6PPR

Cryo-EM structure of AdnA(D934A)-AdnB(D1014A) in complex with AMPPNP and DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures and single-molecule analysis of bacterial motor nuclease AdnAB illuminate the mechanism of DNA double-strand break resection.

Jia, N.Unciuleac, M.C.Xue, C.Greene, E.C.Patel, D.J.Shuman, S.

(2019) Proc.Natl.Acad.Sci.USA 116: 24507-24516

  • DOI: 10.1073/pnas.1913546116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mycobacterial AdnAB is a heterodimeric helicase-nuclease that initiates homologous recombination by resecting DNA double-strand breaks (DSBs). The AdnA and AdnB subunits are each composed of an N-terminal motor domain and a C-terminal nuclease domain ...

    Mycobacterial AdnAB is a heterodimeric helicase-nuclease that initiates homologous recombination by resecting DNA double-strand breaks (DSBs). The AdnA and AdnB subunits are each composed of an N-terminal motor domain and a C-terminal nuclease domain. Here we report cryoelectron microscopy (cryo-EM) structures of AdnAB in three functional states: in the absence of DNA and in complex with forked duplex DNAs before and after cleavage of the 5' single-strand DNA (ssDNA) tail by the AdnA nuclease. The structures reveal the path of the 5' ssDNA through the AdnA nuclease domain and the mechanism of 5' strand cleavage; the path of the 3' tracking strand through the AdnB motor and the DNA contacts that couple ATP hydrolysis to mechanical work; the position of the AdnA iron-sulfur cluster subdomain at the Y junction and its likely role in maintaining the split trajectories of the unwound 5' and 3' strands. Single-molecule DNA curtain analysis of DSB resection reveals that AdnAB is highly processive but prone to spontaneous pausing at random sites on duplex DNA. A striking property of AdnAB is that the velocity of DSB resection slows after the enzyme experiences a spontaneous pause. Our results highlight shared as well as distinctive properties of AdnAB vis-à-vis the RecBCD and AddAB clades of bacterial DSB-resecting motor nucleases.


    Organizational Affiliation

    Molecular Biology Program, Sloan Kettering Institute, New York, NY 10065.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032.,Structural Biology Program, Sloan Kettering Institute, New York, NY 10065; pateld@mskcc.org s-shuman@ski.mskcc.org.,Molecular Biology Program, Sloan Kettering Institute, New York, NY 10065; pateld@mskcc.org s-shuman@ski.mskcc.org.,Structural Biology Program, Sloan Kettering Institute, New York, NY 10065.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UvrD/REP helicase
B
1095Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 1 
Find proteins for I7FZ56 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  I7FZ56
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent DNA helicase (UvrD/REP)
A
1045Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 1 
Find proteins for A0QTR9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QTR9
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (70-MER)X70Mycolicibacterium smegmatis
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ANP
Query on ANP

Download SDF File 
Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2019-12-04
    Type: Database references
  • Version 1.2: 2019-12-18
    Type: Database references