9DES | pdb_00009des

Mycobacterium tuberculosis UvrD1: DNA-bound dimer.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: other
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis for dimerization and activation of UvrD-family helicases.

Chadda, A.Nguyen, B.Lohman, T.M.Galburt, E.A.

(2025) Proc Natl Acad Sci U S A 122: e2422330122-e2422330122

  • DOI: https://doi.org/10.1073/pnas.2422330122
  • Primary Citation of Related Structures:  
    9DCI, 9DES

  • PubMed 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 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, Mycobacterium tuberculosis 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 Escherichia coli 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.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Washington University in Saint Louis School of Medicine, Saint Louis, MO 63110.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent DNA helicase UvrD1A,
C [auth B]
771Mycobacterium tuberculosisMutation(s): 0 
Gene Names: uvrD1ivrdpcrARv0949MTCY10D7.25c
EC: 5.6.2.4
UniProt
Find proteins for P9WMQ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WMQ1 
Go to UniProtKB:  P9WMQ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WMQ1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286:
RECONSTRUCTIONcryoSPARC4.2.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM144282

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release