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 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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
  • Primary Citation of Related Structures:  
    3WUY

  • 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 towards a broad substrate spectrum, ranging from mononitriles to dinitriles and from aromatic nitriles to aliphatic nitriles ...

    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

    RIKEN Systems and Structural Biology Center, Tsurumi-ku, Yokohama, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrilase AB349Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: merR
Find proteins for Q55949 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore Q55949 
Go to UniProtKB:  Q55949
Protein Feature View
Expand
  • Reference Sequence
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

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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