2AHJ

NITRILE HYDRATASE COMPLEXED WITH NITRIC OXIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.3 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 Biol 5: 347-351

  • DOI: 10.1038/nsb0598-347
  • Primary Citation of Related Structures:  
    2AHJ

  • 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 spectrometry revealed the structure of the non-heme iron catalytic center in the nitrosylated state ...

    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

    Organizational Affiliation

    Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China. Electronic address: dongyh@ihep.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NITRILE HYDRATASEA, C206Rhodococcus erythropolisMutation(s): 2 
Gene Names: nthA
EC: 4.2.1.84
UniProt
Find proteins for P13448 (Rhodococcus erythropolis)
Explore P13448 
Go to UniProtKB:  P13448
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NITRILE HYDRATASEB, D212Rhodococcus erythropolisMutation(s): 0 
Gene Names: nthBnha2
EC: 4.2.1.84
UniProt
Find proteins for P13449 (Rhodococcus erythropolis)
Explore P13449 
Go to UniProtKB:  P13449
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A], I [auth B], N [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DIO
Query on DIO

Download Ideal Coordinates CCD File 
J [auth B], O [auth D]1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A], K [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
E [auth A], L [auth C]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
NO
Query on NO

Download Ideal Coordinates CCD File 
H [auth A], M [auth C]NITRIC OXIDE
N O
ODUCDPQEXGNKDN-UHFFFAOYAM
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A, CL-PEPTIDE LINKINGC3 H7 N O4 SCYS
CSO
Query on CSO
A, CL-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.4α = 90
b = 145.6β = 90
c = 52.1γ = 90
Software Package:
Software NamePurpose
DMmodel building
MLPHAREphasing
X-PLORrefinement
WEISdata reduction
CCP4data scaling
DMphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-01-27
    Type: Initial release
  • Version 1.1: 2008-03-10
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-08-21
    Changes: Advisory, Data collection, Derived calculations