3WIA

Crystal structure of the N-terminal 1-37 residues deleted mutant of Geobacillus copper nitrite reductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural and functional characterization of the Geobacillus copper nitrite reductase: involvement of the unique N-terminal region in the interprotein electron transfer with its redox partner

Fukuda, Y.Koteishi, H.Yoneda, R.Tamada, T.Takami, H.Inoue, T.Nojiri, M.

(2014) Biochim.Biophys.Acta 1837: 396-405

  • DOI: 10.1016/j.bbabio.2014.01.004
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structures of copper-containing nitrite reductase (CuNiR) from the thermophilic Gram-positive bacterium Geobacillus kaustophilus HTA426 and the amino (N)-terminal 68 residue-deleted mutant were determined at resolutions of 1.3Å and 1.8Å, ...

    The crystal structures of copper-containing nitrite reductase (CuNiR) from the thermophilic Gram-positive bacterium Geobacillus kaustophilus HTA426 and the amino (N)-terminal 68 residue-deleted mutant were determined at resolutions of 1.3Å and 1.8Å, respectively. Both structures show a striking resemblance with the overall structure of the well-known CuNiRs composed of two Greek key β-barrel domains; however, a remarkable structural difference was found in the N-terminal region. The unique region has one β-strand and one α-helix extended to the northern surface of the type-1 copper site. The superposition of the Geobacillus CuNiR model on the electron-transfer complex structure of CuNiR with the redox partner cytochrome c551 in other denitrifier system led us to infer that this region contributes to the transient binding with the partner protein during the interprotein electron transfer reaction in the Geobacillus system. Furthermore, electron-transfer kinetics experiments using N-terminal residue-deleted mutant and the redox partner, Geobacillus cytochrome c551, were carried out. These structural and kinetics studies demonstrate that the region is directly involved in the specific partner recognition.


    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan; Molecular Biology Research Center, Quantum Beam Science Directorate, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitrite reductase
A, B, C, D, E, F, G, H, I
287Geobacillus kaustophilus (strain HTA426)Mutation(s): 0 
Find proteins for Q5L1X8 (Geobacillus kaustophilus (strain HTA426))
Go to UniProtKB:  Q5L1X8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 89.317α = 90.00
b = 164.991β = 102.27
c = 126.561γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data collection
REFMACrefinement
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-09-09 
  • Released Date: 2014-07-23 
  • Deposition Author(s): Fukuda, Y., Nojiri, M.

Revision History 

  • Version 1.0: 2014-07-23
    Type: Initial release