8XAC | pdb_00008xac

Crystal structure of amidase from Pseudonocardia acaciae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 
    0.259 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.207 (DCC) 

Starting Model: experimental
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Literature

Characterizing an amidase and its operon from actinomycete bacteria responsible for paraben catabolism.

Takenoya, M.Hiratsuka, Y.Shimamura, K.Ito, S.Sasaki, Y.Yajima, S.

(2024) Biosci Biotechnol Biochem 88: 1047-1054

  • DOI: https://doi.org/10.1093/bbb/zbae083
  • Primary Citation of Related Structures:  
    8XAC

  • PubMed Abstract: 

    Hydrazidase from Microbacterium hydrocarbonoxydans was revealed to catalyze synthetic hydrazide compounds, enabling the bacteria to grow with them as a sole carbon source, but natural substrates have remained unknown. In this study, kinetic analyses of hydrazidase with parabens showed that the compounds can be substrates. Then, methylparaben induced gene expressions of the operon containing hydrazidase and ABC transporter, and the compound as a sole carbon source was able to grow the bacteria. Furthermore, homology search was carried out revealing that several actinomycetes possess hydrazidase homologs in the operon. Among those bacteria, an amidase from Pseudonocardia acaciae was subjected to a kinetic analysis and a structure determination revealing similar but not identical to those of hydrazidase. Since parabens are reported to exist in plants and soil, and several actinomycetes code the homologous operon, the enzymes with those operons may play a physiologically important role for bacterial survival with use of parabens.


  • Organizational Affiliation
    • Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amidase family protein
A, B, C, D
467Pseudonocardia acaciaeMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free:  0.259 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.207 (DCC) 
Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 165.28α = 90
b = 165.28β = 90
c = 160.612γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
pointlessdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan21K05351

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release