4TMA

Crystal structure of gyrase bound to its inhibitor YacG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Direct control of type IIA topoisomerase activity by a chromosomally encoded regulatory protein.

Vos, S.M.Lyubimov, A.Y.Hershey, D.M.Schoeffler, A.J.Sengupta, S.Nagaraja, V.Berger, J.M.

(2014) Genes Dev. 28: 1485-1497

  • DOI: 10.1101/gad.241984.114

  • PubMed Abstract: 
  • Precise control of supercoiling homeostasis is critical to DNA-dependent processes such as gene expression, replication, and damage response. Topoisomerases are central regulators of DNA supercoiling commonly thought to act independently in the recog ...

    Precise control of supercoiling homeostasis is critical to DNA-dependent processes such as gene expression, replication, and damage response. Topoisomerases are central regulators of DNA supercoiling commonly thought to act independently in the recognition and modulation of chromosome superstructure; however, recent evidence has indicated that cells tightly regulate topoisomerase activity to support chromosome dynamics, transcriptional response, and replicative events. How topoisomerase control is executed and linked to the internal status of a cell is poorly understood. To investigate these connections, we determined the structure of Escherichia coli gyrase, a type IIA topoisomerase bound to YacG, a recently identified chromosomally encoded inhibitor protein. Phylogenetic analyses indicate that YacG is frequently associated with coenzyme A (CoA) production enzymes, linking the protein to metabolism and stress. The structure, along with supporting solution studies, shows that YacG represses gyrase by sterically occluding the principal DNA-binding site of the enzyme. Unexpectedly, YacG acts by both engaging two spatially segregated regions associated with small-molecule inhibitor interactions (fluoroquinolone antibiotics and the newly reported antagonist GSK299423) and remodeling the gyrase holoenzyme into an inactive, ATP-trapped configuration. This study establishes a new mechanism for the protein-based control of topoisomerases, an approach that may be used to alter supercoiling levels for responding to changes in cellular state.


    Organizational Affiliation

    Department of Molecular and Cell Biology.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit A
A, C, E, G
525N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit B
B, D, F, H
417N/AMutation(s): 1 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase inhibitor YacG
I, J, K, L
65Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: yacG
Find proteins for P0A8H8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8H8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, E, I, J, K, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.243 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 107.210α = 90.00
b = 114.460β = 90.00
c = 462.120γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesR01-CA077373

Revision History 

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy