4TMA

Crystal structure of gyrase bound to its inhibitor YacG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 

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This is version 1.2 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
  • Primary Citation of Related Structures:  
    4TMA

  • 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 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit AA, C, E, G525Escherichia coli str. K-12 substr. MC4100Mutation(s): 0 
Gene Names: gyrABN896_2003
EC: 5.99.1.3
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Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit BB, D, F, H417Escherichia coli str. K-12 substr. MC4100Mutation(s): 1 
Gene Names: gyrBBN896_3389
EC: 5.99.1.3
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Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase inhibitor YacGI, J, K, L65Escherichia coli K-12Mutation(s): 0 
Gene Names: yacGb0101JW5008
UniProt
Find proteins for P0A8H8 (Escherichia coli (strain K12))
Explore P0A8H8 
Go to UniProtKB:  P0A8H8
Entity Groups  
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UniProt GroupP0A8H8
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.21α = 90
b = 114.46β = 90
c = 462.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01-CA077373

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence