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- PDB-5dc7: Crystal structure of D176A-Y306F HDAC8 in complex with a tetrapep... -

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Basic information

Entry
Database: PDB / ID: 5dc7
TitleCrystal structure of D176A-Y306F HDAC8 in complex with a tetrapeptide substrate
Components
  • Fluor-de-Lys tetrapeptide assay substrate
  • Histone deacetylase 8
KeywordsHYDROLASE / histone deacetylase 8 / arginase fold / deacetylase / enzyme-substrate complex
Function / homology
Function and homology information


histone decrotonylase activity / histone deacetylase / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / regulation of telomere maintenance / mitotic sister chromatid cohesion / histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway / histone deacetylase complex ...histone decrotonylase activity / histone deacetylase / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / regulation of telomere maintenance / mitotic sister chromatid cohesion / histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway / histone deacetylase complex / negative regulation of protein ubiquitination / Resolution of Sister Chromatid Cohesion / Hsp70 protein binding / epigenetic regulation of gene expression / HDACs deacetylate histones / Hsp90 protein binding / regulation of protein stability / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Separation of Sister Chromatids / chromatin organization / DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Histone deacetylase / Histone deacetylase domain / Arginase; Chain A / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Histone deacetylase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDecroos, C. / Lee, M.S. / Christianson, D.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49758 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM40602 United States
CitationJournal: Biochemistry / Year: 2016
Title: General Base-General Acid Catalysis in Human Histone Deacetylase 8.
Authors: Gantt, S.M. / Decroos, C. / Lee, M.S. / Gullett, L.E. / Bowman, C.M. / Christianson, D.W. / Fierke, C.A.
History
DepositionAug 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.5Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone deacetylase 8
B: Histone deacetylase 8
C: Fluor-de-Lys tetrapeptide assay substrate
D: Fluor-de-Lys tetrapeptide assay substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,59512
Polymers88,0184
Non-polymers5778
Water4,504250
1
A: Histone deacetylase 8
C: Fluor-de-Lys tetrapeptide assay substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2065
Polymers44,0092
Non-polymers1973
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-42 kcal/mol
Surface area14080 Å2
MethodPISA
2
B: Histone deacetylase 8
D: Fluor-de-Lys tetrapeptide assay substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3907
Polymers44,0092
Non-polymers3815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-44 kcal/mol
Surface area14210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.845, 97.748, 103.616
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Histone deacetylase 8 / HD8


Mass: 43171.984 Da / Num. of mol.: 2 / Mutation: D176A, Y306F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC8, HDACL1, CDA07 / Plasmid: pHD2-Xa-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BY41, histone deacetylase
#2: Protein/peptide Fluor-de-Lys tetrapeptide assay substrate


Mass: 836.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 258 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris (pH 8.0), 15% (w/v) PEG 10000, and 4 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.3→44.203 Å / Num. obs: 37434 / % possible obs: 99.1 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 15
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 8 % / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 2 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIXdev_1833refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EWF

3ewf


Resolution: 2.3→44.203 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.216 1872 5.01 %
Rwork0.1695 --
obs0.1718 37384 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→44.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5695 0 28 250 5973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035897
X-RAY DIFFRACTIONf_angle_d0.7328008
X-RAY DIFFRACTIONf_dihedral_angle_d12.8862092
X-RAY DIFFRACTIONf_chiral_restr0.027872
X-RAY DIFFRACTIONf_plane_restr0.0031024
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35950.34281340.26062632X-RAY DIFFRACTION96
2.3595-2.42890.33071490.23472644X-RAY DIFFRACTION99
2.4289-2.50730.27841430.21912696X-RAY DIFFRACTION99
2.5073-2.59690.28381300.20942701X-RAY DIFFRACTION99
2.5969-2.70090.24021410.19832707X-RAY DIFFRACTION99
2.7009-2.82380.27131420.20052696X-RAY DIFFRACTION99
2.8238-2.97260.25161590.1892694X-RAY DIFFRACTION99
2.9726-3.15880.23931550.17862715X-RAY DIFFRACTION99
3.1588-3.40260.22791410.17242728X-RAY DIFFRACTION99
3.4026-3.74490.18991400.15332769X-RAY DIFFRACTION100
3.7449-4.28640.1551360.13392776X-RAY DIFFRACTION100
4.2864-5.39890.18951510.14142808X-RAY DIFFRACTION100
5.3989-44.21160.17291510.15572946X-RAY DIFFRACTION100

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