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- PDB-9dgy: Mycobacterium tuberculosis UvrD1 monomer-DNA complex -

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Basic information

Entry
Database: PDB / ID: 9dgy
TitleMycobacterium tuberculosis UvrD1 monomer-DNA complex
Components
  • ATP-dependent DNA helicase UvrD1
  • DNA (18-MER)
  • DNA (28-MER)
KeywordsMOTOR PROTEIN/DNA / DNA Helicase / DNA Translocase / ATPase / MOTOR PROTEIN / MOTOR PROTEIN-DNA complex
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
DNA / DNA (> 10) / ATP-dependent DNA helicase UvrD1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 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
DepositionSep 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: ATP-dependent DNA helicase UvrD1
X: DNA (18-MER)
Y: DNA (28-MER)


Theoretical massNumber of molelcules
Total (without water)99,2333
Polymers99,2333
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.: 1
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
#2: DNA chain DNA (18-MER)


Mass: 5422.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)
#3: DNA chain DNA (28-MER)


Mass: 8655.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)
Has protein modificationN

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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: UvrD1 monomer-DNA junction complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Cs: 0.01 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 84 K / Temperature (min): 82 K
Image recordingAverage exposure time: 7.27 sec. / Electron dose: 59 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 4999
EM imaging opticsSpherical aberration corrector: Microscope is outfitted with a Cs image corrector with two hexapole elements
Image scansWidth: 4096 / Height: 4096

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 713562
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 282302 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036307
ELECTRON MICROSCOPYf_angle_d0.7768725
ELECTRON MICROSCOPYf_dihedral_angle_d24.5171188
ELECTRON MICROSCOPYf_chiral_restr0.048981
ELECTRON MICROSCOPYf_plane_restr0.0051019

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