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- PDB-8yik: pP1192R-ATPase-domain -

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Basic information

Entry
Database: PDB / ID: 8yik
TitlepP1192R-ATPase-domain
ComponentsDNA topoisomerase 2
KeywordsISOMERASE / ASFV / PROTEIN BINDING
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 / cytoplasm
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
ADENOSINE-5'-TRIPHOSPHATE / DNA topoisomerase 2
Similarity search - Component
Biological speciesAfrican swine fever virus pig/Kenya/KEN-50/1950
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSun, J.Q. / Liu, R.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270157 China
CitationJournal: Nucleic Acids Res / Year: 2024
Title: Structural basis for difunctional mechanism of m-AMSA against African swine fever virus pP1192R.
Authors: Ruili Liu / Junqing Sun / Lian-Feng Li / Yingxian Cheng / Meilin Li / Lifeng Fu / Su Li / Guorui Peng / Yanjin Wang / Sheng Liu / Xiao Qu / Jiaqi Ran / Xiaomei Li / Erqi Pang / Hua-Ji Qiu / ...Authors: Ruili Liu / Junqing Sun / Lian-Feng Li / Yingxian Cheng / Meilin Li / Lifeng Fu / Su Li / Guorui Peng / Yanjin Wang / Sheng Liu / Xiao Qu / Jiaqi Ran / Xiaomei Li / Erqi Pang / Hua-Ji Qiu / Yanli Wang / Jianxun Qi / Han Wang / George Fu Gao /
Abstract: The African swine fever virus (ASFV) type II topoisomerase (Topo II), pP1192R, is the only known Topo II expressed by mammalian viruses and is essential for ASFV replication in the host cytoplasm. ...The African swine fever virus (ASFV) type II topoisomerase (Topo II), pP1192R, is the only known Topo II expressed by mammalian viruses and is essential for ASFV replication in the host cytoplasm. Herein, we report the structures of pP1192R in various enzymatic stages using both X-ray crystallography and single-particle cryo-electron microscopy. Our data structurally define the pP1192R-modulated DNA topology changes. By presenting the A2+-like metal ion at the pre-cleavage site, the pP1192R-DNA-m-AMSA complex structure provides support for the classical two-metal mechanism in Topo II-mediated DNA cleavage and a better explanation for nucleophile formation. The unique inhibitor selectivity of pP1192R and the difunctional mechanism of pP1192R inhibition by m-AMSA highlight the specificity of viral Topo II in the poison binding site. Altogether, this study provides the information applicable to the development of a pP1192R-targeting anti-ASFV strategy.
History
DepositionFeb 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA topoisomerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4652
Polymers44,9581
Non-polymers5071
Water7,278404
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.753, 85.753, 211.483
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-647-

HOH

21A-905-

HOH

31A-920-

HOH

41A-964-

HOH

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Components

#1: Protein DNA topoisomerase 2 / DNA topoisomerase II


Mass: 44957.844 Da / Num. of mol.: 1 / Fragment: ATPase-domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus pig/Kenya/KEN-50/1950
Gene: BA71V-P1192R (i7R), P1192R
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: A0A0C5B080, DNA topoisomerase (ATP-hydrolysing)
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20%(W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.3→211.48 Å / Num. obs: 111723 / % possible obs: 98.7 % / Redundancy: 5 % / Biso Wilson estimate: 12.27 Å2 / CC1/2: 1 / Net I/σ(I): 0
Reflection shellResolution: 1.3→1.33 Å / Rmerge(I) obs: 0.092 / Num. unique obs: 1531

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→43.07 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2063 5519 4.95 %
Rwork0.2001 --
obs0.2004 111384 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2979 0 0 404 3383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083102
X-RAY DIFFRACTIONf_angle_d0.9024217
X-RAY DIFFRACTIONf_dihedral_angle_d13.1261137
X-RAY DIFFRACTIONf_chiral_restr0.078488
X-RAY DIFFRACTIONf_plane_restr0.008523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.25791430.2572928X-RAY DIFFRACTION83
1.31-1.330.27491470.25553084X-RAY DIFFRACTION87
1.33-1.350.27231720.24133180X-RAY DIFFRACTION90
1.35-1.360.25351640.23383380X-RAY DIFFRACTION95
1.36-1.380.24961820.23953505X-RAY DIFFRACTION99
1.38-1.40.22991830.22453500X-RAY DIFFRACTION100
1.4-1.420.2231740.223531X-RAY DIFFRACTION100
1.42-1.440.22251760.21583540X-RAY DIFFRACTION100
1.44-1.460.19482090.1933508X-RAY DIFFRACTION100
1.46-1.490.21671940.2023524X-RAY DIFFRACTION100
1.49-1.510.211750.20373552X-RAY DIFFRACTION100
1.51-1.540.21842140.20513493X-RAY DIFFRACTION100
1.54-1.570.20841770.20363537X-RAY DIFFRACTION100
1.57-1.60.20481910.20323548X-RAY DIFFRACTION100
1.6-1.640.20021590.19693570X-RAY DIFFRACTION100
1.64-1.680.1951850.20053551X-RAY DIFFRACTION100
1.68-1.720.23811870.2033581X-RAY DIFFRACTION100
1.72-1.760.24371980.19973536X-RAY DIFFRACTION100
1.76-1.820.20271900.19953570X-RAY DIFFRACTION100
1.82-1.870.21991820.20853584X-RAY DIFFRACTION100
1.87-1.940.2341850.21113558X-RAY DIFFRACTION100
1.94-2.020.18841790.19273597X-RAY DIFFRACTION100
2.02-2.110.21482040.19153579X-RAY DIFFRACTION100
2.11-2.220.21431870.1933618X-RAY DIFFRACTION100
2.22-2.360.21322030.19463597X-RAY DIFFRACTION100
2.36-2.540.18671820.19983650X-RAY DIFFRACTION100
2.54-2.80.19552070.20233625X-RAY DIFFRACTION100
2.8-3.210.1981770.19973716X-RAY DIFFRACTION100
3.21-4.040.18651900.18313748X-RAY DIFFRACTION100
4.04-43.070.19312030.1933975X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 32.9626 Å / Origin y: 13.0538 Å / Origin z: 98.4626 Å
111213212223313233
T0.0794 Å2-0.0048 Å2-0.0112 Å2-0.0536 Å20.0021 Å2--0.0602 Å2
L0.622 °20.0362 °2-0.269 °2-0.571 °2-0.0116 °2--0.6268 °2
S-0.0109 Å °0.0376 Å °0.0105 Å °-0.0052 Å °0.0231 Å °-0.0101 Å °-0.0425 Å °-0.0047 Å °-0.008 Å °
Refinement TLS groupSelection details: all

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