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- PDB-9dci: Mycobacterium tuberculosis UvrD1 dimer: apo compact conformation. -

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Basic information

Entry
Database: PDB / ID: 9dci
TitleMycobacterium tuberculosis UvrD1 dimer: apo compact conformation.
ComponentsATP-dependent DNA helicase UvrD1
KeywordsDNA BINDING PROTEIN / DNA Helicase / DNA Translocase / ATPase
Function / homology
Function and homology information


negative regulation of strand invasion / DNA helicase complex / UV protection / recombinational repair / 3'-5' DNA helicase activity / DNA 3'-5' helicase / dATP binding / ATP-dependent activity, acting on DNA / peptidoglycan-based cell wall / isomerase activity ...negative regulation of strand invasion / DNA helicase complex / UV protection / recombinational repair / 3'-5' DNA helicase activity / DNA 3'-5' helicase / dATP binding / ATP-dependent activity, acting on DNA / peptidoglycan-based cell wall / isomerase activity / double-strand break repair / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane / cytosol
Similarity search - Function
ATP-dependent DNA helicase PcrA / PcrA/UvrD tudor domain / DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent DNA helicase UvrD1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.07 Å
AuthorsChadda, A. / Galburt, E.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM144282 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structural basis for dimerization and activation of UvrD-family helicases.
Authors: Ankita Chadda / Binh Nguyen / Timothy M Lohman / Eric A Galburt /
Abstract: UvrD-family helicases are superfamily 1A motor proteins that function during DNA replication, recombination, repair, and transcription. UvrD family monomers translocate along single-stranded (ss) DNA ...UvrD-family helicases are superfamily 1A motor proteins that function during DNA replication, recombination, repair, and transcription. UvrD family monomers translocate along single-stranded (ss) DNA but need to be activated by dimerization to unwind DNA in the absence of force or accessory factors. However, prior structural studies have only revealed monomeric complexes. Here, we report the first structures of a dimeric UvrD-family helicase, UvrD1, both free and bound to a DNA junction. In each structure, the dimer interface occurs between the 2B subdomains of each subunit. The apo UvrD1 dimer is observed in symmetric compact and extended forms indicating substantial flexibility. This symmetry is broken in the DNA-bound dimer complex with leading and trailing subunits adopting distinct conformations. Biochemical experiments reveal that the UvrD dimer shares the same 2B-2B interface. In contrast to the dimeric structures, an inactive, autoinhibited UvrD1 DNA-bound monomer structure reveals 2B subdomain-DNA contacts that are likely inhibitory. The major reorientation of the 2B subdomains that occurs upon UvrD1 dimerization prevents these duplex DNA interactions, thus relieving the autoinhibition. These structures reveal that the 2B subdomain serves a major regulatory role rather than participating directly in DNA unwinding.
History
DepositionAug 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent DNA helicase UvrD1
B: ATP-dependent DNA helicase UvrD1


Theoretical massNumber of molelcules
Total (without water)170,3102
Polymers170,3102
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ATP-dependent DNA helicase UvrD1 / DNA 3'-5' helicase UvrD1


Mass: 85154.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: uvrD1, ivrd, pcrA, Rv0949, MTCY10D7.25c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WMQ1, DNA 3'-5' helicase
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mtb UvrD1 compact dimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.17 MDa / Experimental value: YES
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 0.38 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 9.77 sec. / Electron dose: 46.46 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 6213
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
2EPUimage acquisition
4cryoSPARC4.2.1CTF correction
9PHENIX1.21.1_5286model refinement
10cryoSPARC4.2.1initial Euler assignment
11cryoSPARC4.2.1final Euler assignment
12cryoSPARC4.2.1classification
13cryoSPARC4.2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 350
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 188910 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 104.24 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002311451
ELECTRON MICROSCOPYf_angle_d0.457415518
ELECTRON MICROSCOPYf_chiral_restr0.03981743
ELECTRON MICROSCOPYf_plane_restr0.00362078
ELECTRON MICROSCOPYf_dihedral_angle_d12.20464270

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