9H

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth E]	SCOP2B Superfamily	Metallo-dependent phosphatases	8090756	3001067	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Mre11 C-terminal domain-like	8090757	3002453	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Metallo-dependent phosphatases	8090756	3001067	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Mre11 C-terminal domain-like	8090757	3002453	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth D], D [auth E]	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
C [auth D], D [auth E]	PF04152	Mre11 DNA-binding presumed domain (Mre11_DNA_bind)	Mre11 DNA-binding presumed domain	The Mre11 complex is a multi-subunit nuclease that is composed of Mre11, Rad50 and Nbs1/Xrs2, and is involved in checkpoint signalling and DNA replication [1]. Mre11 has an intrinsic DNA-binding activity that is stimulated by Rad50 on its own or in ...	The Mre11 complex is a multi-subunit nuclease that is composed of Mre11, Rad50 and Nbs1/Xrs2, and is involved in checkpoint signalling and DNA replication [1]. Mre11 has an intrinsic DNA-binding activity that is stimulated by Rad50 on its own or in combination with Nbs1 [2].	Domain
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
F [auth T]	DNA (50-MER)	-	-	-
E [auth P]	DNA (50-MER)	-	-	-
C [auth D], D [auth E]	Double-strand break repair protein MRE11	nuclease activity catalytic activity, acting on a nucleic acid catalytic activity cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding hydrolase activity, acting on ester bonds 3'-5' exonuclease activity hydrolase activity exonuclease activity nuclease activity catalytic activity, acting on a nucleic acid catalytic activity cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding hydrolase activity, acting on ester bonds 3'-5' exonuclease activity hydrolase activity exonuclease activity DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA single-stranded DNA endodeoxyribonuclease activity DNA nuclease activity cell adhesion molecule binding cadherin binding protein binding identical protein binding DNA exonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters 3'-5'-DNA exonuclease activity DNA binding double-stranded DNA binding nucleic acid binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process double-strand break repair DNA double-strand break processing primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process metabolic process macromolecule metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process double-strand break repair DNA double-strand break processing primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process metabolic process macromolecule metabolic process DNA repair homologous recombination sexual reproduction reproductive process meiotic cell cycle process cellular component organization meiosis I meiotic nuclear division cell cycle cellular component organization or biogenesis reciprocal homologous recombination cell cycle process DNA recombination meiotic cell cycle organelle fission reciprocal meiotic recombination nuclear division organelle organization meiosis I cell cycle process cell population proliferation chromosome organization sister chromatid cohesion mitochondrial double-strand break repair mitochondrial double-strand break repair via homologous recombination recombinational repair positive regulation of organelle organization regulation of telomere maintenance regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization positive regulation of biological process telomere organization regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process positive regulation of telomere maintenance regulation of biological process biological regulation regulation of chromosome organization regulation of macromolecule metabolic process regulation of organelle organization positive regulation of chromosome organization telomere maintenance positive regulation of DNA metabolic process regulation of metabolic process regulation of DNA metabolic process DNA damage checkpoint signaling regulation of cell cycle phase transition 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 cell communication regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction mitotic intra-S DNA damage checkpoint signaling regulation of cell cycle regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling mitotic cell cycle checkpoint signaling mitotic cell cycle process signal transduction in response to DNA damage G2/M transition of mitotic cell cycle mitotic G2/M transition checkpoint cell cycle G2/M phase transition negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle G2/M phase transition regulation of mitotic cell cycle phase transition negative regulation of cell cycle G2/M phase transition negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition regulation of double-strand break repair regulation of cellular response to stress positive regulation of response to stimulus positive regulation of DNA repair regulation of response to stress positive regulation of double-strand break repair regulation of DNA repair regulation of response to stimulus telomere maintenance via telomerase nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA-templated DNA biosynthetic process telomere maintenance via telomere lengthening nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process chromatin organization chromatin remodeling R-loop processing negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death negative regulation of double-strand break repair via nonhomologous end joining negative regulation of DNA repair negative regulation of double-strand break repair negative regulation of nucleobase-containing compound metabolic process regulation of double-strand break repair via nonhomologous end joining negative regulation of macromolecule metabolic process double-strand break repair via nonhomologous end joining negative regulation of response to stimulus negative regulation of metabolic process negative regulation of DNA metabolic process meiotic chromosome segregation chromosome organization involved in meiotic cell cycle homologous chromosome pairing at meiosis nuclear chromosome segregation homologous chromosome segregation chromosome segregation telomeric 3' overhang formation DNA strand elongation telomere capping meiotic DNA double-strand break formation regulation of DNA recombination mitotic recombination regulation of mitotic recombination DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity DNA replication DNA strand resection involved in replication fork processing replication fork processing mitotic G2 DNA damage checkpoint signaling double-strand break repair via homologous recombination	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure BRCA1-C complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cytoplasm cytosol membraneless organelle intracellular membraneless organelle membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure BRCA1-C complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cytoplasm cytosol membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen replication fork Mre11 complex site of double-strand break site of DNA damage nuclear body PML body
A, B	DNA repair protein RAD50	DNA binding G-quadruplex DNA binding binding nucleic acid binding protein-macromolecule adaptor activity molecular adaptor activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding DNA binding G-quadruplex DNA binding binding nucleic acid binding protein-macromolecule adaptor activity molecular adaptor activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding sequence-specific DNA binding double-stranded telomeric DNA binding double-stranded DNA binding telomeric DNA binding 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 enzyme regulator activity protein serine/threonine kinase activator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity cation binding metal ion binding identical protein binding protein binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process regulation of double-strand break repair positive regulation of biological process regulation of cellular response to stress regulation of primary metabolic process positive regulation of response to stimulus nucleobase-containing compound metabolic process positive regulation of metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process regulation of double-strand break repair positive regulation of biological process regulation of cellular response to stress regulation of primary metabolic process positive regulation of response to stimulus nucleobase-containing compound metabolic process positive regulation of metabolic process positive regulation of DNA repair regulation of response to stress positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process DNA repair double-strand break repair regulation of biological process biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process positive regulation of double-strand break repair nucleic acid metabolic process regulation of DNA repair positive regulation of DNA metabolic process regulation of response to stimulus metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process DNA double-strand break processing 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 component organization or biogenesis cell cycle cell cycle process telomere maintenance via telomerase telomere organization nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA-templated DNA biosynthetic process telomere maintenance via telomere lengthening telomere maintenance nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process chromatin organization chromatin remodeling R-loop processing homologous recombination meiosis I meiotic nuclear division reciprocal homologous recombination DNA recombination organelle fission reciprocal meiotic recombination nuclear division meiosis I cell cycle process mitotic recombination telomere maintenance via recombination telomeric 3' overhang formation DNA strand elongation telomere capping regulation of DNA recombination regulation of mitotic recombination DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity DNA replication DNA strand resection involved in replication fork processing replication fork processing recombinational repair double-strand break repair via homologous recombination positive regulation of organelle organization regulation of telomere maintenance regulation of cellular component organization positive regulation of cellular component organization positive regulation of telomere maintenance regulation of chromosome organization regulation of organelle organization positive regulation of chromosome organization regulation of cell cycle phase transition signaling G2/M transition of mitotic cell cycle 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 negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction regulation of cell cycle cell cycle G2/M phase transition negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process 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 negative regulation of cell cycle G2/M phase transition negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition negative regulation of telomere maintenance negative regulation of chromosome organization negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of cellular component organization negative regulation of metabolic process negative regulation of organelle organization negative regulation of telomere capping negative regulation of DNA metabolic process regulation of telomere capping	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure BRCA1-C complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle membrane condensed nuclear chromosome membrane-enclosed lumen intracellular membraneless organelle membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure BRCA1-C complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle membrane condensed nuclear chromosome membrane-enclosed lumen intracellular membraneless organelle nuclear chromosome chromosome intracellular organelle lumen organelle lumen membraneless organelle condensed chromosome nuclear lumen nucleoplasm chromosomal region Mre11 complex site of double-strand break site of DNA damage chromosome, telomeric region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth D], D [auth E]	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily
C [auth D], D [auth E]	IPR038487	Mre11, capping domain	Homologous Superfamily
C [auth D], D [auth E]	IPR003701	DNA double-strand break repair protein Mre11	Family
C [auth D], D [auth E]	IPR004843	Calcineurin-like, phosphoesterase domain	Domain
C [auth D], D [auth E]	IPR007281	Mre11, DNA-binding	Domain
C [auth D], D [auth E]	IPR041796	DNA double-strand break repair protein Mre11, N-terminal metallophosphatase domain	Domain
A, B	IPR038729	Rad50/SbcC-type AAA domain	Domain
A, B	IPR004584	DNA repair protein Rad50, eukaryotes	Family
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR013134	RAD50, zinc hook	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth D], D [auth E]	Pharos: P49959	ataxia-telangiectasia-like disorder 1 microcephaly osteosarcoma ataxia-telangiectasia-like disorder ataxia, early-onset, with oculomotor apraxia and hypoalbuminemia BAP1-related tumor predisposition syndrome hereditary breast carcinoma intellectual disability malignant colon neoplasm Malignant neoplasm of ovary Nijmegen breakage syndrome-like disorder cancer hereditary breast ovarian cancer syndrome large cell medulloblastoma malignant ependymoma ataxia-telangiectasia-like disorder 1 microcephaly osteosarcoma ataxia-telangiectasia-like disorder ataxia, early-onset, with oculomotor apraxia and hypoalbuminemia BAP1-related tumor predisposition syndrome hereditary breast carcinoma intellectual disability malignant colon neoplasm Malignant neoplasm of ovary Nijmegen breakage syndrome-like disorder cancer hereditary breast ovarian cancer syndrome large cell medulloblastoma malignant ependymoma medulloblastoma obstructive sleep apnea syndrome atypical teratoid rhabdoid tumor Charcot-Marie-Tooth disease hereditary hemorrhagic telangiectasia lung cancer
A, B	Pharos: Q92878	Nijmegen breakage syndrome-like disorder psoriasis polycystic ovary syndrome asthma ovarian cancer Pick disease allergic rhinitis atopic eczema Crohn disease hereditary breast ovarian cancer syndrome juvenile idiopathic arthritis pancreatic intraductal papillary-mucinous carcinoma alopecia areata atypical teratoid rhabdoid tumor glioblastoma Nijmegen breakage syndrome-like disorder psoriasis polycystic ovary syndrome asthma ovarian cancer Pick disease allergic rhinitis atopic eczema Crohn disease hereditary breast ovarian cancer syndrome juvenile idiopathic arthritis pancreatic intraductal papillary-mucinous carcinoma alopecia areata atypical teratoid rhabdoid tumor glioblastoma Hodgkins lymphoma lung cancer osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia progressive supranuclear palsy cancer hereditary breast carcinoma intellectual disability Malignant neoplasm of ovary

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.