4OFA

Structural basis for thymine glycosylase activity on T:O6-methylG mismatch by methyl-CpG binding domain protein 4: Implications for roles of Arg468 in mismatch recognition and catalysis

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Mismatch glycosylase	8089627	4001144	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DNA-glycosylase	8089628	3000905	SCOP2 (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	HhH-GPD	e4ofaA1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: DNA-glycosylase	F: HhH-GPD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.340.30	Mainly Alpha	Orthogonal Bundle	Endonuclease III	domain 1	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Methyl-CpG-binding domain protein 4	DNA binding binding organic cyclic compound binding nucleic acid binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding satellite DNA binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid DNA binding binding organic cyclic compound binding nucleic acid binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding satellite DNA binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity DNA nuclease activity hydrolase activity, acting on glycosyl bonds DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds mismatch base pair DNA N-glycosylase activity pyrimidine-specific mismatch base pair DNA N-glycosylase activity	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair deoxyribonucleotide catabolic process pyrimidine deoxyribonucleotide metabolic process pyrimidine-containing compound catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process pyrimidine nucleotide metabolic process DNA modification phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process organonitrogen compound catabolic process pyrimidine-containing compound metabolic process cellular metabolic process nucleotide metabolic process nucleobase-containing compound catabolic process macromolecule modification base-excision repair, AP site formation pyrimidine deoxyribonucleotide catabolic process catabolic process deoxyribose phosphate catabolic process pyrimidine nucleotide catabolic process base-excision repair deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process depyrimidination nucleotide catabolic process carbohydrate derivative catabolic process organonitrogen compound metabolic process 2'-deoxyribonucleotide metabolic process deoxyribose phosphate metabolic process organic cyclic compound catabolic process organophosphate metabolic process organic substance catabolic process response to organic substance response to lipid response to chemical response to estradiol response to oxygen-containing compound response to organic cyclic compound	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
B [auth C]	12-mer DNA(T)	-	-	-
C [auth D]	12-mer DNA(G)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001739	Methyl-CpG DNA binding	Domain
A	IPR045138	Methyl-CpG binding protein MeCP2/MBD4	Family
A	IPR017352	Methyl-CpG-binding domain protein 4	Family
A	IPR011257	DNA glycosylase	Homologous Superfamily
A	IPR016177	DNA-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O95243	primitive neuroectodermal tumor ulcerative colitis astrocytic tumor dermatomyositis juvenile dermatomyositis malignant mesothelioma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma Pick disease psoriasis autism esophageal adenocarcinoma lymphoplasmacytic lymphoma medulloblastoma ovarian cancer primitive neuroectodermal tumor ulcerative colitis astrocytic tumor dermatomyositis juvenile dermatomyositis malignant mesothelioma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma Pick disease psoriasis autism esophageal adenocarcinoma lymphoplasmacytic lymphoma medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm plasma cell myeloma Sjogren syndrome Autistic Disorder glioblastoma malignant ependymoma oligodendroglioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.