6LYF | pdb_00006lyf

Crystal structure of the mouse endonuclease EndoG(H138A/Se-Met)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	His-Me finger endonucleases	8098092	3001893	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	His-Me finger endonucleases	8098092	3001893	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	His-Me finger endonucleases	8098092	3001893	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	His-Me finger endonucleases	8098092	3001893	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)
D	Endonuclease_NS	e6lyfD1	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: Endonuclease_NS	ECOD (1.6)
C	Endonuclease_NS	e6lyfC1	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: Endonuclease_NS	ECOD (1.6)
B	Endonuclease_NS	e6lyfB1	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: Endonuclease_NS	ECOD (1.6)
A	Endonuclease_NS	e6lyfA1	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: Endonuclease_NS	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.570.10	Alpha Beta	3-Layer(aba) Sandwich	Extracellular Endonuclease	Chain A	CATH (utative)
C	3.40.570.10	Alpha Beta	3-Layer(aba) Sandwich	Extracellular Endonuclease	Chain A	CATH (utative)
B	3.40.570.10	Alpha Beta	3-Layer(aba) Sandwich	Extracellular Endonuclease	Chain A	CATH (utative)
A	3.40.570.10	Alpha Beta	3-Layer(aba) Sandwich	Extracellular Endonuclease	Chain A	CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Endonuclease G, mitochondrial	binding nucleic acid binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid catalytic activity DNA nuclease activity cation binding magnesium ion binding ion binding metal ion binding small molecule binding binding nucleic acid binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid catalytic activity DNA nuclease activity cation binding magnesium ion binding ion binding metal ion binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process positive regulation of mitochondrial DNA metabolic process positive regulation of organelle organization regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization positive regulation of DNA replication positive regulation of biological process positive regulation of mitochondrial DNA replication cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process positive regulation of mitochondrial DNA metabolic process positive regulation of organelle organization regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization positive regulation of DNA replication positive regulation of biological process positive regulation of mitochondrial DNA replication mitochondrial DNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process cellular component organization positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process cellular component organization or biogenesis positive regulation of cellular process mitochondrion organization regulation of biological process DNA-templated DNA replication biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of organelle organization organelle organization DNA replication positive regulation of DNA metabolic process mitochondrial DNA replication regulation of mitochondrion organization regulation of DNA-templated DNA replication positive regulation of DNA-templated DNA replication metabolic process regulation of mitochondrial DNA replication macromolecule metabolic process regulation of metabolic process regulation of mitochondrial DNA metabolic process regulation of DNA metabolic process regulation of DNA replication catabolic process macromolecule catabolic process nucleobase-containing compound catabolic process DNA catabolic process nucleic acid catabolic process response to decreased oxygen levels cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus response to hypoxia response to chemical response to oxygen levels response to abiotic stimulus response to antibiotic homeostatic process response to oxygen-containing compound cellular response to glucose stimulus intracellular glucose homeostasis cellular response to oxygen-containing compound response to hexose cellular response to carbohydrate stimulus cellular homeostasis response to monosaccharide response to carbohydrate chemical homeostasis response to glucose glucose homeostasis carbohydrate homeostasis cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus mitochondrial DNA catabolic process positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death response to oxidative stress cellular response to oxidative stress cellular response to chemical stress developmental process multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development anatomical structure development embryo development in utero embryonic development cellular response to metal ion response to metal ion cellular response to calcium ion response to calcium ion regulation of DNA catabolic process execution phase of apoptosis positive regulation of DNA catabolic process apoptotic nuclear changes regulation of apoptotic DNA fragmentation cellular component disassembly positive regulation of apoptotic DNA fragmentation regulation of catabolic process positive regulation of catabolic process apoptotic DNA fragmentation cellular component disassembly involved in execution phase of apoptosis response to mechanical stimulus response to external stimulus regulation of hydrogen peroxide-mediated programmed cell death positive regulation of hydrogen peroxide-mediated programmed cell death programmed cell death in response to reactive oxygen species cellular response to reactive oxygen species hydrogen peroxide-mediated programmed cell death response to reactive oxygen species negative regulation of signaling signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction negative regulation of cell communication intracellular signal transduction cell communication negative regulation of TOR signaling regulation of intracellular signal transduction negative regulation of cellular process signal transduction TOR signaling regulation of signaling regulation of TOR signaling negative regulation of response to stimulus negative regulation of signal transduction regulation of response to stimulus regulation of cell communication positive regulation of autophagy autophagy regulation of autophagy process utilizing autophagic mechanism response to lipid response to estradiol response to peptide response to cytokine response to tumor necrosis factor	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle somatodendritic compartment cell body perikaryon neuronal cell body perinuclear region of cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR018524	DNA/RNA non-specific endonuclease, active site	Active Site
A, B, C, D	IPR044929	DNA/RNA non-specific endonuclease superfamily	Homologous Superfamily
A, B, C, D	IPR020821	ENPP1-3/EXOG-like, endonuclease/phosphodiesterase domain	Domain
A, B, C, D	IPR044925	His-Me finger superfamily	Homologous Superfamily
A, B, C, D	IPR040255	Non-specific endonuclease	Family
A, B, C, D	IPR001604	DNA/RNA non-specific endonuclease/pyrophosphatase/phosphodiesterase 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.