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- PDB-9ckg: Crystal structure of SMYD2 active site mutant -

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Basic information

Entry
Database: PDB / ID: 9ckg
TitleCrystal structure of SMYD2 active site mutant
ComponentsN-lysine methyltransferase SMYD2
KeywordsTRANSFERASE / SMYD2 / PARP1 / protein lysine-methyltransferase / SET and MYND-containing protein
Function / homology
Function and homology information


lysine N-methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K4 trimethyltransferase activity / histone H3K36 methyltransferase activity / protein-lysine N-methyltransferase activity / regulation of DNA damage response, signal transduction by p53 class mediator / histone H3 methyltransferase activity / RNA polymerase II complex binding ...lysine N-methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K4 trimethyltransferase activity / histone H3K36 methyltransferase activity / protein-lysine N-methyltransferase activity / regulation of DNA damage response, signal transduction by p53 class mediator / histone H3 methyltransferase activity / RNA polymerase II complex binding / Transferases; Transferring one-carbon groups; Methyltransferases / regulation of signal transduction by p53 class mediator / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / p53 binding / heart development / negative regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
SMYD2, SET domain / : / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. ...SMYD2, SET domain / : / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
ETHANOL / DI(HYDROXYETHYL)ETHER / S-ADENOSYL-L-HOMOCYSTEINE / N-lysine methyltransferase SMYD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsSobota, J. / Zhang, Y. / Spellmon, N. / Perry, E. / Brunzelle, J. / Yang, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: Biorxiv / Year: 2024
Title: Structure of the SMYD2-PARP1 Complex Reveals Both Productive and Allosteric Modes of Peptide Binding.
Authors: Zhang, Y. / Alshammari, E. / Sobota, J. / Spellmon, N. / Perry, E. / Cao, T. / Mugunamalwaththa, T. / Smith, S. / Brunzelle, J. / Wu, G. / Stemmler, T. / Jin, J. / Li, C. / Yang, Z.
History
DepositionJul 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-lysine methyltransferase SMYD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,80910
Polymers49,6841
Non-polymers1,1259
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.822, 151.822, 53.377
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein N-lysine methyltransferase SMYD2 / HSKM-B / Histone methyltransferase SMYD2 / Lysine N-methyltransferase 3C / SET and MYND domain- ...HSKM-B / Histone methyltransferase SMYD2 / Lysine N-methyltransferase 3C / SET and MYND domain-containing protein 2


Mass: 49684.008 Da / Num. of mol.: 1 / Mutation: F184A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD2, KMT3C / Plasmid: pCDF-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9NRG4, Transferases; Transferring one-carbon groups; Methyltransferases, [histone H3]-lysine4 N-trimethyltransferase

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Non-polymers , 6 types, 9 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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Details

Has ligand of interestN
Has protein modificationN

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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: 3.1 Å3/Da / Density % sol: 60.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350, 100 mM Tris pH 7.5, 5% ethanol, 1 mM PARP1 peptide, and 0.6 mM AdoHcy

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.75→107.35 Å / Num. obs: 8636 / % possible obs: 89.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 87.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.053 / Rrim(I) all: 0.132 / Net I/σ(I): 9.3
Reflection shellResolution: 2.75→3.162 Å / Rmerge(I) obs: 1.013 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 8635 / CC1/2: 0.997 / Rpim(I) all: 0.455 / Rsym value: 1.113

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→48.01 Å / SU ML: 0.3375 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.3761
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2229 870 10.09 %
Rwork0.1935 7756 -
obs0.1965 8626 53.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.61 Å2
Refinement stepCycle: LAST / Resolution: 2.75→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3432 0 65 0 3497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00623568
X-RAY DIFFRACTIONf_angle_d1.07514797
X-RAY DIFFRACTIONf_chiral_restr0.0691509
X-RAY DIFFRACTIONf_plane_restr0.006614
X-RAY DIFFRACTIONf_dihedral_angle_d14.91921363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.920.521350.397861X-RAY DIFFRACTION2.51
2.92-3.150.2494300.3316314X-RAY DIFFRACTION13.08
3.15-3.470.3559790.3026754X-RAY DIFFRACTION31.42
3.47-3.970.27332070.24921758X-RAY DIFFRACTION74.23
3.97-50.20583000.18392388X-RAY DIFFRACTION99.56
5-48.010.20452490.16742481X-RAY DIFFRACTION98.84
Refinement TLS params.Method: refined / Origin x: 49.406 Å / Origin y: -20.4 Å / Origin z: -24.778 Å
111213212223313233
T0.609218065132 Å2-0.0795366725266 Å20.00260842576003 Å2-0.67954619884 Å20.048573962021 Å2--0.638260124153 Å2
L2.22098569581 °20.832682751503 °2-0.13379532039 °2-2.90572704294 °20.0294993895372 °2--3.08259831761 °2
S0.026772247297 Å °0.1736254849 Å °0.0506793495635 Å °-0.0869957541925 Å °-0.0738033218246 Å °-0.095805337621 Å °0.268152294604 Å °-0.183365900257 Å °-3.31273267991E-10 Å °
Refinement TLS groupSelection details: ( CHAIN A AND RESID 5:432 )

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