1JNI

Structure of the NapB subunit of the periplasmic nitrate reductase from Haemophilus influenzae.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The 1.25 A resolution structure of the diheme NapB subunit of soluble nitrate reductase reveals a novel cytochrome c fold with a stacked heme arrangement.

Brige, A.Leys, D.Meyer, T.E.Cusanovich, M.A.Van Beeumen, J.J.

(2002) Biochemistry 41: 4827-4836

  • Also Cited By: 1OGY, 3U99

  • PubMed Abstract: 
  • The diheme cytochrome NapB constitutes the small subunit of a periplasmic nitrate reductase found in a wide variety of bacterial species, including pathogens. The NapB protein is essential in transferring electrons to the large catalytic subunit NapA ...

    The diheme cytochrome NapB constitutes the small subunit of a periplasmic nitrate reductase found in a wide variety of bacterial species, including pathogens. The NapB protein is essential in transferring electrons to the large catalytic subunit NapA, which subsequently reduces nitrate to nitrite. Here we present the crystal structure of a proteolyzed form of recombinant NapB from Haemophilus influenzae, which was determined by the multiple-wavelength anomalous dispersion (MAD) method at 1.25 A resolution. This structure shows an unprecedented fold, confirming that NapB proteins belong to a new class of cytochromes. The two heme groups have nearly parallel heme planes and are stacked at van der Waals distances with an iron-to-iron distance of only 9.9 A, two structural features that are also present in the split-Soret diheme cytochrome c from Desulfovibrio desulfuricans ATCC 27774, which is otherwise unrelated in the peptide chain folding pattern. The two propionate side chains on both heme groups are hydrogen-bonded to each other, a structural characteristic that to date also has not been reported in any other heme protein. The propionates of one of the heme groups are pulled toward the interior of the molecule due to a salt bridge and a number of hydrogen bonds between the propionates and conserved residues. We propose a hypothetical but plausible model of the NapAB complex in which the four redox centers are positioned in a virtually linear configuration which spans a distance of nearly 40 A, suggesting an efficient pathway for the transfer of electrons from NapC, the physiological electron donor of NapB, to a nitrate molecule at the catalytic site of NapA.


    Organizational Affiliation

    Laboratory of Protein Biochemistry and Protein Engineering, State University of Gent, Ledeganckstraat 35, B-9000 Gent, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIHEME CYTOCHROME C NAPB
A
123Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)Gene Names: napB
Find proteins for P44654 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Go to UniProtKB:  P44654
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.170 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.752α = 90.00
b = 78.752β = 90.00
c = 29.047γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MLPHAREphasing
SHELXL-97refinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-17
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance