2ZCF | pdb_00002zcf

Mutational study on Alpha-Gln90 of Fe-type nitrile hydratase from Rhodococcus sp. N771


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 
    0.211 (Depositor) 
  • R-Value Work: 
    0.169 (Depositor) 
  • R-Value Observed: 
    0.169 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2ZCF

This is version 2.0 of the entry. See complete history

Literature

Mutational study on alphaGln90 of Fe-type nitrile hydratase from Rhodococcus sp. N771

Takarada, H.Kawano, Y.Hashimoto, K.Nakayama, H.Ueda, S.Yohda, M.Kamiya, N.Dohmae, N.Maeda, M.Odaka, M.

(2006) Biosci Biotechnol Biochem 70: 881-889

  • DOI: https://doi.org/10.1271/bbb.70.881
  • Primary Citation Related Structures: 
    2ZCF

  • PubMed Abstract: 

    Nitrile hydratase (NHase) from Rhodococcus sp. N771 is a non-heme iron enzyme having post-translationally modified cysteine ligands, alphaCys112-SO2H and alphaCys114-SOH. We replaced alphaGln90, which is conserved in all known NHases and involved in the hydrogen-bond network around the catalytic center, with glutamic acid or asparagine. The kcat of alphaQ90E and alphaQ90N mutants decreased to 24% and 5% that of wild type respectively, but the effect of mutations on Km was not very significant. In both mutants, the alphaCys114-SOH modification appeared to be responsible for the catalysis as in native NHase. We crystallized the nitrosylated alphaQ90N mutant and determined its structure at a resolution of 1.43 A. The structure was basically identical to that of native nitrosylated NHase except for the mutated site and its vicinity. The structural difference between native and alphaQ90N mutant NHases suggested the importance of the hydrogen bond networks between alphaGln90 and the iron center for the catalytic activity.


  • Organizational Affiliation
    • United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan.

Macromolecule Content 

  • Total Structure Weight: 46.51 kDa 
  • Atom Count: 3,867 
  • Modeled Residue Count: 410 
  • Deposited Residue Count: 418 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitrile hydratase subunit alpha206Rhodococcus erythropolisMutation(s): 1 
Gene Names: nthA
EC: 4.2.1.84
UniProt
Find proteins for P13448 (Rhodococcus erythropolis)
Explore P13448 
Go to UniProtKB:  P13448
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13448
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitrile hydratase subunit beta212Rhodococcus erythropolisMutation(s): 0 
Gene Names: nthB
EC: 4.2.1.84
UniProt
Find proteins for P13449 (Rhodococcus erythropolis)
Explore P13449 
Go to UniProtKB:  P13449
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13449
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE

Query on FE



Download:Ideal Coordinates CCD File
C [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free:  0.211 (Depositor) 
  • R-Value Work:  0.169 (Depositor) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.838α = 90
b = 60.554β = 125.05
c = 82.187γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection
  • Version 1.5: 2024-10-09
    Changes: Structure summary
  • Version 2.0: 2025-10-29
    Changes: Advisory, Atomic model, Data collection, Derived calculations