8DF8

Structure of M. kandleri topoisomerase V in complex with DNA. 40 base pair symmetric DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 

Starting Model: experimental
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Literature

Structures of topoisomerase V in complex with DNA reveal unusual DNA binding mode and novel relaxation mechanism.

Osterman, A.Mondragon, A.

(2022) Elife 11

  • DOI: https://doi.org/10.7554/eLife.72702
  • Primary Citation of Related Structures:  
    8DF7, 8DF8, 8DF9, 8DFB

  • PubMed Abstract: 

    Topoisomerase V is a unique topoisomerase that combines DNA repair and topoisomerase activities. The enzyme has an unusual arrangement, with a small topoisomerase domain followed by 12 tandem (HhH) 2 domains, which include 3 AP lyase repair domains. The uncommon architecture of this enzyme bears no resemblance to any other known topoisomerase. Here, we present structures of topoisomerase V in complex with DNA. The structures show that the (HhH) 2 domains wrap around the DNA and in this manner appear to act as a processivity factor. There is a conformational change in the protein to expose the topoisomerase active site. The DNA bends sharply to enter the active site, which melts the DNA and probably facilitates relaxation. The structures show a DNA-binding mode not observed before and provide information on the way this atypical topoisomerase relaxes DNA. In common with type IB enzymes, topoisomerase V relaxes DNA using a controlled rotation mechanism, but the structures show that topoisomerase V accomplishes this in different manner. Overall, the structures firmly establish that type IC topoisomerases form a distinct type of topoisomerases, with no similarities to other types at the sequence, structural, or mechanistic level. They represent a completely different solution to DNA relaxation.


  • Organizational Affiliation

    Department of Molecular Biosciences, Northwestern University, Evanston, United States.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Topoisomerase V
A, B
854Methanopyrus kandleriMutation(s): 6 
Gene Names: top5HA336_03250
UniProt
Find proteins for Q977W1 (Methanopyrus kandleri)
Explore Q977W1 
Go to UniProtKB:  Q977W1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ977W1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (42-MER)C [auth U]42synthetic construct
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (42-MER)D [auth V]42synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth B],
J [auth B],
K [auth U],
M [auth U]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
PO3
Query on PO3

Download Ideal Coordinates CCD File 
L [auth U],
N [auth V]
PHOSPHITE ION
O3 P
AQSJGOWTSHOLKH-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
H [auth B],
I [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.941α = 90
b = 120.941β = 90
c = 497.569γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
Aimlessdata scaling
PHASERphasing

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 StatesR35GM118108

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-31
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description