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

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Basic information

Entry
Database: PDB / ID: 8kgs
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 negative supercoiling 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 / : / 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 ...C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / DNA topoisomerase II, eukaryotic-type / : / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA topoisomerase 2
Similarity search - Component
Biological speciesAfrican swine fever virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.603 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)50,0503
Polymers49,5191
Non-polymers5312
Water2,180121
1
A: DNA topoisomerase 2
hetero molecules

A: DNA topoisomerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0996
Polymers99,0382
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area7230 Å2
ΔGint-45 kcal/mol
Surface area33170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.077, 85.077, 210.180
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-633-

HOH

21A-667-

HOH

31A-719-

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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 21% PEG 3350, 100 mM Hepes (pH 7.2) and 200 mM MgCl2

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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 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 14604 / % possible obs: 100 % / Redundancy: 19 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.203 / Net I/σ(I): 11
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 9 % / Rmerge(I) obs: 1.019 / Mean I/σ(I) obs: 1.38 / Num. unique obs: 708 / CC1/2: 0.76 / CC star: 0.929 / Rpim(I) all: 0.339 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.603→42.78 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2441 670 4.61 %
Rwork0.2003 --
obs0.2023 14538 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.603→42.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3141 0 32 121 3294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013239
X-RAY DIFFRACTIONf_angle_d1.064390
X-RAY DIFFRACTIONf_dihedral_angle_d23.8791198
X-RAY DIFFRACTIONf_chiral_restr0.056509
X-RAY DIFFRACTIONf_plane_restr0.005546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6031-2.8040.28311200.26262692X-RAY DIFFRACTION100
2.804-3.08610.29531360.23782702X-RAY DIFFRACTION100
3.0861-3.53250.26451530.2092707X-RAY DIFFRACTION100
3.5325-4.44990.2161230.1692790X-RAY DIFFRACTION100
4.4499-42.780.22121380.1882977X-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)
12.9170.75230.55052.5430.54512.1582-0.06910.0420.1769-0.061-0.06280.0512-0.12450.03740.08040.31290.0350.00780.1451-0.01920.182331.605712.18595.5373
24.43550.45620.7862.9888-0.62452.18370.02940.24290.1435-0.2793-0.07760.3044-0.2006-0.23910.02950.37640.0633-0.03240.1802-0.0250.197519.189617.3886-11.3144
32.18040.59980.60381.53040.34591.7623-0.0560.050.3031-0.1572-0.01160.2012-0.3733-0.39290.01210.30210.0778-0.01790.22420.04580.19820.290417.895-3.7262
40.7344-0.5130.29111.38150.05570.89890.04990.20520.5552-1.18340.0926-0.42-0.92420.53170.14920.6364-0.08970.00010.23330.0380.360734.847225.121-13.3786
53.34430.49310.62831.3522-0.54052.2260.00580.003-0.08830.0777-0.0435-0.25580.07850.16120.0290.2734-0.03850.00760.14170.01530.222749.13047.5049-13.38
63.06990.8329-0.29825.5613-1.74076.4768-0.7133-1.5059-0.91720.98560.2888-1.16140.41751.2750.16550.93060.06740.01090.88040.04740.923566.133-4.7979-8.5013
70.87310.5321-0.52950.69010.37861.6521-0.21580.0327-0.2703-0.0619-0.026-0.11510.378-0.04950.21180.3769-0.0212-0.01040.1099-0.00630.233740.87611.5879-13.4743
81.73970.6210.78859.16381.62067.4522-0.4269-0.06470.50.2278-0.0917-1.218-0.34771.33040.38970.2757-0.0635-0.0160.41530.08420.428564.11885.6585-12.6413
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:54)
2X-RAY DIFFRACTION2(chain A and resid 55:118)
3X-RAY DIFFRACTION3(chain A and resid 119:231)
4X-RAY DIFFRACTION4(chain A and resid 232:248)
5X-RAY DIFFRACTION5(chain A and resid 249:332)
6X-RAY DIFFRACTION6(chain A and resid 333:346)
7X-RAY DIFFRACTION7(chain A and resid 347:387)
8X-RAY DIFFRACTION8(chain A and resid 388:405)

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