4OB0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 

wwPDB Validation   3D Report Full Report


This is version 1.1 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:  
    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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cobalt-containing nitrile hydratase subunit alpha A210Pseudonocardia thermophilaMutation(s): 0 
EC: 4.2.1.84
Find proteins for Q7SID2 (Pseudonocardia thermophila)
Explore Q7SID2 
Go to UniProtKB:  Q7SID2
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cobalt-containing nitrile hydratase subunit beta B233Pseudonocardia thermophilaMutation(s): 0 
EC: 4.2.1.84
Find proteins for Q7SID3 (Pseudonocardia thermophila)
Explore Q7SID3 
Go to UniProtKB:  Q7SID3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PBC
Query on PBC

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.68α = 90
b = 65.68β = 90
c = 185.691γ = 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