2YPD | pdb_00002ypd

Crystal structure of the Jumonji domain of human Jumonji domain containing 1C protein

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d2ypdb1	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2ypdb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2ypda1	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2ypda2	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e2ypdB1	A: Rubredoxin-like	X: Rubredoxin-related	H: Rubredoxin-related	T: Peptidase_M99_C	F:	ECOD (20:10:01)
A		e2ypdA1	A: Immunoglobulin-like beta-sandwich	X: Immunoglobulin-related	H: PEBP-like	T: Myosin_head	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (4.3.0)
A	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02373	JmjC domain, hydroxylase (JmjC)	JmjC domain, hydroxylase	The JmjC domain belongs to the Cupin superfamily [3]. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the ...	The JmjC domain belongs to the Cupin superfamily [3]. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	PROBABLE JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROT EIN 2C	DNA binding binding chromatin binding nucleic acid binding chromatin DNA binding transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding nuclear thyroid hormone receptor binding protein binding DNA binding binding chromatin binding nucleic acid binding chromatin DNA binding transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding nuclear thyroid hormone receptor binding protein binding DNA-binding transcription factor binding oxidoreductase activity catalytic activity dioxygenase activity catalytic activity, acting on a protein protein demethylase activity histone H3K9 demethylase activity histone H3 demethylase activity histone modifying activity histone demethylase activity demethylase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding regulation of cellular process RNA metabolic process regulation of primary metabolic process multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process 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 cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen histone deacetylase complex intracellular organelle cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen histone deacetylase complex intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR054503	Lysine-specific demethylase 3A/B, tudor domain	Domain
A, B	IPR003347	JmjC domain	Domain
A, B	IPR054504	Lysine-specific demethylase 3B, PWWP domain	Domain
A, B	IPR045109	Lysine-specific demethylase LSDs-like	Family
A, B	IPR054294	Lysine-specific demethylase 3A/B-like, DUF7030	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q15652	juvenile idiopathic arthritis salivary gland adenoid cystic carcinoma adenoid cystic carcinoma gastric cancer interstitial lung disease large cell medulloblastoma 22q11 Deletion Syndrome malignant pancreatic neoplasm acute myeloid leukemia non-small cell lung carcinoma pancreatic ductal adenocarcinoma autism Pick disease breast carcinoma exocrine pancreatic carcinoma juvenile idiopathic arthritis salivary gland adenoid cystic carcinoma adenoid cystic carcinoma gastric cancer interstitial lung disease large cell medulloblastoma 22q11 Deletion Syndrome malignant pancreatic neoplasm acute myeloid leukemia non-small cell lung carcinoma pancreatic ductal adenocarcinoma autism Pick disease breast carcinoma exocrine pancreatic carcinoma gastric carcinoma lung cancer medulloblastoma oligodendroglioma atrial fibrillation pancreatic intraductal papillary-mucinous carcinoma pituitary cancer central nervous system germinoma diabetes mellitus gallbladder disease glioblastoma juvenile dermatomyositis malignant ependymoma 22q11.2 deletion syndrome metabolic syndrome X astrocytic tumor ovarian cancer atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia breast cancer rheumatoid arthritis cholelithiasis spina bifida DiGeorge syndrome

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.