2AHJ

NITRILE HYDRATASE COMPLEXED WITH NITRIC OXIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Novel non-heme iron center of nitrile hydratase with a claw setting of oxygen atoms.

Nagashima, S.Nakasako, M.Dohmae, N.Tsujimura, M.Takio, K.Odaka, M.Yohda, M.Kamiya, N.Endo, I.

(1998) Nat.Struct.Mol.Biol. 5: 347-351


  • PubMed Abstract: 
  • The iron-containing nitrile hydratase (NHase) is a photoreactive enzyme that is inactivated in the dark because of persistent association with NO and activated by photo-dissociation of NO. The crystal structure at 1.7 A resolution and mass spectromet ...

    The iron-containing nitrile hydratase (NHase) is a photoreactive enzyme that is inactivated in the dark because of persistent association with NO and activated by photo-dissociation of NO. The crystal structure at 1.7 A resolution and mass spectrometry revealed the structure of the non-heme iron catalytic center in the nitrosylated state. Two Cys residues coordinated to the iron were post-translationally modified to Cys-sulfenic and -sulfinic acids. Together with another oxygen atom of the Ser ligand, these modifications induced a claw setting of oxygen atoms capturing an NO molecule. This unprecedented structure is likely to enable the photo-regulation of NHase and will provide an excellent model for designing photo-controllable chelate complexes and, ultimately, proteins.


    Related Citations: 
    • Crystallization of a Photosensitive Nitrile Hydratase from Rhodococcus Sp. N-771
      Nagamune, T.,Honda, J.,Cho, W.D.,Kamiya, N.,Teratani, Y.,Hirata, A.,Sasabe, H.,Endo, I.
      (1991) J.Mol.Biol. 220: 221



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NITRILE HYDRATASE
A, C
206Rhodococcus erythropolisMutation(s): 0 
Gene Names: nthA
EC: 4.2.1.84
Find proteins for P13448 (Rhodococcus erythropolis)
Go to UniProtKB:  P13448
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NITRILE HYDRATASE
B, D
212Rhodococcus erythropolisMutation(s): 0 
Gene Names: nthB (nha2)
EC: 4.2.1.84
Find proteins for P13449 (Rhodococcus erythropolis)
Go to UniProtKB:  P13449
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, C
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
DIO
Query on DIO

Download SDF File 
Download CCD File 
B, D
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
NO
Query on NO

Download SDF File 
Download CCD File 
A, C
NITRIC OXIDE
Nitrogen monoxide
N O
ODUCDPQEXGNKDN-UHFFFAOYAM
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A, C
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
CSD
Query on CSD
A, C
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 117.400α = 90.00
b = 145.600β = 90.00
c = 52.100γ = 90.00
Software Package:
Software NamePurpose
DMphasing
DMmodel building
X-PLORrefinement
WEISdata reduction
MLPHAREphasing
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-27
    Type: Initial release
  • Version 1.1: 2008-03-10
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance