5TSP

Crystal structure of the catalytic domain of Clostridium perfringens neuraminidase (NanI) in complex with a CHES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the catalytic domain of Clostridium perfringens neuraminidase in complex with a non-carbohydrate-based inhibitor, 2-(cyclohexylamino)ethanesulfonic acid

Lee, Y.Youn, H.-S.Lee, J.-G.An, J.Y.Park, K.R.Kang, J.Y.Ryu, Y.B.Jin, M.S.Park, K.H.Eom, S.H.

(2017) Biochem Biophys Res Commun 486: 470-475

  • DOI: https://doi.org/10.1016/j.bbrc.2017.03.064
  • Primary Citation of Related Structures:  
    5TSP

  • PubMed Abstract: 

    Anti-bacterial and anti-viral neuraminidase agents inhibit neuraminidase activity catalyzing the hydrolysis of terminal N-acetylneuraminic acid (Neu5Ac) from glycoconjugates and help to prevent the host pathogenesis that lead to fatal infectious diseases including influenza, bacteremia, sepsis, and cholera. Emerging antibiotic and drug resistances to commonly used anti-neuraminidase agents such as oseltamivir (Tamiflu) and zanamivir (Relenza) have highlighted the need to develop new anti-neuraminidase drugs. We obtained a serendipitous complex crystal of the catalytic domain of Clostridium perfringens neuraminidase (CpNanI CD ) with 2-(cyclohexylamino)ethanesulfonic acid (CHES) as a buffer. Here, we report the crystal structure of CpNanI CD in complex with CHES at 1.24 Å resolution. Amphipathic CHES binds to the catalytic site of CpNanI CD similar to the substrate (Neu5Ac) binding site. The 2-aminoethanesulfonic acid moiety and cyclohexyl groups of CHES interact with the cluster of three arginine residues and with the hydrophobic pocket of the CpNanI CD catalytic site. In addition, a structural comparison with other bacterial and human neuraminidases suggests that CHES could serve as a scaffold for the development of new anti-neuraminidase agents targeting CpNanI.


  • Organizational Affiliation

    School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea; Steitz Center for Structural Biology, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sialidase
A, B
461Clostridium perfringens ATCC 13124Mutation(s): 0 
Gene Names: nanI
EC: 3.2.1.18
UniProt
Find proteins for A0A0H2YQR1 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A))
Explore A0A0H2YQR1 
Go to UniProtKB:  A0A0H2YQR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2YQR1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.386α = 90
b = 98.007β = 90.99
c = 72.648γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data processing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-04-19
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description