2AHJ

NITRILE HYDRATASE COMPLEXED WITH NITRIC OXIDE

• PDB DOI: https://doi.org/10.2210/pdb2AHJ/pdb

• Classification: LYASE
• Organism(s): Rhodococcus erythropolis
• Mutation(s): Yes 


• Deposited: 1997-12-24 Released: 1999-01-27 
• Deposition Author(s): Nagashima, S., Nakasako, M., Dohmae, N., Tsujimura, M., Takio, K., Odaka, M., Yohda, M., Kamiya, N., Endo, I.

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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 

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

• PubMed: 9586994 
• DOI: https://doi.org/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. 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 93.66 kDa 
• Atom Count: 7,082 
• Modelled Residue Count: 812 
• Deposited Residue Count: 836 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NITRILE HYDRATASE	A, C	206	Rhodococcus erythropolis	Mutation(s): 2  EC: 4.2.1.84
UniProt
Find proteins for P13448 (Rhodococcus erythropolis) Explore P13448  Go to UniProtKB:  P13448

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NITRILE HYDRATASE	B, D	212	Rhodococcus erythropolis	Mutation(s): 0  EC: 4.2.1.84
UniProt
Find proteins for P13449 (Rhodococcus erythropolis) Explore P13449  Go to UniProtKB:  P13449

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], I [auth B], N [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DIO	J [auth B], O [auth D]	1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-UHFFFAOYSA-N
ZN	F [auth A], K [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE	E [auth A], L [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
NO	H [auth A], M [auth C]	NITRIC OXIDE N O ODUCDPQEXGNKDN-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A, C	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS
CSO	A, C	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

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 = 117.4	α = 90
b = 145.6	β = 90
c = 52.1	γ = 90

Software Package:

Software Name	Purpose
DM	model building
MLPHARE	phasing
X-PLOR	refinement
WEIS	data reduction
CCP4	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-01-27 
Deposition Author(s): Nagashima, S., Nakasako, M., Dohmae, N., Tsujimura, M., Takio, K., Odaka, M., Yohda, M., Kamiya, N., Endo, I.

Revision History  

• 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
• Version 1.4: 2022-12-21
  Changes: Database references, Derived calculations