MultifacetedProtDB - Bologna Biocomputing Group

EC number	EC number description
3.5.1.-	Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides;
3.5.1.98	Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides; histone deacetylase

Structure

PDB	Resolution (Å)	PDB name
4BKX	3.0	The structure of HDAC1 in complex with the dimeric ELM2-SANT domain of MTA1 from the NuRD complex
5ICN	3.3	HDAC1:MTA1 in complex with inositol-6-phosphate and a novel peptide inhibitor based on histone H4
6Z2J	4.0	The structure of the dimeric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex
6Z2K	4.5	The structure of the tetrameric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex
7AO8	4.5	Structure of the MTA1/HDAC1/MBD2 NURD deacetylase complex
7AO9	6.1	Structure of the core MTA1/HDAC1/MBD2 NURD deacetylase complex
7AOA	19.4	Structure of the extended MTA1/HDAC1/MBD2/RBBP4 NURD deacetylase complex
7SME	2.64	p107 pocket domain complexed with HDAC1 peptide

GO term

GO ontology	GO term	GO description
Biological Process	GO:0006346	DNA methylation-dependent heterochromatin formation
Biological Process	GO:0036120	cellular response to platelet-derived growth factor stimulus
Biological Process	GO:0006325	chromatin organization
Biological Process	GO:0006338	chromatin remodeling
Biological Process	GO:0032922	circadian regulation of gene expression
Biological Process	GO:0042733	embryonic digit morphogenesis
Biological Process	GO:0007492	endoderm development
Biological Process	GO:0009913	epidermal cell differentiation
Biological Process	GO:0061029	eyelid development in camera-type eye
Biological Process	GO:0061198	fungiform papilla formation
Biological Process	GO:0060789	hair follicle placode formation
Biological Process	GO:0021766	hippocampus development
Biological Process	GO:0070932	histone H3 deacetylation
Biological Process	GO:0070933	histone H4 deacetylation
Biological Process	GO:0016575	histone deacetylation
Biological Process	GO:0043922	negative regulation by host of viral transcription
Biological Process	GO:0045892	negative regulation of DNA-templated transcription
Biological Process	GO:0043124	negative regulation of I-kappaB kinase/NF-kappaB signaling
Biological Process	GO:0060766	negative regulation of androgen receptor signaling pathway
Biological Process	GO:0043066	negative regulation of apoptotic process
Biological Process	GO:0090090	negative regulation of canonical Wnt signaling pathway
Biological Process	GO:0030336	negative regulation of cell migration
Biological Process	GO:0010629	negative regulation of gene expression
Biological Process	GO:2001243	negative regulation of intrinsic apoptotic signaling pathway
Biological Process	GO:1902455	negative regulation of stem cell population maintenance
Biological Process	GO:0000122	negative regulation of transcription by RNA polymerase II
Biological Process	GO:0030512	negative regulation of transforming growth factor beta receptor signaling pathway
Biological Process	GO:0030182	neuron differentiation
Biological Process	GO:0042475	odontogenesis of dentin-containing tooth
Biological Process	GO:0048709	oligodendrocyte differentiation
Biological Process	GO:0045893	positive regulation of DNA-templated transcription
Biological Process	GO:0008284	positive regulation of cell population proliferation
Biological Process	GO:0010628	positive regulation of gene expression
Biological Process	GO:0048714	positive regulation of oligodendrocyte differentiation
Biological Process	GO:2000273	positive regulation of signaling receptor activity
Biological Process	GO:0048661	positive regulation of smooth muscle cell proliferation
Biological Process	GO:1902459	positive regulation of stem cell population maintenance
Biological Process	GO:0045944	positive regulation of transcription by RNA polymerase II
Biological Process	GO:0006476	protein deacetylation
Biological Process	GO:1900221	regulation of amyloid-beta clearance
Biological Process	GO:0042659	regulation of cell fate specification
Biological Process	GO:0052548	regulation of endopeptidase activity
Biological Process	GO:2000736	regulation of stem cell differentiation
Biological Process	GO:0006357	regulation of transcription by RNA polymerase II
Molecular Function	GO:0140297	DNA-binding transcription factor binding
Molecular Function	GO:0070888	E-box binding
Molecular Function	GO:0035851	Krueppel-associated box domain binding
Molecular Function	GO:0051059	NF-kappaB binding
Molecular Function	GO:0000978	RNA polymerase II cis-regulatory region sequence-specific DNA binding
Molecular Function	GO:0000979	RNA polymerase II core promoter sequence-specific DNA binding
Molecular Function	GO:0061629	RNA polymerase II-specific DNA-binding transcription factor binding
Molecular Function	GO:0001046	core promoter sequence-specific DNA binding
Molecular Function	GO:0019899	enzyme binding
Molecular Function	GO:0004407	histone deacetylase activity
Molecular Function	GO:0042826	histone deacetylase binding
Molecular Function	GO:0160009	histone decrotonylase activity
Molecular Function	GO:0002039	p53 binding
Molecular Function	GO:1990841	promoter-specific chromatin binding
Molecular Function	GO:0033558	protein lysine deacetylase activity
Molecular Function	GO:0003714	transcription corepressor activity
Molecular Function	GO:0001222	transcription corepressor binding
Cellular Component	GO:0016581	NuRD complex
Cellular Component	GO:0016580	Sin3 complex
Cellular Component	GO:0000785	chromatin
Cellular Component	GO:0005737	cytoplasm
Cellular Component	GO:0005829	cytosol
Cellular Component	GO:0000792	heterochromatin
Cellular Component	GO:0000118	histone deacetylase complex
Cellular Component	GO:0043025	neuronal cell body
Cellular Component	GO:0005654	nucleoplasm
Cellular Component	GO:0005634	nucleus
Cellular Component	GO:0032991	protein-containing complex
Cellular Component	GO:0017053	transcription repressor complex

InterPro / Pfam

InterPro	InterPro name
IPR000286	Histone deacetylase family
IPR003084	Histone deacetylase
IPR023696	Ureohydrolase domain superfamily
IPR023801	Histone deacetylase domain
IPR037138	Histone deacetylase domain superfamily

Pfam	Pfam name
PF00850	Histone deacetylase domain

Reactome

Reactome	Reactome Name	Node type	Reactome Root	Reactome Root Name
R-HSA-1362277	Transcription of E2F targets under negative control by DREAM complex	Leaf	R-HSA-1640170	Cell Cycle
R-HSA-1362300	Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1	Leaf	R-HSA-1640170	Cell Cycle
R-HSA-1538133	G0 and Early G1	Internal node	R-HSA-1640170	Cell Cycle
R-HSA-193670	p75NTR negatively regulates cell cycle via SC1	Leaf	R-HSA-162582	Signal Transduction
R-HSA-201722	Formation of the beta-catenin:TCF transactivating complex	Internal node	R-HSA-162582	Signal Transduction
R-HSA-2122947	NOTCH1 Intracellular Domain Regulates Transcription	Leaf	R-HSA-162582	Signal Transduction
R-HSA-2173795	Downregulation of SMAD2/3:SMAD4 transcriptional activity	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-2173796	SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-2644606	Constitutive Signaling by NOTCH1 PEST Domain Mutants	Leaf	R-HSA-1643685	Disease
R-HSA-2894862	Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants	Leaf	R-HSA-1643685	Disease
R-HSA-3214815	HDACs deacetylate histones	Leaf	R-HSA-4839726	Chromatin organization
R-HSA-350054	Notch-HLH transcription pathway	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-3769402	Deactivation of the beta-catenin transactivating complex	Leaf	R-HSA-162582	Signal Transduction
R-HSA-427389	ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-427413	NoRC negatively regulates rRNA expression	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-4551638	SUMOylation of chromatin organization proteins	Leaf	R-HSA-392499	Metabolism of proteins
R-HSA-4641265	Repression of WNT target genes	Leaf	R-HSA-162582	Signal Transduction
R-HSA-6804758	Regulation of TP53 Activity through Acetylation	Internal node	R-HSA-74160	Gene expression (Transcription)
R-HSA-69205	G1/S-Specific Transcription	Leaf	R-HSA-1640170	Cell Cycle
R-HSA-73762	RNA Polymerase I Transcription Initiation	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-8936459	RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-8943724	Regulation of PTEN gene transcription	Leaf	R-HSA-162582	Signal Transduction
R-HSA-9018519	Estrogen-dependent gene expression	Leaf	R-HSA-162582	Signal Transduction
R-HSA-9022538	Loss of MECP2 binding ability to 5mC-DNA	Leaf	R-HSA-1643685	Disease
R-HSA-9022692	Regulation of MECP2 expression and activity	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-9022699	MECP2 regulates neuronal receptors and channels	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-9022702	MECP2 regulates transcription of neuronal ligands	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-9615017	FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-9679191	Potential therapeutics for SARS	Leaf	R-HSA-1643685	Disease
R-HSA-9701898	STAT3 nuclear events downstream of ALK signaling	Leaf	R-HSA-162582	Signal Transduction
R-HSA-983231	Factors involved in megakaryocyte development and platelet production	Internal node	R-HSA-109582	Hemostasis

Subcellular location

Location	ECO term	Pubmed
Nucleus	ECO:0000269	PubMed:10846170
Nucleus	ECO:0000269	PubMed:20523938
Nucleus	ECO:0000269	PubMed:28977666
Nucleus	ECO:0000269	PubMed:33283408

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Tissue	Cell type	Expression level	Reliability
adipose tissue	adipocytes	Low	Enhanced
appendix	glandular cells	High	Enhanced
appendix	lymphoid tissue	High	Enhanced
bone marrow	hematopoietic cells	High	Enhanced
breast	glandular cells	Medium	Enhanced
breast	myoepithelial cells	Medium	Enhanced
bronchus	respiratory epithelial cells	High	Enhanced
caudate	glial cells	Low	Enhanced
cerebral cortex	endothelial cells	Low	Enhanced
cervix	glandular cells	Low	Enhanced
cervix	squamous epithelial cells	High	Enhanced
colon	endothelial cells	Low	Enhanced
colon	glandular cells	High	Enhanced
colon	peripheral nerve/ganglion	Low	Enhanced
duodenum	glandular cells	High	Enhanced
endometrium 1	cells in endometrial stroma	Medium	Enhanced
endometrium 1	glandular cells	Medium	Enhanced
endometrium 2	cells in endometrial stroma	Medium	Enhanced
endometrium 2	glandular cells	Medium	Enhanced
epididymis	glandular cells	High	Enhanced
esophagus	squamous epithelial cells	High	Enhanced
fallopian tube	glandular cells	High	Enhanced
gallbladder	glandular cells	High	Enhanced
heart muscle	cardiomyocytes	Low	Enhanced
kidney	cells in glomeruli	Medium	Enhanced
kidney	cells in tubules	Medium	Enhanced
liver	cholangiocytes	Medium	Enhanced
liver	hepatocytes	Medium	Enhanced
lung	alveolar cells type I	Medium	Enhanced
lung	alveolar cells type II	Medium	Enhanced
lung	macrophages	Medium	Enhanced
lymph node	germinal center cells	Low	Enhanced
lymph node	non-germinal center cells	Medium	Enhanced
nasopharynx	respiratory epithelial cells	Medium	Enhanced
oral mucosa	squamous epithelial cells	High	Enhanced
ovary	ovarian stroma cells	Medium	Enhanced
pancreas	exocrine glandular cells	Medium	Enhanced
pancreas	pancreatic endocrine cells	Medium	Enhanced
parathyroid gland	glandular cells	Medium	Enhanced
placenta	decidual cells	High	Enhanced
placenta	trophoblastic cells	Medium	Enhanced
prostate	glandular cells	Medium	Enhanced
rectum	glandular cells	High	Enhanced
salivary gland	glandular cells	Medium	Enhanced
seminal vesicle	glandular cells	Medium	Enhanced
skin 1	Langerhans	Medium	Enhanced
skin 1	fibroblasts	Low	Enhanced
skin 1	keratinocytes	Medium	Enhanced
skin 1	melanocytes	Medium	Enhanced
skin 2	epidermal cells	Medium	Enhanced
small intestine	glandular cells	High	Enhanced
smooth muscle	smooth muscle cells	Medium	Enhanced
soft tissue 1	chondrocytes	Medium	Enhanced
soft tissue 1	fibroblasts	Medium	Enhanced
soft tissue 2	fibroblasts	Low	Enhanced
spleen	cells in red pulp	Medium	Enhanced
spleen	cells in white pulp	Medium	Enhanced
stomach 1	glandular cells	High	Enhanced
stomach 2	glandular cells	High	Enhanced
testis	Leydig cells	Medium	Enhanced
testis	preleptotene spermatocytes	Medium	Enhanced
testis	spermatogonia cells	High	Enhanced
thyroid gland	glandular cells	High	Enhanced
tonsil	germinal center cells	High	Enhanced
tonsil	non-germinal center cells	High	Enhanced
tonsil	squamous epithelial cells	High	Enhanced
urinary bladder	urothelial cells	High	Enhanced
vagina	squamous epithelial cells	Medium	Enhanced

Summary of Q13547

Gene: HDAC1, RPD3L1
Protein: Histone deacetylase 1

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Summary of Q13547

Gene: HDAC1, RPD3L1 Protein: Histone deacetylase 1

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Gene: HDAC1, RPD3L1
Protein: Histone deacetylase 1