4OB0

Crystal Structure of Nitrile Hydratase from Pseudonocardia thermophila bound to Phenyl Boronic Acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The active site sulfenic acid ligand in nitrile hydratases can function as a nucleophile.

Martinez, S.Wu, R.Sanishvili, R.Liu, D.Holz, R.

(2014) J.Am.Chem.Soc. 136: 1186-1189

  • DOI: 10.1021/ja410462j
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nitrile hydratase (NHase) catalyzes the hydration of nitriles to their corresponding commercially valuable amides at ambient temperatures and physiological pH. Several reaction mechanisms have been proposed for NHase enzymes; however, the source of t ...

    Nitrile hydratase (NHase) catalyzes the hydration of nitriles to their corresponding commercially valuable amides at ambient temperatures and physiological pH. Several reaction mechanisms have been proposed for NHase enzymes; however, the source of the nucleophile remains a mystery. Boronic acids have been shown to be potent inhibitors of numerous hydrolytic enzymes due to the open shell of boron, which allows it to expand from a trigonal planar (sp(2)) form to a tetrahedral form (sp(3)). Therefore, we examined the inhibition of the Co-type NHase from Pseudonocardia thermophila JCM 3095 (PtNHase) by boronic acids via kinetics and X-ray crystallography. Both 1-butaneboronic acid (BuBA) and phenylboronic acid (PBA) function as potent competitive inhibitors of PtNHase. X-ray crystal structures for BuBA and PBA complexed to PtNHase were solved and refined at 1.5, 1.6, and 1.2 Å resolution. The resulting PtNHase-boronic acid complexes represent a "snapshot" of reaction intermediates and implicate the cysteine-sulfenic acid ligand as the catalytic nucleophile, a heretofore unknown role for the αCys(113)-OH sulfenic acid ligand. Based on these data, a new mechanism of action for the hydration of nitriles by NHase is presented.


    Organizational Affiliation

    Department of Chemistry, Marquette University , Milwaukee, Wisconsin 53201, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cobalt-containing nitrile hydratase subunit alpha
A
210Pseudonocardia thermophilaMutation(s): 0 
EC: 4.2.1.84
Find proteins for Q7SID2 (Pseudonocardia thermophila)
Go to UniProtKB:  Q7SID2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cobalt-containing nitrile hydratase subunit beta
B
233Pseudonocardia thermophilaMutation(s): 0 
EC: 4.2.1.84
Find proteins for Q7SID3 (Pseudonocardia thermophila)
Go to UniProtKB:  Q7SID3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PBC
Query on PBC

Download SDF File 
Download CCD File 
A
PHENYL BORONIC ACID
C6 H7 B O2
HXITXNWTGFUOAU-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PBCKi: 5000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.152 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 65.680α = 90.00
b = 65.680β = 90.00
c = 185.691γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-26
    Type: Initial release