1WYW | pdb_00001wyw

Crystal Structure of SUMO1-conjugated thymine DNA glycosylase

External Resource: Annotation

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1wywb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1wywa_	Alpha and beta proteins (a/b)	Uracil-DNA glycosylase-like	Uracil-DNA glycosylase-like	Mug-like	G/T mismatch-specific thymine DNA glycosylase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Ubiquitin-like	8043414	3000157	SCOP2B (2022-06-29)
A	SCOP2 Family	Mug-like	8020074	4003607	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Uracil-DNA glycosylase-like	8032454	3001106	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)
B		e1wywB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
A		e1wywA1	A: Globin-like	X: Globin-like	H: Globin-like	T: C1-set	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
A	3.40.470.10	Alpha Beta	3-Layer(aba) Sandwich	Uracil-DNA Glycosylase, subunit E	Uracil-DNA glycosylase-like domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF11976	Ubiquitin-2 like Rad60 SUMO-like (Rad60-SLD)	Ubiquitin-2 like Rad60 SUMO-like	-	Family
A	PF03167	Uracil DNA glycosylase superfamily (UDG)	Uracil DNA glycosylase superfamily		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Ubiquitin-like protein SMT3C	protein binding binding small protein activating enzyme binding enzyme binding RNA binding nucleic acid binding ubiquitin-specific protease binding protease binding ubiquitin-like protein ligase binding transporter activator activity molecular function activator activity molecular function regulator activity transporter regulator activity protein tag activity protein binding binding small protein activating enzyme binding enzyme binding RNA binding nucleic acid binding ubiquitin-specific protease binding protease binding ubiquitin-like protein ligase binding transporter activator activity molecular function activator activity molecular function regulator activity transporter regulator activity protein tag activity molecular tag activity potassium channel regulator activity channel regulator activity ion channel regulator activity ubiquitin protein ligase binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process negative regulation of transcription initiation by RNA polymerase II regulation of DNA-templated transcription initiation transcription by RNA polymerase II transcription initiation at RNA polymerase II promoter regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II DNA-templated transcription initiation regulation of transcription initiation by RNA polymerase II negative regulation of DNA-templated transcription initiation heart process multicellular organismal process system process regulation of actin filament-based process regulation of heart contraction regulation of system process cardiac muscle contraction striated muscle contraction circulatory system process actin filament-based process regulation of multicellular organismal process blood circulation cardiac muscle cell contraction regulation of cardiac muscle contraction actin filament-based movement muscle contraction muscle system process regulation of muscle system process regulation of blood circulation regulation of striated muscle contraction regulation of actin filament-based movement regulation of muscle contraction regulation of cardiac muscle cell contraction actin-mediated cell contraction heart contraction negative regulation of protein transport regulation of localization establishment of protein localization cellular localization negative regulation of nucleocytoplasmic transport nucleocytoplasmic transport regulation of protein localization transport nuclear transport negative regulation of intracellular protein transport regulation of protein localization to nucleus negative regulation of transport negative regulation of protein import into nucleus localization import into nucleus regulation of protein import into nucleus establishment of localization in cell protein import into nucleus intracellular protein localization regulation of intracellular transport negative regulation of protein localization negative regulation of intracellular transport regulation of transport regulation of establishment of protein localization negative regulation of establishment of protein localization intracellular transport regulation of nucleocytoplasmic transport protein localization to nucleus regulation of protein transport establishment of localization negative regulation of protein localization to nucleus establishment of protein localization to organelle protein transport regulation of cellular localization macromolecule localization protein localization to organelle regulation of intracellular protein transport intracellular protein transport regulation of protein stability regulation of biological quality protein stabilization positive regulation of cellular component organization regulation of cellular component organization protein-containing complex organization positive regulation of cellular component biogenesis positive regulation of biological process regulation of cellular component biogenesis cellular component organization cellular component biogenesis positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly cellular component organization or biogenesis positive regulation of cellular process cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus protein localization to nuclear pore protein localization to nuclear envelope peptidyl-lysine modification protein sumoylation macromolecule modification peptidyl-amino acid modification protein metabolic process protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal positive regulation of proteasomal protein catabolic process catabolic process positive regulation of protein metabolic process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process macromolecule catabolic process positive regulation of metabolic process positive regulation of ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process positive regulation of macromolecule metabolic process regulation of protein metabolic process proteasomal protein catabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of protein catabolic process nuclear body organization nucleus organization organelle organization PML body organization regulation of action potential negative regulation of action potential action potential regulation of membrane potential DNA metabolic process DNA damage response DNA repair cellular response to metal ion cellular response to chemical stimulus response to metal ion response to chemical cellular response to cadmium ion response to cadmium ion regulation of calcium ion transport monoatomic ion transmembrane transport regulation of monoatomic ion transmembrane transport calcium ion transport metal ion transport regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport monoatomic ion transport monoatomic cation transport regulation of metal ion transport regulation of monoatomic ion transport transmembrane transport regulation of transmembrane transport regulation of monoatomic cation transmembrane transport calcium ion transmembrane transport developmental process anatomical structure development roof of mouth development	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen nuclear speck ribonucleoprotein granule nuclear body nucleoplasm supramolecular complex nuclear ribonucleoprotein granule nuclear membrane membrane endomembrane system organelle envelope nuclear envelope organelle membrane cytoplasm cytosol XY body sex chromosome chromosome presynapse presynaptic cytosol synapse cell junction cell periphery plasma membrane protein-containing complex nuclear protein-containing complex nuclear pore glutamatergic synapse nuclear stress granule PML body postsynapse postsynaptic cytosol
A	G/T mismatch-specific thymine DNA glycosylase	binding nucleic acid binding protein binding protein domain specific binding transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity uracil DNA N-glycosylase activity hydrolase activity, acting on glycosyl bonds deaminated base DNA N-glycosylase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid hydrolase activity binding nucleic acid binding protein binding protein domain specific binding transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity uracil DNA N-glycosylase activity hydrolase activity, acting on glycosyl bonds deaminated base DNA N-glycosylase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid hydrolase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity DNA binding damaged DNA binding mismatch base pair DNA N-glycosylase activity pyrimidine-specific mismatch base pair DNA N-glycosylase activity ion binding anion binding chloride ion binding small molecule binding cation binding magnesium ion binding metal ion binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding double-stranded DNA binding G/T mismatch-specific thymine-DNA glycosylase activity G/U mismatch-specific uracil-DNA glycosylase activity transcription factor binding DNA-binding transcription factor binding mismatched DNA binding SUMO binding ubiquitin-like protein binding kinase binding protein kinase C binding enzyme binding protein kinase binding alkali metal ion binding sodium ion binding	regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process cellular component organization regulation of gene expression biosynthetic process chromatin organization chromatin remodeling cellular process regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process cellular component organization regulation of gene expression biosynthetic process chromatin organization chromatin remodeling cellular process regulation of macromolecule biosynthetic process metabolic process cellular component organization or biogenesis macromolecule metabolic process regulation of metabolic process cellular response to stimulus pyrimidine deoxyribonucleotide catabolic process deoxyribonucleotide catabolic process catabolic process response to stimulus pyrimidine deoxyribonucleotide metabolic process pyrimidine-containing compound catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process deoxyribose phosphate catabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process pyrimidine nucleotide catabolic process base-excision repair DNA modification cellular response to stress deoxyribonucleotide metabolic process response to stress nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process depyrimidination nucleotide catabolic process DNA repair nucleoside phosphate metabolic process carbohydrate derivative catabolic process pyrimidine-containing compound metabolic process 2'-deoxyribonucleotide metabolic process primary metabolic process DNA metabolic process nucleotide metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process DNA damage response organophosphate metabolic process macromolecule modification base-excision repair, AP site formation developmental process multicellular organismal process regulation of embryonic development regulation of multicellular organismal development regulation of developmental process embryo development multicellular organism development anatomical structure development regulation of multicellular organismal process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process nucleobase-containing compound biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process chromosomal 5-methylcytosine DNA demethylation, oxidation pathway positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process chromosomal 5-methylcytosine DNA demethylation pathway positive regulation of gene expression	cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen intracellular membraneless organelle nuclear body membraneless organelle PML body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR046332	Small ubiquitin-related modifier 1, Ubl domain	Domain
B	IPR000626	Ubiquitin-like domain	Domain
B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B	IPR022617	Rad60/SUMO-like domain	Domain
A	IPR036895	Uracil-DNA glycosylase-like domain superfamily	Homologous Superfamily
A	IPR003310	G/T mismatch-specific thymine DNA glycosylasee TDG-like, eukaryotes	Family
A	IPR005122	Uracil-DNA glycosylase-like	Domain
A	IPR015637	Uracil DNA glycosylase family 2	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P63165	orofacial cleft 10 cleft palate Neoplasm Invasiveness cleft lip pancreatic intraductal papillary-mucinous neoplasm
A	Pharos: Q13569	atypical teratoid rhabdoid tumor invasive ductal breast carcinoma lymphoplasmacytic lymphoma Pick disease progressive supranuclear palsy dermatomyositis large cell medulloblastoma medulloblastoma plasma cell myeloma glioblastoma lung cancer osteosarcoma primitive neuroectodermal tumor

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.