Crystal structure of Rhodococcus sp. N-771 Amidase complexed with Benzamide

Experimental Data Snapshot

  • Resolution: 2.32 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.199 

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Structure and Characterization of Amidase from Rhodococcus sp. N-771: Insight into the Molecular Mechanism of Substrate Recognition

Ohtaki, A.Murata, K.Sato, Y.Noguchi, K.Miyatake, H.Dohmae, N.Yamada, K.Yohda, M.Odaka, M.

(2009) Biochim Biophys Acta 

  • DOI: https://doi.org/10.1016/j.bbapap.2009.10.001
  • Primary Citation of Related Structures:  
    3A1I, 3A1K

  • PubMed Abstract: 

    In this study, we have structurally characterized the amidase of a nitrile-degrading bacterium, Rhodococcus sp. N-771 (RhAmidase). RhAmidase belongs to amidase signature (AS) family, a group of amidase families, and is responsible for the degradation of amides produced from nitriles by nitrile hydratase. Recombinant RhAmidase exists as a dimer of about 107 kDa. RhAmidase can hydrolyze acetamide, propionamide, acrylamide and benzamide with kcat/Km values of 1.14+/-0.23 mM(-1)s(-1), 4.54+/-0.09 mM(-1)s(-1), 0.087+/-0.02 mM(-1)s(-1) and 153.5+/-7.1 mM(-1)s(-1), respectively. The crystal structures of RhAmidase and its inactive mutant complex with benzamide (S195A/benzamide) were determined at resolutions of 2.17 A and 2.32 A, respectively. RhAmidase has three domains: an N-terminal alpha-helical domain, a small domain and a large domain. The N-terminal alpha-helical domain is not found in other AS family enzymes. This domain is involved in the formation of the dimer structure and, together with the small domain, forms a narrow substrate-binding tunnel. The large domain showed high structural similarities to those of other AS family enzymes. The Ser-cis Ser-Lys catalytic triad is located in the large domain. But the substrate-binding pocket of RhAmidase is relatively narrow, due to the presence of the helix alpha13 in the small domain. The hydrophobic residues from the small domain are involved in recognizing the substrate. The small domain likely participates in substrate recognition and is related to the difference of substrate specificities among the AS family amidases.

  • Organizational Affiliation

    Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amidase521Rhodococcus sp. N-771Mutation(s): 0 
Gene Names: ami
Find proteins for Q7DKE4 (Rhodococcus sp. N-771)
Explore Q7DKE4 
Go to UniProtKB:  Q7DKE4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7DKE4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on UNU

Download Ideal Coordinates CCD File 
C7 H7 N O
Experimental Data & Validation

Experimental Data

  • Resolution: 2.32 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.199 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.272α = 90
b = 92.272β = 90
c = 161.799γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description