5YTL

Crystal structure of Geobacillus thermodenitrificans copper-containing nitrite reductase determined with an anaerobically manipulated crystal


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.113 
  • R-Value Observed: 0.115 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystallographic study of dioxygen chemistry in a copper-containing nitrite reductase from Geobacillus thermodenitrificans.

Fukuda, Y.Matsusaki, T.Tse, K.M.Mizohata, E.Murphy, M.E.P.Inoue, T.

(2018) Acta Crystallogr D Struct Biol 74: 769-777

  • DOI: https://doi.org/10.1107/S2059798318010082
  • Primary Citation of Related Structures:  
    5YTL, 5YTM, 5YTN

  • PubMed Abstract: 

    Copper-containing nitrite reductases (CuNIRs) are multifunctional enzymes that catalyse the one-electron reduction of nitrite (NO 2 - ) to nitric oxide (NO) and the two-electron reduction of dioxygen (O 2 ) to hydrogen peroxide (H 2 O 2 ). In contrast to the mechanism of nitrite reduction, that of dioxygen reduction is poorly understood. Here, results from anaerobic synchrotron-radiation crystallography (SRX) and aerobic in-house radiation crystallography (iHRX) with a CuNIR from the thermophile Geobacillus thermodenitrificans (GtNIR) support the hypothesis that the dioxygen present in an aerobically manipulated crystal can bind to the catalytic type 2 copper (T2Cu) site of GtNIR during SRX experiments. The anaerobic SRX structure showed a dual conformation of one water molecule as an axial ligand in the T2Cu site, while previous aerobic SRX GtNIR structures were refined as diatomic molecule-bound states. Moreover, an SRX structure of the C135A mutant of GtNIR with peroxide bound to the T2Cu atom was determined. The peroxide molecule was mainly observed in a side-on binding manner, with a possible minor end-on conformation. The structures provide insights into dioxygen chemistry in CuNIRs and hence help to unmask the other face of CuNIRs.


  • Organizational Affiliation

    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Copper-containing nitrite reductase323Geobacillus thermodenitrificansMutation(s): 0 
Gene Names: nirKGTHT12_00198
EC: 1.7.2.1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
H [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
MRD
Query on MRD

Download Ideal Coordinates CCD File 
G [auth A](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
CU
Query on CU

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
ACY
Query on ACY

Download Ideal Coordinates CCD File 
I [auth A]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.113 
  • R-Value Observed: 0.115 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.314α = 90
b = 115.314β = 90
c = 84.534γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan--
The Natural Sciences and Engineering Research Council of CanadaCanada--

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references, Derived calculations