4OB3 | pdb_00004ob3

Crystal Structure of Nitrile Hydratase from Pseudonocardia thermophila : A Reference Structure to Boronic Acid Inhibition of Nitrile Hydratase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 
    0.202 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.175 (Depositor) 
  • R-Value Observed: 
    0.176 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4OB3

This is version 1.2 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: https://doi.org/10.1021/ja410462j
  • Primary Citation Related Structures: 
    4OB0, 4OB1, 4OB2, 4OB3

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 50.85 kDa 
  • Atom Count: 4,003 
  • Modeled Residue Count: 433 
  • Deposited Residue Count: 444 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cobalt-containing nitrile hydratase subunit alpha211Pseudonocardia thermophilaMutation(s): 0 
EC: 4.2.1.84
UniProt
Find proteins for Q7SID2 (Pseudonocardia thermophila)
Explore Q7SID2 
Go to UniProtKB:  Q7SID2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SID2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cobalt-containing nitrile hydratase subunit beta233Pseudonocardia thermophilaMutation(s): 0 
EC: 4.2.1.84
UniProt
Find proteins for Q7SID3 (Pseudonocardia thermophila)
Explore Q7SID3 
Go to UniProtKB:  Q7SID3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SID3
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free:  0.202 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.175 (Depositor) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.234α = 90
b = 65.234β = 90
c = 184.308γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary