4XMC

Crystal structure of nitrophorin 7 from Rhodnius prolixus at pH 5.8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.421 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7.

Knipp, M.Ogata, H.Soavi, G.Cerullo, G.Allegri, A.Abbruzzetti, S.Bruno, S.Viappiani, C.Bidon-Chanal, A.Luque, F.J.

(2015) F1000Res 4: 45-45

  • DOI: 10.12688/f1000research.6060.1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nitrophorins represent a unique class of heme proteins that are able to perform the delicate transportation and release of the free-radical gaseous messenger nitric oxide (NO) in a pH-triggered manner. Besides its ability to bind to phospholipid memb ...

    Nitrophorins represent a unique class of heme proteins that are able to perform the delicate transportation and release of the free-radical gaseous messenger nitric oxide (NO) in a pH-triggered manner. Besides its ability to bind to phospholipid membranes, the N-terminus contains an additional Leu-Pro-Gly stretch, which is a unique sequence trait, and the heme cavity is significantly altered with respect to other nitrophorins. These distinctive features encouraged us to solve the X-ray crystallographic structures of NP7 at low and high pH and bound with different heme ligands (nitric oxide, histamine, imidazole). The overall fold of the lipocalin motif is well preserved in the different X-ray structures and resembles the fold of other nitrophorins. However, a chain-like arrangement in the crystal lattice due to a number of head-to-tail electrostatic stabilizing interactions is found in NP7. Furthermore, the X-ray structures also reveal ligand-dependent changes in the orientation of the heme, as well as in specific interactions between the A-B and G-H loops, which are considered to be relevant for the biological function of nitrophorins. Fast and ultrafast laser triggered ligand rebinding experiments demonstrate the pH-dependent ligand migration within the cavities and the exit route. Finally, the topological distribution of pockets located around the heme as well as from inner cavities present at the rear of the protein provides a distinctive feature in NP7, so that while a loop gated exit mechanism to the solvent has been proposed for most nitrophorins, a more complex mechanism that involves several interconnected gas hosting cavities is proposed for NP7.


    Organizational Affiliation

    Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr, 45470, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitrophorin-7
A
184Rhodnius prolixusMutation(s): 0 
EC: 1.7.6.1
Find proteins for Q6PQK2 (Rhodnius prolixus)
Go to UniProtKB:  Q6PQK2
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: 1.421 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 38.419α = 90.00
b = 66.999β = 116.57
c = 38.997γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-01-14 
  • Released Date: 2015-07-29 
  • Deposition Author(s): Ogata, H.

Revision History 

  • Version 1.0: 2015-07-29
    Type: Initial release