4OB2 | pdb_00004ob2

Crystal Structure of Nitrile Hydratase from Pseudonocardia thermophila bound to Butaneboronic Acid via Crystal Soaking


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 
    0.183 (Depositor), 0.183 (DCC) 
  • R-Value Work: 
    0.152 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 
    0.153 (Depositor) 

wwPDB Validation   3D Report Full Report


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 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. 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cobalt-containing nitrile hydratase subunit alpha209Pseudonocardia 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:  (by identity cutoff)  |  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
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BUB
Query on BUB

Download Ideal Coordinates CCD File 
C [auth A]1-BUTANE BORONIC ACID
C4 H11 B O2
QPKFVRWIISEVCW-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
R [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CO
Query on CO

Download Ideal Coordinates CCD File 
D [auth A]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
MOH
Query on MOH

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
METHANOL
C H4 O
OKKJLVBELUTLKV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free:  0.183 (Depositor), 0.183 (DCC) 
  • R-Value Work:  0.152 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 0.153 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.601α = 90
b = 65.601β = 90
c = 185.658γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
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: 2014-11-26
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-12-25
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary