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- PDB-5dc6: Crystal structure of D176N-Y306F HDAC8 in complex with a tetrapep... -

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Basic information

Entry
Database: PDB / ID: 5dc6
TitleCrystal structure of D176N-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 H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / histone H3K4 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / histone H4K12 deacetylase activity, hydrolytic mechanism / histone deacetylase / histone H3K9 deacetylase activity, hydrolytic mechanism / regulation of telomere maintenance ...histone decrotonylase activity / histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / histone H3K4 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / histone H4K12 deacetylase activity, hydrolytic mechanism / histone deacetylase / histone H3K9 deacetylase activity, hydrolytic mechanism / regulation of telomere maintenance / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / mitotic sister chromatid cohesion / histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway / histone deacetylase complex / negative regulation of protein ubiquitination / Hsp70 protein binding / Resolution of Sister Chromatid Cohesion / 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 / heterochromatin formation / chromatin organization / DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / 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: 1.553 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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 23, 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)88,58911
Polymers88,1044
Non-polymers4857
Water10,647591
1
A: Histone deacetylase 8
C: Fluor-de-Lys tetrapeptide assay substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2495
Polymers44,0522
Non-polymers1973
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-42 kcal/mol
Surface area14360 Å2
MethodPISA
2
B: Histone deacetylase 8
D: Fluor-de-Lys tetrapeptide assay substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3416
Polymers44,0522
Non-polymers2894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-43 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.332, 98.206, 104.281
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: 43215.008 Da / Num. of mol.: 2 / Mutation: D176N, 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, 598 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / 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: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris (pH 8.0), 13% (w/v) PEG 8000, and 4 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 20, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.55→49.103 Å / Num. obs: 122036 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.6
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.039 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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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: 1.553→49.103 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1663 6116 5.02 %
Rwork0.1467 --
obs0.1477 121931 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.553→49.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5744 0 22 591 6357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016400
X-RAY DIFFRACTIONf_angle_d1.2468743
X-RAY DIFFRACTIONf_dihedral_angle_d12.7332339
X-RAY DIFFRACTIONf_chiral_restr0.059931
X-RAY DIFFRACTIONf_plane_restr0.0071153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.553-1.57020.26771660.24033611X-RAY DIFFRACTION93
1.5702-1.58870.25192070.23373822X-RAY DIFFRACTION100
1.5887-1.60810.21382100.21923817X-RAY DIFFRACTION100
1.6081-1.62840.23312080.213799X-RAY DIFFRACTION100
1.6284-1.64990.23422070.20063822X-RAY DIFFRACTION100
1.6499-1.67250.23612250.19193793X-RAY DIFFRACTION100
1.6725-1.69640.22032030.19163838X-RAY DIFFRACTION100
1.6964-1.72170.23071740.18143883X-RAY DIFFRACTION100
1.7217-1.74860.20391940.17363854X-RAY DIFFRACTION100
1.7486-1.77730.18522040.16183826X-RAY DIFFRACTION100
1.7773-1.80790.17252240.15343828X-RAY DIFFRACTION100
1.8079-1.84080.16211840.15183826X-RAY DIFFRACTION100
1.8408-1.87620.18552170.14423831X-RAY DIFFRACTION100
1.8762-1.91450.172100.14023856X-RAY DIFFRACTION100
1.9145-1.95610.16541860.1443845X-RAY DIFFRACTION100
1.9561-2.00160.18242030.14873860X-RAY DIFFRACTION100
2.0016-2.05170.16152000.14453834X-RAY DIFFRACTION100
2.0517-2.10720.1932110.14373848X-RAY DIFFRACTION100
2.1072-2.16920.15771950.13853874X-RAY DIFFRACTION100
2.1692-2.23920.16011880.13763886X-RAY DIFFRACTION100
2.2392-2.31920.17452040.14073859X-RAY DIFFRACTION100
2.3192-2.41210.16392020.14253877X-RAY DIFFRACTION100
2.4121-2.52180.18372180.14353868X-RAY DIFFRACTION100
2.5218-2.65480.17522010.14733902X-RAY DIFFRACTION100
2.6548-2.82110.15332190.14553872X-RAY DIFFRACTION100
2.8211-3.03890.18181990.14723913X-RAY DIFFRACTION100
3.0389-3.34460.17392290.14253887X-RAY DIFFRACTION100
3.3446-3.82840.13922080.13383953X-RAY DIFFRACTION100
3.8284-4.82280.11932030.12113986X-RAY DIFFRACTION100
4.8228-49.12760.15732170.1524145X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.12740.0591-0.25252.0730.46411.06740.05050.20890.0741-0.2752-0.0213-0.2125-0.14820.0858-0.03270.2361-0.00880.04130.22350.03110.1979-1.1845-2.1915-9.0896
21.8292-0.3781-0.58811.45380.4711.73990.02010.2544-0.1402-0.1308-0.11560.09980.0497-0.19750.09830.15760.01120.00420.1599-0.02520.141-13.728-15.6511-7.0142
31.2758-0.8547-0.13691.3850.3931.2981-0.0578-0.0775-0.13860.11270.06360.00360.17310.0507-0.01170.15740.0067-0.0010.14480.00740.1754-5.7489-19.33019.2334
40.6742-0.1889-0.01311.4343-0.0450.7885-0.0339-0.08350.06470.11810.0309-0.2015-0.07080.1340.01010.145-0.0092-0.02120.1784-0.00810.1838-0.7693-2.88889.5266
50.998-0.141-0.23761.8829-0.67841.7058-0.0304-0.24330.09380.39870.1134-0.0044-0.08860.0442-0.0750.221-0.0114-0.03510.2125-0.02580.1542-6.7985-1.056417.6555
61.4638-0.26830.20842.3669-0.00981.5799-0.00330.1736-0.1031-0.24560.01150.17420.10760.086-0.00840.21890.0085-0.03290.2229-0.01680.1911-38.9110.8384-6.5714
71.16620.9434-0.42571.0848-0.07120.6938-0.01640.1522-0.0309-0.19950.07640.37590.0458-0.1822-0.0630.1951-0.0048-0.05820.2384-0.00970.2576-46.1072-2.2093-3.2999
82.20730.1849-0.24872.77960.24222.00650.0120.5480.1021-0.4789-0.08760.054-0.2525-0.11890.0230.31420.011-0.01930.28080.04650.2126-30.298718.38-12.3955
92.2075-0.17230.69011.3669-0.32471.4991-0.00090.3656-0.0111-0.199-0.0461-0.0416-0.07150.15490.04480.25040.008-0.02170.18770.00360.1593-30.002211.8235-8.2006
101.2903-0.2213-0.10661.5338-0.1271.2775-0.03810.0580.08250.01130.00350.1206-0.1462-0.10040.03590.18880.0309-0.01860.15820.00280.1707-36.893611.4875-0.1226
111.2545-0.38020.28111.7217-0.41082.3915-0.09810.0330.1383-0.04830.00680.2072-0.3438-0.15530.03410.23370.054-0.01930.17090.00440.2422-44.497120.01343.4499
120.9366-1.05550.23982.6254-0.40841.0408-0.1575-0.00360.08650.09120.08270.0149-0.2437-0.04190.05410.19620.0241-0.01410.1584-0.00720.1812-33.700617.626710.4444
131.4947-0.969-0.03841.85550.13491.3261-0.1056-0.13930.29850.08010.1096-0.1286-0.37980.03040.04850.26640.0001-0.03080.174-0.01450.1866-28.687120.476615.0984
141.0532-0.87870.26132.5357-0.42691.2009-0.0826-0.1372-0.0320.32530.05910.2063-0.1178-0.12410.02620.26820.05340.04160.2283-0.01280.1769-38.266710.541821.583
150.9909-0.3632-0.00121.18960.04951.0512-0.0698-0.12910.0090.13180.06460.1749-0.0407-0.1350.03110.17030.01570.03030.1840.00630.2039-40.48484.960212.2256
161.3209-0.21160.30622.52060.53331.6191-0.039-0.0441-0.07790.07160.00170.37340.164-0.22550.02230.1678-0.01960.01010.18850.00320.2141-43.5414-8.39256.201
170.78050.14180.31082.05160.77531.7931-0.0407-0.1483-0.00670.26820.1035-0.0596-0.0783-0.0068-0.04250.1910.01340.01990.21170.01470.1513-32.423.08221.1073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 156 )
3X-RAY DIFFRACTION3chain 'A' and (resid 157 through 225 )
4X-RAY DIFFRACTION4chain 'A' and (resid 226 through 336 )
5X-RAY DIFFRACTION5chain 'A' and (resid 337 through 376 )
6X-RAY DIFFRACTION6chain 'B' and (resid 14 through 36 )
7X-RAY DIFFRACTION7chain 'B' and (resid 37 through 63 )
8X-RAY DIFFRACTION8chain 'B' and (resid 64 through 85 )
9X-RAY DIFFRACTION9chain 'B' and (resid 86 through 127 )
10X-RAY DIFFRACTION10chain 'B' and (resid 128 through 156 )
11X-RAY DIFFRACTION11chain 'B' and (resid 157 through 176 )
12X-RAY DIFFRACTION12chain 'B' and (resid 177 through 202 )
13X-RAY DIFFRACTION13chain 'B' and (resid 203 through 225 )
14X-RAY DIFFRACTION14chain 'B' and (resid 226 through 255 )
15X-RAY DIFFRACTION15chain 'B' and (resid 256 through 307 )
16X-RAY DIFFRACTION16chain 'B' and (resid 308 through 336 )
17X-RAY DIFFRACTION17chain 'B' and (resid 337 through 377 )

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