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- PDB-8ja1: ASFV Topoisomerase ATPase domain in complex with AMP-PNP and Mg2+... -

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Basic information

Entry
Database: PDB / ID: 8ja1
TitleASFV Topoisomerase ATPase domain in complex with AMP-PNP and Mg2+ (oxidized form)
ComponentsDNA topoisomerase 2
KeywordsISOMERASE / GHKL NUCLEOTIDE-BINDING FOLD / Topoisomerase / AMP-PNP / ASFV
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 / host cell cytoplasm / 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
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA topoisomerase 2
Similarity search - Component
Biological speciesAfrican swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsChang, C.-W. / Pang, A.H. / Tsai, M.-D.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-KPQ-109-TPP2 Taiwan
CitationJournal: Commun Chem / Year: 2024
Title: A unified view on enzyme catalysis by cryo-EM study of a DNA topoisomerase.
Authors: Chiung-Wen Mary Chang / Shun-Chang Wang / Chun-Hsiung Wang / Allan H Pang / Cheng-Han Yang / Yao-Kai Chang / Wen-Jin Wu / Ming-Daw Tsai /
Abstract: The theories for substrate recognition in enzyme catalysis have evolved from lock-key to induced fit, then conformational selection, and conformational selection followed by induced fit. However, the ...The theories for substrate recognition in enzyme catalysis have evolved from lock-key to induced fit, then conformational selection, and conformational selection followed by induced fit. However, the prevalence and consensus of these theories require further examination. Here we use cryogenic electron microscopy and African swine fever virus type 2 topoisomerase (AsfvTop2) to demonstrate substrate binding theories in a joint and ordered manner: catalytic selection by the enzyme, conformational selection by the substrates, then induced fit. The apo-AsfvTop2 pre-exists in six conformers that comply with the two-gate mechanism directing DNA passage and release in the Top2 catalytic cycle. The structures of AsfvTop2-DNA-inhibitor complexes show that substantial induced-fit changes occur locally from the closed apo-conformer that however is too far-fetched for the open apo-conformer. Furthermore, the ATPase domain of AsfvTop2 in the MgAMP-PNP-bound crystal structures coexist in reduced and oxidized forms involving a disulfide bond, which can regulate the AsfvTop2 function.
History
DepositionMay 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)45,9943
Polymers45,4641
Non-polymers5312
Water9,386521
1
A: DNA topoisomerase 2
hetero molecules

A: DNA topoisomerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9886
Polymers90,9272
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area6370 Å2
ΔGint-46 kcal/mol
Surface area30060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.759, 85.759, 212.302
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
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-907-

HOH

21A-1022-

HOH

31A-1044-

HOH

41A-1054-

HOH

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Components

#1: Protein DNA topoisomerase 2


Mass: 45463.555 Da / Num. of mol.: 1 / Fragment: ATPase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: P1192R / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A1E3Q0
#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.: 521 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, LiSO4, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.14→43.18 Å / Num. obs: 166668 / % possible obs: 99.8 % / Redundancy: 20 % / Biso Wilson estimate: 11.37 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Net I/σ(I): 15.1
Reflection shellResolution: 1.14→1.2 Å / Num. unique obs: 23634 / CC1/2: 0.696

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PHENIX1.19_4092refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.14→37.13 Å / SU ML: 0.1069 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.8135
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.187 8242 4.95 %
Rwork0.1838 158266 -
obs0.184 166508 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.28 Å2
Refinement stepCycle: LAST / Resolution: 1.14→37.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2899 0 32 521 3452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00743051
X-RAY DIFFRACTIONf_angle_d1.03734158
X-RAY DIFFRACTIONf_chiral_restr0.0912488
X-RAY DIFFRACTIONf_plane_restr0.0079520
X-RAY DIFFRACTIONf_dihedral_angle_d12.82521093
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.150.31572430.29864903X-RAY DIFFRACTION94.53
1.15-1.170.26442900.27735143X-RAY DIFFRACTION99.09
1.17-1.180.26162600.2595209X-RAY DIFFRACTION99.6
1.18-1.20.25812720.24065209X-RAY DIFFRACTION100
1.2-1.210.22842690.22695222X-RAY DIFFRACTION99.98
1.21-1.230.22542690.22055221X-RAY DIFFRACTION100
1.23-1.250.22362730.22075217X-RAY DIFFRACTION100
1.25-1.270.23142700.2155211X-RAY DIFFRACTION100
1.27-1.290.18962620.21085225X-RAY DIFFRACTION100
1.29-1.310.22832460.20685272X-RAY DIFFRACTION99.96
1.31-1.330.20752740.20745203X-RAY DIFFRACTION99.96
1.33-1.350.19652760.2015226X-RAY DIFFRACTION100
1.35-1.380.2052860.1945256X-RAY DIFFRACTION99.98
1.38-1.410.19942730.19265245X-RAY DIFFRACTION99.98
1.41-1.440.22262770.18945223X-RAY DIFFRACTION99.98
1.44-1.470.18912640.18365250X-RAY DIFFRACTION100
1.47-1.510.19862730.18165266X-RAY DIFFRACTION100
1.51-1.550.1972830.17845239X-RAY DIFFRACTION100
1.55-1.590.18242790.17375272X-RAY DIFFRACTION99.98
1.59-1.650.17462890.17165277X-RAY DIFFRACTION100
1.65-1.70.17372840.17095259X-RAY DIFFRACTION100
1.7-1.770.17972980.1715264X-RAY DIFFRACTION99.98
1.77-1.850.17312680.17225316X-RAY DIFFRACTION100
1.85-1.950.17142620.17525344X-RAY DIFFRACTION100
1.95-2.070.19243040.16825295X-RAY DIFFRACTION100
2.07-2.230.18342690.16945364X-RAY DIFFRACTION100
2.23-2.460.18182380.1735432X-RAY DIFFRACTION100
2.46-2.810.18662830.17745414X-RAY DIFFRACTION100
2.81-3.540.17112840.17625512X-RAY DIFFRACTION100
3.54-37.130.16953240.18245777X-RAY DIFFRACTION99.82

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