7AO8

Structure of the 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	0006355	biological_process	regulation of DNA-templated transcription
A	0007165	biological_process	signal transduction
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	0043231	cellular_component	intracellular membrane-bounded organelle
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 heterochromatin formation
B	0006357	biological_process	regulation of transcription by RNA polymerase II
B	0006476	biological_process	protein deacetylation
B	0007492	biological_process	endoderm development
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	0017053	cellular_component	transcription repressor complex
B	0019899	molecular_function	enzyme binding
B	0021766	biological_process	hippocampus development
B	0030182	biological_process	neuron differentiation
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	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	0043124	biological_process	negative regulation of canonical NF-kappaB signal transduction
B	0043922	biological_process	negative regulation by host 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	0048511	biological_process	rhythmic process
B	0048661	biological_process	positive regulation of smooth muscle cell proliferation
B	0048709	biological_process	oligodendrocyte differentiation
B	0048714	biological_process	positive regulation of oligodendrocyte differentiation
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	0160008	molecular_function	protein decrotonylase activity
B	0160009	molecular_function	histone decrotonylase 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	2000273	biological_process	positive regulation of signaling receptor activity
B	2000736	biological_process	regulation of stem cell differentiation
B	2001243	biological_process	negative regulation of intrinsic apoptotic signaling pathway
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	0005829	cellular_component	cytosol
C	0006338	biological_process	chromatin remodeling
C	0006346	biological_process	DNA methylation-dependent heterochromatin formation
C	0008327	molecular_function	methyl-CpG binding
C	0009612	biological_process	response to mechanical stimulus
C	0014070	biological_process	response to organic cyclic compound
C	0016055	biological_process	Wnt signaling pathway
C	0016581	cellular_component	NuRD complex
C	0019904	molecular_function	protein domain specific binding
C	0030177	biological_process	positive regulation of Wnt signaling pathway
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	0042127	biological_process	regulation of cell population proliferation
C	0042711	biological_process	maternal behavior
C	0042802	molecular_function	identical protein binding
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	0065003	biological_process	protein-containing complex assembly
C	0070742	molecular_function	C2H2 zinc finger domain binding
C	0071407	biological_process	cellular response to organic cyclic compound
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	0006355	biological_process	regulation of DNA-templated transcription
D	0007165	biological_process	signal transduction
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	0043231	cellular_component	intracellular membrane-bounded organelle
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 heterochromatin formation
E	0006357	biological_process	regulation of transcription by RNA polymerase II
E	0006476	biological_process	protein deacetylation
E	0007492	biological_process	endoderm development
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	0017053	cellular_component	transcription repressor complex
E	0019899	molecular_function	enzyme binding
E	0021766	biological_process	hippocampus development
E	0030182	biological_process	neuron differentiation
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	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	0043124	biological_process	negative regulation of canonical NF-kappaB signal transduction
E	0043922	biological_process	negative regulation by host 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	0048511	biological_process	rhythmic process
E	0048661	biological_process	positive regulation of smooth muscle cell proliferation
E	0048709	biological_process	oligodendrocyte differentiation
E	0048714	biological_process	positive regulation of oligodendrocyte differentiation
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	0160008	molecular_function	protein decrotonylase activity
E	0160009	molecular_function	histone decrotonylase 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	2000273	biological_process	positive regulation of signaling receptor activity
E	2000736	biological_process	regulation of stem cell differentiation
E	2001243	biological_process	negative regulation of intrinsic apoptotic signaling pathway

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	ACT_SITE: ACT_SITE => ECO:0000269|PubMed:19182791, ECO:0000269|PubMed:28497810

Chain	Residue	Details
E	HIS141
B	HIS141

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	MOD_RES: N6-acetyllysine; alternate => ECO:0007744|PubMed:19608861

Chain	Residue	Details
E	LYS74
B	LYS74

---

site_id	SWS_FT_FI3
Number of Residues	2
Details	MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861

Chain	Residue	Details
E	LYS220
B	LYS220

---

site_id	SWS_FT_FI4
Number of Residues	4
Details	MOD_RES: S-nitrosocysteine => ECO:0000250|UniProtKB:P70288

Chain	Residue	Details
E	CYS261
E	CYS273
B	CYS261
B	CYS273

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:17487921, ECO:0007744|PubMed:18691976, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569

Chain	Residue	Details
E	SER393
B	SER393
A	SER522
A	SER576

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q92769

Chain	Residue	Details
E	SER406
B	SER406

---

site_id	SWS_FT_FI7
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163

Chain	Residue	Details
E	SER409
B	SER409

---

site_id	SWS_FT_FI8
Number of Residues	2
Details	MOD_RES: Phosphoserine; by CK2 => ECO:0000269|PubMed:11602581, ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18318008, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163

Chain	Residue	Details
E	SER421
B	SER421

---

site_id	SWS_FT_FI9
Number of Residues	2
Details	MOD_RES: Phosphoserine; by CK2 => ECO:0000269|PubMed:11602581, ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18318008, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163

Chain	Residue	Details
E	SER423
B	SER423

---

site_id	SWS_FT_FI10
Number of Residues	2
Details	MOD_RES: N6-methylated lysine; by EHMT2 => ECO:0000269|PubMed:18438403

Chain	Residue	Details
E	LYS432
B	LYS432

---

site_id	SWS_FT_FI11
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0000250|UniProtKB:Q92769

Chain	Residue	Details
E	LYS74
B	LYS74
A	LYS626

---

site_id	SWS_FT_FI12
Number of Residues	6
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733

Chain	Residue	Details
D	LYS509
E	LYS438
E	LYS480
B	LYS438
B	LYS480

---

site_id	SWS_FT_FI13
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:25218447, ECO:0007744|PubMed:25755297

Chain	Residue	Details
E	LYS444
B	LYS444

---

site_id	SWS_FT_FI14
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0000250|UniProtKB:Q92769

Chain	Residue	Details
E	LYS456
E	LYS473
B	LYS456
B	LYS473

---

site_id	SWS_FT_FI15
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25218447

Chain	Residue	Details
E	LYS457
B	LYS457

---

site_id	SWS_FT_FI16
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:25218447, ECO:0007744|PubMed:25755297, ECO:0007744|PubMed:25772364, ECO:0007744|PubMed:28112733

Chain	Residue	Details
E	LYS476
B	LYS476

---