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- PDB-9imj: Bacteriophage T6 topoisomerase II ATPase domain crystal strcuture -

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Basic information

Entry
Database: PDB / ID: 9imj
TitleBacteriophage T6 topoisomerase II ATPase domain crystal strcuture
ComponentsDNA topoisomerase (ATP-hydrolyzing)
KeywordsISOMERASE / topoisomerase II ATPase domain
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
Similarity search - Function
: / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / 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-, DNA gyrase B-, and HSP90-like ATPase ...: / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / 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-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / 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 (ATP-hydrolyzing)
Similarity search - Component
Biological speciesEnterobacteria phage T6 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsXin, Y.H. / Chen, Y.T.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2024
Title: Structural and functional insights into the T-even type bacteriophage topoisomerase II.
Authors: Yuhui Xin / Runqi Xian / Yunge Yang / Jingyuan Cong / Zihe Rao / Xuemei Li / Yutao Chen /
Abstract: T-even type bacteriophages are virulent phages commonly used as model organisms, playing a crucial role in understanding various biological processes. One such process involves the regulation of DNA ...T-even type bacteriophages are virulent phages commonly used as model organisms, playing a crucial role in understanding various biological processes. One such process involves the regulation of DNA topology during phage replication upon host infection, governed by type IIA DNA topoisomerases. In spite of various studies on prokaryotic and eukaryotic counterparts, viral topoisomerase II remains insufficiently understood, especially the unique domain composition of T4 phage. In this study, we determine the cryo-EM structures of topoisomerase II from T4 and T6 phages, including full-length structures of both apo and DNA-binding states which have never been determined before. Together with other conformational states, these structures provide an explicit blueprint of mechanisms of phage topoisomerase II. Particularly, the asymmetric dimeric interactions observed in cryo-EM structures of T6 phage topoisomerase II ATPase domain and central domain bound with DNA shed light on the asynchronous ATP usage and asynchronous cleavage of the G-segment DNA, respectively. The elucidation of phage topoisomerase II's structures and functions not only enhances our understanding of mechanisms and evolutionary parallels with prokaryotic and eukaryotic homologs but also highlights its potential as a model for developing type IIA topoisomerase inhibitors.
History
DepositionJul 3, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA topoisomerase (ATP-hydrolyzing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2153
Polymers43,6851
Non-polymers5312
Water32418
1
A: DNA topoisomerase (ATP-hydrolyzing)
hetero molecules

A: DNA topoisomerase (ATP-hydrolyzing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4316
Polymers87,3702
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area7870 Å2
ΔGint-37 kcal/mol
Surface area29720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.989, 90.989, 102.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein DNA topoisomerase (ATP-hydrolyzing)


Mass: 43684.969 Da / Num. of mol.: 1 / Fragment: ATPase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T6 (virus) / Gene: EcT6_00003 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A346FJ89, DNA topoisomerase (ATP-hydrolysing)
#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: isolated from a natural source / 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.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG3350, succinic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 13967 / % possible obs: 100 % / Redundancy: 16.1 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.026 / Rrim(I) all: 0.104 / Χ2: 2.127 / Net I/σ(I): 12.1 / Num. measured all: 225456
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.7-2.7515.80.7366850.9720.9930.1890.761.053100
2.75-2.8160.6936690.9840.9960.1780.7161.046100
2.8-2.8516.10.637130.9830.9960.1610.651.064100
2.85-2.9116.30.5116740.9860.9970.130.5281.064100
2.91-2.9716.40.4916700.9860.9960.1240.5061.17100
2.97-3.0416.40.3567210.9930.9980.0910.3671.304100
3.04-3.1216.80.2926680.9950.9990.0730.3011.477100
3.12-3.216.60.2586970.9950.9990.0650.2661.525100
3.2-3.316.50.26680.9960.9990.0510.2061.688100
3.3-3.416.70.1696960.9970.9990.0430.1741.975100
3.4-3.5216.60.1457020.99910.0370.152.271100
3.52-3.6616.50.1246910.99810.0310.1282.514100
3.66-3.8316.30.1116950.9980.9990.0280.1152.914100
3.83-4.0316.20.0946970.99810.0240.0973.006100
4.03-4.2916.10.0867070.99810.0220.0893.171100
4.29-4.6215.80.0756990.99910.0190.0773.51100
4.62-5.0816.20.0727070.99910.0180.0743.095100
5.08-5.81160.0657060.99910.0170.0672.905100
5.81-7.3215.90.0597290.99910.0150.0612.719100
7.32-50140.0477730.9980.9990.0130.0493.00599.2

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Processing

Software
NameVersionClassification
PHENIXv1.20refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→36.79 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2895 594 5.05 %
Rwork0.2333 --
obs0.236 11766 93.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→36.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2970 0 32 18 3020
Refine LS restraintsType: f_plane_restr / Dev ideal: 0.01 / Number: 530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.080.48971450.36312714X-RAY DIFFRACTION93
3.08-3.530.33231660.27052670X-RAY DIFFRACTION91
3.53-4.440.28481330.22082796X-RAY DIFFRACTION94
4.44-36.790.21971500.19792992X-RAY DIFFRACTION97

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