7AO9

Structure of the core MTA1/HDAC1/MBD2 NURD deacetylase complex

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000122	biological_process	negative regulation of transcription by RNA polymerase II
A	0000978	molecular_function	RNA polymerase II cis-regulatory region sequence-specific DNA binding
A	0003677	molecular_function	DNA binding
A	0003682	molecular_function	chromatin binding
A	0003713	molecular_function	transcription coactivator activity
A	0003714	molecular_function	transcription corepressor activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005635	cellular_component	nuclear envelope
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0005856	cellular_component	cytoskeleton
A	0005874	cellular_component	microtubule
A	0006302	biological_process	double-strand break repair
A	0006338	biological_process	chromatin remodeling
A	0006351	biological_process	DNA-templated transcription
A	0006355	biological_process	regulation of DNA-templated transcription
A	0007165	biological_process	signal transduction
A	0008270	molecular_function	zinc ion binding
A	0010212	biological_process	response to ionizing radiation
A	0016581	cellular_component	NuRD complex
A	0032922	biological_process	circadian regulation of gene expression
A	0042659	biological_process	regulation of cell fate specification
A	0042826	molecular_function	histone deacetylase binding
A	0043153	biological_process	entrainment of circadian clock by photoperiod
A	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
A	0043565	molecular_function	sequence-specific DNA binding
A	0045475	biological_process	locomotor rhythm
A	0045814	biological_process	negative regulation of gene expression, epigenetic
A	0045892	biological_process	negative regulation of DNA-templated transcription
A	0045893	biological_process	positive regulation of DNA-templated transcription
A	0046872	molecular_function	metal ion binding
A	0048511	biological_process	rhythmic process
A	0061629	molecular_function	RNA polymerase II-specific DNA-binding transcription factor binding
A	1902499	biological_process	positive regulation of protein autoubiquitination
A	2000736	biological_process	regulation of stem cell differentiation
B	0000118	cellular_component	histone deacetylase complex
B	0000122	biological_process	negative regulation of transcription by RNA polymerase II
B	0000785	cellular_component	chromatin
B	0000792	cellular_component	heterochromatin
B	0000976	molecular_function	transcription cis-regulatory region binding
B	0000978	molecular_function	RNA polymerase II cis-regulatory region sequence-specific DNA binding
B	0000979	molecular_function	RNA polymerase II core promoter sequence-specific DNA binding
B	0001046	molecular_function	core promoter sequence-specific DNA binding
B	0001222	molecular_function	transcription corepressor binding
B	0002039	molecular_function	p53 binding
B	0003677	molecular_function	DNA binding
B	0003682	molecular_function	chromatin binding
B	0003714	molecular_function	transcription corepressor activity
B	0004407	molecular_function	histone deacetylase activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005667	cellular_component	transcription regulator complex
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006325	biological_process	chromatin organization
B	0006338	biological_process	chromatin remodeling
B	0006346	biological_process	DNA methylation-dependent constitutive heterochromatin formation
B	0006351	biological_process	DNA-templated transcription
B	0006357	biological_process	regulation of transcription by RNA polymerase II
B	0007623	biological_process	circadian rhythm
B	0008284	biological_process	positive regulation of cell population proliferation
B	0009913	biological_process	epidermal cell differentiation
B	0010628	biological_process	positive regulation of gene expression
B	0010629	biological_process	negative regulation of gene expression
B	0010832	biological_process	negative regulation of myotube differentiation
B	0016581	cellular_component	NuRD complex
B	0016787	molecular_function	hydrolase activity
B	0016811	molecular_function	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
B	0017053	cellular_component	transcription repressor complex
B	0019899	molecular_function	enzyme binding
B	0030336	biological_process	negative regulation of cell migration
B	0030512	biological_process	negative regulation of transforming growth factor beta receptor signaling pathway
B	0031492	molecular_function	nucleosomal DNA binding
B	0031507	biological_process	heterochromatin formation
B	0032922	biological_process	circadian regulation of gene expression
B	0032991	cellular_component	protein-containing complex
B	0033148	biological_process	positive regulation of intracellular estrogen receptor signaling pathway
B	0033558	molecular_function	protein lysine deacetylase activity
B	0035851	molecular_function	Krueppel-associated box domain binding
B	0036120	biological_process	cellular response to platelet-derived growth factor stimulus
B	0042475	biological_process	odontogenesis of dentin-containing tooth
B	0042659	biological_process	regulation of cell fate specification
B	0042733	biological_process	embryonic digit morphogenesis
B	0042826	molecular_function	histone deacetylase binding
B	0043025	cellular_component	neuronal cell body
B	0043066	biological_process	negative regulation of apoptotic process
B	0043922	biological_process	host-mediated suppression of viral transcription
B	0045814	biological_process	negative regulation of gene expression, epigenetic
B	0045892	biological_process	negative regulation of DNA-templated transcription
B	0045893	biological_process	positive regulation of DNA-templated transcription
B	0045944	biological_process	positive regulation of transcription by RNA polymerase II
B	0045995	biological_process	regulation of embryonic development
B	0046872	molecular_function	metal ion binding
B	0048511	biological_process	rhythmic process
B	0048661	biological_process	positive regulation of smooth muscle cell proliferation
B	0051059	molecular_function	NF-kappaB binding
B	0060766	biological_process	negative regulation of androgen receptor signaling pathway
B	0060789	biological_process	hair follicle placode formation
B	0061029	biological_process	eyelid development in camera-type eye
B	0061198	biological_process	fungiform papilla formation
B	0061629	molecular_function	RNA polymerase II-specific DNA-binding transcription factor binding
B	0070822	cellular_component	Sin3-type complex
B	0070888	molecular_function	E-box binding
B	0090090	biological_process	negative regulation of canonical Wnt signaling pathway
B	0140297	molecular_function	DNA-binding transcription factor binding
B	0141221	molecular_function	histone deacetylase activity, hydrolytic mechanism
B	0160008	molecular_function	protein decrotonylase activity
B	0160009	molecular_function	histone decrotonylase activity
B	0160216	molecular_function	protein lysine delactylase activity
B	1902455	biological_process	negative regulation of stem cell population maintenance
B	1902459	biological_process	positive regulation of stem cell population maintenance
B	1990841	molecular_function	promoter-specific chromatin binding
B	1990904	cellular_component	ribonucleoprotein complex
B	2000736	biological_process	regulation of stem cell differentiation
C	0000118	cellular_component	histone deacetylase complex
C	0000122	biological_process	negative regulation of transcription by RNA polymerase II
C	0000785	cellular_component	chromatin
C	0000792	cellular_component	heterochromatin
C	0003229	biological_process	ventricular cardiac muscle tissue development
C	0003677	molecular_function	DNA binding
C	0003682	molecular_function	chromatin binding
C	0003696	molecular_function	satellite DNA binding
C	0003729	molecular_function	mRNA binding
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005694	cellular_component	chromosome
C	0005737	cellular_component	cytoplasm
C	0006338	biological_process	chromatin remodeling
C	0006346	biological_process	DNA methylation-dependent constitutive heterochromatin formation
C	0006351	biological_process	DNA-templated transcription
C	0006357	biological_process	regulation of transcription by RNA polymerase II
C	0008327	molecular_function	methyl-CpG binding
C	0009612	biological_process	response to mechanical stimulus
C	0016581	cellular_component	NuRD complex
C	0019904	molecular_function	protein domain specific binding
C	0031492	molecular_function	nucleosomal DNA binding
C	0031667	biological_process	response to nutrient levels
C	0032355	biological_process	response to estradiol
C	0032991	cellular_component	protein-containing complex
C	0035197	molecular_function	siRNA binding
C	0040029	biological_process	epigenetic regulation of gene expression
C	0042711	biological_process	maternal behavior
C	0045892	biological_process	negative regulation of DNA-templated transcription
C	0045893	biological_process	positive regulation of DNA-templated transcription
C	0048568	biological_process	embryonic organ development
C	0060090	molecular_function	molecular adaptor activity
C	0070742	molecular_function	C2H2 zinc finger domain binding
C	1903925	biological_process	response to bisphenol A
C	1904015	biological_process	cellular response to serotonin
D	0000122	biological_process	negative regulation of transcription by RNA polymerase II
D	0000978	molecular_function	RNA polymerase II cis-regulatory region sequence-specific DNA binding
D	0003677	molecular_function	DNA binding
D	0003682	molecular_function	chromatin binding
D	0003713	molecular_function	transcription coactivator activity
D	0003714	molecular_function	transcription corepressor activity
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005635	cellular_component	nuclear envelope
D	0005654	cellular_component	nucleoplasm
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0005856	cellular_component	cytoskeleton
D	0005874	cellular_component	microtubule
D	0006302	biological_process	double-strand break repair
D	0006338	biological_process	chromatin remodeling
D	0006351	biological_process	DNA-templated transcription
D	0006355	biological_process	regulation of DNA-templated transcription
D	0007165	biological_process	signal transduction
D	0008270	molecular_function	zinc ion binding
D	0010212	biological_process	response to ionizing radiation
D	0016581	cellular_component	NuRD complex
D	0032922	biological_process	circadian regulation of gene expression
D	0042659	biological_process	regulation of cell fate specification
D	0042826	molecular_function	histone deacetylase binding
D	0043153	biological_process	entrainment of circadian clock by photoperiod
D	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
D	0043565	molecular_function	sequence-specific DNA binding
D	0045475	biological_process	locomotor rhythm
D	0045814	biological_process	negative regulation of gene expression, epigenetic
D	0045892	biological_process	negative regulation of DNA-templated transcription
D	0045893	biological_process	positive regulation of DNA-templated transcription
D	0046872	molecular_function	metal ion binding
D	0048511	biological_process	rhythmic process
D	0061629	molecular_function	RNA polymerase II-specific DNA-binding transcription factor binding
D	1902499	biological_process	positive regulation of protein autoubiquitination
D	2000736	biological_process	regulation of stem cell differentiation
E	0000118	cellular_component	histone deacetylase complex
E	0000122	biological_process	negative regulation of transcription by RNA polymerase II
E	0000785	cellular_component	chromatin
E	0000792	cellular_component	heterochromatin
E	0000976	molecular_function	transcription cis-regulatory region binding
E	0000978	molecular_function	RNA polymerase II cis-regulatory region sequence-specific DNA binding
E	0000979	molecular_function	RNA polymerase II core promoter sequence-specific DNA binding
E	0001046	molecular_function	core promoter sequence-specific DNA binding
E	0001222	molecular_function	transcription corepressor binding
E	0002039	molecular_function	p53 binding
E	0003677	molecular_function	DNA binding
E	0003682	molecular_function	chromatin binding
E	0003714	molecular_function	transcription corepressor activity
E	0004407	molecular_function	histone deacetylase activity
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005667	cellular_component	transcription regulator complex
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0006325	biological_process	chromatin organization
E	0006338	biological_process	chromatin remodeling
E	0006346	biological_process	DNA methylation-dependent constitutive heterochromatin formation
E	0006351	biological_process	DNA-templated transcription
E	0006357	biological_process	regulation of transcription by RNA polymerase II
E	0007623	biological_process	circadian rhythm
E	0008284	biological_process	positive regulation of cell population proliferation
E	0009913	biological_process	epidermal cell differentiation
E	0010628	biological_process	positive regulation of gene expression
E	0010629	biological_process	negative regulation of gene expression
E	0010832	biological_process	negative regulation of myotube differentiation
E	0016581	cellular_component	NuRD complex
E	0016787	molecular_function	hydrolase activity
E	0016811	molecular_function	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
E	0017053	cellular_component	transcription repressor complex
E	0019899	molecular_function	enzyme binding
E	0030336	biological_process	negative regulation of cell migration
E	0030512	biological_process	negative regulation of transforming growth factor beta receptor signaling pathway
E	0031492	molecular_function	nucleosomal DNA binding
E	0031507	biological_process	heterochromatin formation
E	0032922	biological_process	circadian regulation of gene expression
E	0032991	cellular_component	protein-containing complex
E	0033148	biological_process	positive regulation of intracellular estrogen receptor signaling pathway
E	0033558	molecular_function	protein lysine deacetylase activity
E	0035851	molecular_function	Krueppel-associated box domain binding
E	0036120	biological_process	cellular response to platelet-derived growth factor stimulus
E	0042475	biological_process	odontogenesis of dentin-containing tooth
E	0042659	biological_process	regulation of cell fate specification
E	0042733	biological_process	embryonic digit morphogenesis
E	0042826	molecular_function	histone deacetylase binding
E	0043025	cellular_component	neuronal cell body
E	0043066	biological_process	negative regulation of apoptotic process
E	0043922	biological_process	host-mediated suppression of viral transcription
E	0045814	biological_process	negative regulation of gene expression, epigenetic
E	0045892	biological_process	negative regulation of DNA-templated transcription
E	0045893	biological_process	positive regulation of DNA-templated transcription
E	0045944	biological_process	positive regulation of transcription by RNA polymerase II
E	0045995	biological_process	regulation of embryonic development
E	0046872	molecular_function	metal ion binding
E	0048511	biological_process	rhythmic process
E	0048661	biological_process	positive regulation of smooth muscle cell proliferation
E	0051059	molecular_function	NF-kappaB binding
E	0060766	biological_process	negative regulation of androgen receptor signaling pathway
E	0060789	biological_process	hair follicle placode formation
E	0061029	biological_process	eyelid development in camera-type eye
E	0061198	biological_process	fungiform papilla formation
E	0061629	molecular_function	RNA polymerase II-specific DNA-binding transcription factor binding
E	0070822	cellular_component	Sin3-type complex
E	0070888	molecular_function	E-box binding
E	0090090	biological_process	negative regulation of canonical Wnt signaling pathway
E	0140297	molecular_function	DNA-binding transcription factor binding
E	0141221	molecular_function	histone deacetylase activity, hydrolytic mechanism
E	0160008	molecular_function	protein decrotonylase activity
E	0160009	molecular_function	histone decrotonylase activity
E	0160216	molecular_function	protein lysine delactylase activity
E	1902455	biological_process	negative regulation of stem cell population maintenance
E	1902459	biological_process	positive regulation of stem cell population maintenance
E	1990841	molecular_function	promoter-specific chromatin binding
E	1990904	cellular_component	ribonucleoprotein complex
E	2000736	biological_process	regulation of stem cell differentiation

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	104
Details	Domain: {"description":"SANT","evidences":[{"source":"PROSITE-ProRule","id":"PRU00624","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"19805145","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	624
Details	Region: {"description":"Histone deacetylase"}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	Active site: {"evidences":[{"source":"PubMed","id":"19182791","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"28497810","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"O15379","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine; alternate","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	4
Details	Modified residue: {"description":"S-nitrosocysteine","evidences":[{"source":"UniProtKB","id":"P70288","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate","evidences":[{"source":"UniProtKB","id":"Q92769","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---