3WUY

Crystal structure of Nit6803


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

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Literature

Structural insights into enzymatic activity and substrate specificity determination by a single amino acid in nitrilase from Syechocystis sp. PCC6803

Zhang, L.Yin, B.Wang, C.Jiang, S.Wang, H.Yuan, Y.A.Wei, D.

(2014) J Struct Biol 188: 93-101

  • DOI: 10.1016/j.jsb.2014.10.003
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Nitrilases are enzymes widely expressed in prokaryotes and eukaryotes that utilize a Cys–Glu–Lys catalytic triad to hydrolyze non-peptide carbon–nitrogen bonds. Nitrilase from Syechocystis sp. Strain PCC6803 (Nit6803) shows hydrolysis activity toward ...

    Nitrilases are enzymes widely expressed in prokaryotes and eukaryotes that utilize a Cys–Glu–Lys catalytic triad to hydrolyze non-peptide carbon–nitrogen bonds. Nitrilase from Syechocystis sp. Strain PCC6803 (Nit6803) shows hydrolysis activity towards a broad substrate spectrum, ranging from mononitriles to dinitriles and from aromatic nitriles to aliphatic nitriles. Yet, the structural principle of the substrate specificity of this nitrilase is still unknown. We report the crystal structure of Nit6803 at 3.1 Å resolution and propose a structural mechanism of substrate selection. Our mutagenesis data exhibited that the aromaticity of the amino acid at position 146 of Nit6803 is absolutely required for its nitrilase activity towards any substrates tested. Moreover, molecular docking and dynamic simulation analysis indicated that the distance between the sulfhydryl group of the catalytic cysteine residue and the cyano carbon of the substrate plays a crucial role in determining the nitrilase catalytic activity of Nit6803 and its mutants towards different nitrile substrates.


    Organizational Affiliation

    Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, France.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitrilase
A, B
349Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: merR
Find proteins for Q55949 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  Q55949
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.545α = 90
b = 113.545β = 90
c = 161.009γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SHARPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-31
    Type: Initial release