1U0X

Crystal structure of nitrophorin 4 under pressure of xenon (200 psi)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural dynamics controls nitric oxide affinity in nitrophorin 4

Nienhaus, K.Maes, E.M.Weichsel, A.Montfort, W.R.Nienhaus, G.U.

(2004) J.Biol.Chem. 279: 39401-39407

  • DOI: 10.1074/jbc.M406178200

  • PubMed Abstract: 
  • Nitrophorin 4 (NP4) is one of seven nitric oxide (NO) transporting proteins in the blood-sucking insect Rhodnius prolixus. In its physiological function, NO binds to a ferric iron centered in a highly ruffled heme plane. Carbon monoxide (CO) also bin ...

    Nitrophorin 4 (NP4) is one of seven nitric oxide (NO) transporting proteins in the blood-sucking insect Rhodnius prolixus. In its physiological function, NO binds to a ferric iron centered in a highly ruffled heme plane. Carbon monoxide (CO) also binds after reduction of the heme iron. Here we have used Fourier transform infrared spectroscopy at cryogenic temperatures to study CO and NO binding and migration in NP4, complemented by x-ray cryo-crystallography on xenon-containing NP4 crystals to identify cavities that may serve as ligand docking sites. Multiple infrared stretching bands of the heme-bound ligands indicate different active site conformations with varying degrees of hydrophobicity. Narrow infrared stretching bands are observed for photodissociated CO and NO; temperature-derivative spectroscopy shows that these bands are associated with ligand docking sites close to the extremely reactive heme iron. No rebinding from distinct secondary sites was detected, although two xenon binding cavities were observed in the x-ray structure. Photolysis studies at approximately 200 K show efficient NO photoproduct formation in the more hydrophilic, open NP4 conformation. This result suggests that ligand escape is facilitated in this conformation, and blockage of the active site by water hinders immediate reassociation of NO to the ferric iron. In the closed, low-pH conformation, ligand escape from the active site of NP4 is prevented by an extremely reactive heme iron and the absence of secondary ligand docking sites.


    Related Citations: 
    • Nitric Oxide Binding to Nitrophorin 4 Induces Complete Distal Pocket Burial
      Weichsel, A.,Andersen, J.F.,Roberts, S.A.,Montfort, W.R.
      (2000) Nat.Struct.Mol.Biol. 7: 551
    • Ligand-Induced Heme Ruffling and Bent NO Geometry in Ultra-High-Resolution Structures of Nitrophorin 4
      Roberts, S.A.,Weichsel, A.,Qui, Y.,Shelnutt, J.A.,Walker, F.A.,Montfort, W.R.
      (2001) Biochemistry 40: 11327


    Organizational Affiliation

    Department of Biophysics, University of Ulm, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitrophorin 4
A
184Rhodnius prolixusMutation(s): 0 
EC: 1.7.6.1
Find proteins for Q94734 (Rhodnius prolixus)
Go to UniProtKB:  Q94734
Small Molecules
Ligands 3 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
XE
Query on XE

Download SDF File 
Download CCD File 
A
XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
 Ligand Interaction
NH3
Query on NH3

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Download CCD File 
A
AMMONIA
H3 N
QGZKDVFQNNGYKY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.143 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 70.196α = 90.00
b = 42.461β = 94.24
c = 52.990γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
CrystalCleardata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance