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Information on EC 3.5.1.98 - histone deacetylase

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EC Tree
     3 Hydrolases
         3.5 Acting on carbon-nitrogen bonds, other than peptide bonds
             3.5.1 In linear amides
                3.5.1.98 histone deacetylase
IUBMB Comments
A class of enzymes that remove acetyl groups from N6-acetyl-lysine residues on a histone. The reaction of this enzyme is opposite to that of EC 2.3.1.48, histone acetyltransferase. Histone deacetylases (HDACs) can be organized into three classes, HDAC1, HDAC2 and HDAC3, depending on sequence similarity and domain organization. Histone acetylation plays an important role in regulation of gene expression. In eukaryotes, HDACs play a key role in the regulation of transcription and cell proliferation . May be identical to EC 3.5.1.17, acyl-lysine deacylase.
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UNIPROT: Q8WUI4
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Word Map
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
Reaction Schemes
hydrolysis of an N6-acetyl-lysine residue of a histone to yield a deacetylated histone
Synonyms
histone deacetylase, hdac1, hdac6, hdac2, hdac3, hdac4, hdac5, hdac8, hdac9, hdac7, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
class IIa HDAC
-
class IIa histone deacetylase
-
histone deacetylase 7
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
deacetylation
-
SYSTEMATIC NAME
IUBMB Comments
histone amidohydrolase
A class of enzymes that remove acetyl groups from N6-acetyl-lysine residues on a histone. The reaction of this enzyme is opposite to that of EC 2.3.1.48, histone acetyltransferase. Histone deacetylases (HDACs) can be organized into three classes, HDAC1, HDAC2 and HDAC3, depending on sequence similarity and domain organization. Histone acetylation plays an important role in regulation of gene expression. In eukaryotes, HDACs play a key role in the regulation of transcription and cell proliferation [4]. May be identical to EC 3.5.1.17, acyl-lysine deacylase.
CAS REGISTRY NUMBER
COMMENTARY hide
9076-57-7
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
Fluor de Lys HDAC substrate + H2O
?
show the reaction diagram
commercially available kit
-
-
?
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(2E)-N-hydroxy-3-[3-(phenylsulfamoyl)phenyl]prop-2-enamide
-
oxamflatin
-
suberoylanilide hydroxamic acid
SAHA
trichostatin A
TSA
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.013 - 0.017
Fluor de Lys HDAC substrate
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0002 - 1.1
Fluor de Lys HDAC substrate
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00002 - 0.0043
(2E)-N-hydroxy-3-[3-(phenylsulfamoyl)phenyl]prop-2-enamide
0.0036 - 0.553
LAQ824
0.00013 - 0.0154
LBH589
0.0026 - 0.098
oxamflatin
0.0003 - 0.113
suberoylanilide hydroxamic acid
0.00004 - 0.0003
trichostatin A
0.0008 - 0.225
tubacin
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
class I and class IIa histone deacetylases (HDACs) are overexpressed in non-type and basal human bladder cancer (BC) cell lines at the mRNA level, overview
Manually annotated by BRENDA team
additional information
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
shuttling of isoform HDAC7 between cytoplasm and nucleus. Catalytic activity of HDAC7 requires interaction with isoform HDAC3 in the nucleus
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
histone deacetylase 7 (HDAC7) controls the thymic effector programming of natural killer T (NKT) cells, and interference with this function contributes to tissue-specific autoimmunity. Gain of HDAC7 function in thymocytes blocks both negative selection and NKT development, and diverts Va14/Ja18 TCR transgenic thymocytes into a Tconv-like lineage. Conversely, HDAC7 deletion promotes thymocyte apoptosis and causes expansion of innate-effector cells, mechanisms, overview. A mutation in HDAC7 can create problems only for specific organs in the body. In humans, mutations in HDAC7 are also associated with autoimmune disorders of the digestive tract and liver. These include inflammatory bowel diseases such as ulcerative colitis or Crohn's disease. Alteration of HDAC7 function dysregulates thymic innate effector programming and interferes with iNKT development
metabolism
epigenetic modifications including DNA methylation and histone post-translational modifications are closely associated with bladder cancer initiation and development, some HDACs play roles in the tumorigenicity of bladder cancer, overview
physiological function
histone deacetylase 7 mediates tissue-specific autoimmunity via control of innate effector function in invariant natural killer T cells. HDAC7 binds transcription factor promyelocytic leukemia zinc finger protein (PLZF, ZBTB16) and modulates PLZF-dependent transcription. HDAC7 and many of its transcriptional targets are human risk loci for IBD and PSC, autoimmune diseases that strikingly resemble the disease observed in HDAC7 gain-of-function in mice. Association between HDAC7 and hepatobiliary autoimmunity. Tconv development is regulated by the class IIA histone deacetylase histone deacetylase 7 (HDAC7), a TCR signal-regulated corepressor abundantly expressed in thymocytes. The activity of HDAC7 is controlled by nuclear exclusion in response to phosphorylation of conserved serine residues in their N-terminal adapter domains. HDAC7 regulates the effector programming of NKT cells in a manner that mirrors the function of PLZF. HDAC7 and PLZF inversely regulate a shared innate effector gene network that is highly relevant to autoimmune disease. HDAC7 nuclear export licenses innate effector development. HDAC7 serves as a gatekeeper of this developmental fate decision in the thymus
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
HDAC7_HUMAN
952
0
102927
Swiss-Prot
Mitochondrion (Reliability: 5)
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phosphoprotein
in thymocytes, TCR stimulation results in HDAC7 phosphorylation and nuclear exclusion via protein kinase D
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
the crystal structures of the catalytic domain of HDAC7 and its complexes with suberoylanilide hydroxamic acid and trichostatin A are solved
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
H843A
mutant, constructed to assess the role of the active site His-843
H843F
mutant, constructed to assess the role of the active site His-843
H843Y
mutant, constructed to assess the role of the active site His-843
additional information
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
by affinity chromatography on a 5-ml HiTrap Chelating column charged with Ni2+ and by anion exchange chromatography on a Source 30Q column
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene HDAC7, histone deacetylase expression within in vitro and in vivo bladder cancer model systems, quantitative real-time PCR enzyme expression analysis, overview
residues 483 to 903 of isoform 1 of chHDAC7 are cloned into a modified pET28a vector for expression in Escherichia coli BL21DE3 Codon Plus RIL cells
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Fischle, W.; Dequiedt, F.; Fillion, M.; Hendzel, M.J.; Voelter, W.; Verdin, E.
Human HDAC7 histone deacetylase activity is associated with HDAC3 in vivo
J. Biol. Chem.
276
35826-35835
2001
Homo sapiens (Q8WUI4), Homo sapiens
Manually annotated by BRENDA team
Schuetz, A.; Min, J.; Allali-Hassani, A.; Schapira, M.; Shuen, M.; Loppnau, P.; Mazitschek, R.; Kwiatkowski, N.P.; Lewis, T.A.; Maglathin, R.L.; McLean, T.H.; Bochkarev, A.; Plotnikov, A.N.; Vedadi, M.; Arrowsmith, C.H.
Human HDAC7 harbors a class IIa histone deacetylase-specific zinc binding motif and cryptic deacetylase activity
J. Biol. Chem.
283
11355-11363
2008
Homo sapiens (Q8WUI4), Homo sapiens
Manually annotated by BRENDA team
Kasler, H.G.; Lee, I.S.; Lim, H.W.; Verdin, E.
Histone deacetylase 7 mediates tissue-specific autoimmunity via control of innate effector function in invariant natural killer T cells
eLife
7
e32109
2018
Mus musculus (Q8C2B3), Homo sapiens (Q8WUI4), Homo sapiens, Mus musculus C57BL/6 (Q8C2B3)
Manually annotated by BRENDA team
Buckwalter, J.M.; Chan, W.; Shuman, L.; Wildermuth, T.; Ellis-Mohl, J.; Walter, V.; Warrick, J.I.; Wu, X.R.; Kaag, M.; Raman, J.D.; DeGraff, D.J.
Characterization of histone deacetylase expression within in vitro and in vivo bladder cancer model systems
Int. J. Mol. Sci.
20
E2599
2019
Homo sapiens (P56524), Homo sapiens (Q8WUI4), Homo sapiens (Q9UKV0), Homo sapiens
Manually annotated by BRENDA team