8Q9R | pdb_00008q9r

Crystal structure of MADS-box/MEF2D N-terminal domain bound to dsDNA and HDAC9 deacetylase binding motif

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A], C [auth B], G [auth E], H [auth F]	PF00319	SRF-type transcription factor (DNA-binding and dimerisation domain) (SRF-TF)	SRF-type transcription factor (DNA-binding and dimerisation domain)		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth L], J [auth H]	MADS box dsDNA: TCTTATAAATAGT	-	-	-
D [auth K], I [auth G]	MADS box dsDNA: AACTATTTATAAGA	-	-	-
B [auth A], C [auth B], G [auth E], H [auth F]	MEF2D protein	DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity protein binding binding protein dimerization activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding	developmental process animal organ development anatomical structure development multicellular organism development multicellular organismal process nervous system development system development regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process developmental process animal organ development anatomical structure development multicellular organism development multicellular organismal process nervous system development system development regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
A [auth X], F [auth C]	Histone deacetylase 9 (HDAC9) binding motif peptide: EVKQKLQEFLLSKS	histone deacetylase binding protein binding binding enzyme binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein deacylase activity catalytic activity histone H4K16 deacetylase activity, hydrolytic mechanism hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides histone deacetylase binding protein binding binding enzyme binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein deacylase activity catalytic activity histone H4K16 deacetylase activity, hydrolytic mechanism hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds histone deacetylase activity histone H4K deacetylase activity histone deacetylase activity, hydrolytic mechanism histone modifying activity transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity histone H3K14 deacetylase activity, hydrolytic mechanism histone H3K deacetylase activity histone H3K9 deacetylase activity, hydrolytic mechanism kinase binding protein kinase C binding protein kinase binding cation binding ion binding metal ion binding small molecule 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 developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process leukocyte differentiation peptidyl-lysine deacetylation peptidyl-lysine modification macromolecule deacylation protein deacetylation protein deacylation macromolecule modification peptidyl-amino acid modification protein metabolic process protein modification process epigenetic regulation of gene expression cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis sterol homeostasis chemical homeostasis homeostatic process cholesterol homeostasis lipid homeostasis negative regulation of gene expression negative regulation of gene expression, epigenetic cytokine production regulation of cytokine production regulation of multicellular organismal process negative regulation of cytokine production negative regulation of multicellular organismal process regulation of developmental process regulation of cell differentiation regulation of striated muscle cell differentiation muscle cell differentiation muscle structure development regulation of muscle cell differentiation striated muscle cell differentiation response to stimulus defense response response to stress inflammatory response cellular response to stimulus cellular response to nitrogen compound response to endogenous stimulus response to peptide hormone response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical response to insulin cellular response to insulin stimulus cellular response to hormone stimulus transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II positive regulation of locomotion regulation of cell motility cell migration involved in sprouting angiogenesis regulation of blood vessel endothelial cell migration endothelial cell migration positive regulation of biological process angiogenesis positive regulation of cell migration tube morphogenesis positive regulation of cell motility regulation of cell migration blood vessel endothelial cell migration regulation of endothelial cell migration cell migration positive regulation of cell migration involved in sprouting angiogenesis cell motility locomotion positive regulation of cellular process blood vessel development blood vessel morphogenesis tube development regulation of cell migration involved in sprouting angiogenesis sprouting angiogenesis vasculature development positive regulation of blood vessel endothelial cell migration anatomical structure morphogenesis regulation of locomotion positive regulation of endothelial cell migration anatomical structure formation involved in morphogenesis skeletal muscle tissue development myotube differentiation striated muscle tissue development regulation of cell development skeletal muscle organ development striated muscle cell development regulation of skeletal muscle fiber development muscle cell development regulation of myotube differentiation muscle tissue development muscle organ development myotube cell development skeletal muscle fiber development tissue development	membrane-bounded organelle protein-containing complex histone methyltransferase complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm membrane-bounded organelle protein-containing complex histone methyltransferase complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle methyltransferase complex nuclear lumen transcription regulator complex cytoplasm histone deacetylase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A], C [auth B], G [auth E], H [auth F]	IPR022102	Holliday junction regulator protein family C-terminal	Domain
B [auth A], C [auth B], G [auth E], H [auth F]	IPR036879	Transcription factor, MADS-box superfamily	Homologous Superfamily
B [auth A], C [auth B], G [auth E], H [auth F]	IPR033896	MADS MEF2-like, N-terminal	Domain
B [auth A], C [auth B], G [auth E], H [auth F]	IPR002100	Transcription factor, MADS-box	Domain
A [auth X], F [auth C]	IPR023801	Histone deacetylase domain	Domain
A [auth X], F [auth C]	IPR000286	Histone deacetylase HDAC	Family
A [auth X], F [auth C]	IPR024643	Histone deacetylase, glutamine rich N-terminal domain	Domain
A [auth X], F [auth C]	IPR046949	Histone deacetylase 4/5/7/9	Family
A [auth X], F [auth C]	IPR037138	Histone deacetylase domain superfamily	Homologous Superfamily
A [auth X], F [auth C]	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth X], F [auth C]	Pharos: Q9UKV0	cerebrovascular disorder myocardial infarction osteoarthritis, hip peripheral arterial disease primitive neuroectodermal tumor Acute Cerebrovascular Accidents tuberculosis atypical teratoid rhabdoid tumor cystic fibrosis heart disease lung cancer malignant glioma medulloblastoma oligodendroglioma osteosarcoma cerebrovascular disorder myocardial infarction osteoarthritis, hip peripheral arterial disease primitive neuroectodermal tumor Acute Cerebrovascular Accidents tuberculosis atypical teratoid rhabdoid tumor cystic fibrosis heart disease lung cancer malignant glioma medulloblastoma oligodendroglioma osteosarcoma plasma cell myeloma pulmonary hypertension androgenetic alopecia depressive disorder interstitial cystitis lung carcinoma malignant mesothelioma osteoarthritis pancreatic intraductal papillary-mucinous neoplasm primary cutaneous T-cell lymphoma schizophrenia astrocytic tumor glioblastoma large cell medulloblastoma malignant ependymoma mature T-cell and NK-cell non-Hodgkin lymphoma

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.