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- PDB-8kgt: Structure of African swine fever virus topoisomerase II in comple... -

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Basic information

Entry
Database: PDB / ID: 8kgt
TitleStructure of African swine fever virus topoisomerase II in complex with dsDNA
ComponentsDNA topoisomerase 2
KeywordsVIRAL PROTEIN / topo 2
Function / homology
Function and homology information


sister chromatid segregation / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA binding / ATP binding / metal ion binding
Similarity search - Function
C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / DNA topoisomerase II, eukaryotic-type / : / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV ...C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / DNA topoisomerase II, eukaryotic-type / : / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / DNA topoisomerase, type IIA-like domain superfamily / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA topoisomerase 2
Similarity search - Component
Biological speciesAfrican swine fever virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCong, J. / Xin, Y. / Li, X. / Chen, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Structural insights into the DNA topoisomerase II of the African swine fever virus.
Authors: Jingyuan Cong / Yuhui Xin / Huiling Kang / Yunge Yang / Chenlong Wang / Dongming Zhao / Xuemei Li / Zihe Rao / Yutao Chen /
Abstract: Type II topoisomerases are ubiquitous enzymes that play a pivotal role in modulating the topological configuration of double-stranded DNA. These topoisomerases are required for DNA metabolism and ...Type II topoisomerases are ubiquitous enzymes that play a pivotal role in modulating the topological configuration of double-stranded DNA. These topoisomerases are required for DNA metabolism and have been extensively studied in both prokaryotic and eukaryotic organisms. However, our understanding of virus-encoded type II topoisomerases remains limited. One intriguing example is the African swine fever virus, which stands as the sole mammalian-infecting virus encoding a type II topoisomerase. In this work, we use several approaches including cryo-EM, X-ray crystallography, and biochemical assays to investigate the structure and function of the African swine fever virus type II topoisomerase, pP1192R. We determine the structures of pP1192R in different conformational states and confirm its enzymatic activity in vitro. Collectively, our results illustrate the basic mechanisms of viral type II topoisomerases, increasing our understanding of these enzymes and presenting a potential avenue for intervention strategies to mitigate the impact of the African swine fever virus.
History
DepositionAug 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9462
Polymers49,5191
Non-polymers4271
Water1,946108
1
A: DNA topoisomerase 2
hetero molecules

A: DNA topoisomerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,8924
Polymers99,0382
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area6810 Å2
ΔGint-33 kcal/mol
Surface area32600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.234, 85.234, 209.809
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-656-

HOH

21A-705-

HOH

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Components

#1: Protein DNA topoisomerase 2


Mass: 49519.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: P1192R CDS / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2X0THW2
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 21% PEG 3350, 100 mM Hepes (pH 7.2) and 200 mM Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 20799 / % possible obs: 99.4 % / Redundancy: 8.2 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.055 / Rrim(I) all: 0.159 / Net I/σ(I): 14.22
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.945 / Mean I/σ(I) obs: 2.24 / Num. unique obs: 996 / CC1/2: 0.629 / CC star: 0.879 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX5.8.0405refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→42.79 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.478 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.31 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24593 988 4.8 %RANDOM
Rwork0.19314 ---
obs0.19559 19793 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.263 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20.31 Å2-0 Å2
2--0.61 Å2-0 Å2
3----1.98 Å2
Refinement stepCycle: 1 / Resolution: 2.3→42.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3080 0 27 108 3215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0123173
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163057
X-RAY DIFFRACTIONr_angle_refined_deg1.1351.6474301
X-RAY DIFFRACTIONr_angle_other_deg0.3831.5727072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.595394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.408511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37510567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0550.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023557
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02668
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6844.1591582
X-RAY DIFFRACTIONr_mcbond_other2.6834.1591582
X-RAY DIFFRACTIONr_mcangle_it4.2277.4561974
X-RAY DIFFRACTIONr_mcangle_other4.2257.461975
X-RAY DIFFRACTIONr_scbond_it3.134.5481591
X-RAY DIFFRACTIONr_scbond_other3.134.5481591
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0638.1762328
X-RAY DIFFRACTIONr_long_range_B_refined7.13739.993528
X-RAY DIFFRACTIONr_long_range_B_other7.12739.853515
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 71 -
Rwork0.277 1415 -
obs--99.46 %

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