Crystal Structure of Staph GyraseB 24kDa in complex with Novobiocin

Experimental Data Snapshot

  • Resolution: 2.59 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

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Structures of Kibdelomycin Bound to Staphylococcus Aureus Gyrb and Pare Showed a Novel U-Shaped Binding Mode.

Lu, J.Patel, S.Sharma, N.Soisson, S.M.Kishii, R.Takei, M.Fukuda, Y.Lumb, K.J.Singh, S.B.

(2014) ACS Chem Biol 9: 2023

  • DOI: https://doi.org/10.1021/cb5001197
  • Primary Citation of Related Structures:  
    4URL, 4URM, 4URN, 4URO

  • PubMed Abstract: 

    Bacterial resistance to antibiotics continues to pose serious challenges as the discovery rate for new antibiotics fades. Kibdelomycin is one of the rare, novel, natural product antibiotics discovered recently that inhibits the bacterial DNA synthesis enzymes gyrase and topoisomerase IV. It is a broad-spectrum, Gram-positive antibiotic without cross-resistance to known gyrase inhibitors, including clinically effective quinolones. To understand its mechanism of action, binding mode, and lack of cross-resistance, we have co-crystallized kibdelomycin and novobiocin with the N-terminal domains of Staphylococcus aureus gyrase B (24 kDa) and topo IV (ParE, 24 and 43 kDa). Kibdelomycin shows a unique "dual-arm", U-shaped binding mode in both crystal structures. The pyrrolamide moiety in the lower part of kibdelomycin penetrates deeply into the ATP-binding site pocket, whereas the isopropyl-tetramic acid and sugar moiety of the upper part thoroughly engage in polar interactions with a surface patch of the protein. The isoproramic acid (1,3-dioxopyrrolidine) and a tetrahydropyran acetate group (Sugar A) make polar contact with a surface area consisting of helix α4 and the flexible loop connecting helices α3 and α4. The two arms are connected together by a rigid decalin linker that makes van del Waals contacts with the protein backbone. This "dual-arm", U-shaped, multicontact binding mode of kibdelomycin is unique and distinctively different from binding modes of other known gyrase inhibitors (e.g., coumarins and quinolones), which explains its lack of cross-resistance and low frequency of resistance. The crystal structures reported in this paper should enable design and discovery of analogues with better properties and antibacterial spectrum.

  • Organizational Affiliation

    Merck Research Laboratories, West Point, Pennsylvania 19486, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
231Staphylococcus aureusMutation(s): 0 
Find proteins for P0A0K8 (Staphylococcus aureus)
Explore P0A0K8 
Go to UniProtKB:  P0A0K8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A0K8
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
NOV BindingDB:  4URO Ki: 10 (nM) from 1 assay(s)
IC50: min: 4, max: 457 (nM) from 8 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.59 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.28α = 90
b = 68.59β = 91.72
c = 85.72γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description