1S5Y

The crystal structure of Trematomus bernacchii hemoglobin oxidized by ferricyanide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The oxidation process of Antarctic fish hemoglobins

Vitagliano, L.Bonomi, G.Riccio, A.Di Prisco, G.Smulevich, G.Mazzarella, L.

(2004) Eur.J.Biochem. 271: 1651-1659

  • DOI: 10.1111/j.1432-1033.2004.04054.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Analysis of the molecular properties of proteins extracted from organisms living under extreme conditions often highlights peculiar features. We investigated by UV-visible spectroscopy and X-ray crystallography the oxidation process, promoted by air ...

    Analysis of the molecular properties of proteins extracted from organisms living under extreme conditions often highlights peculiar features. We investigated by UV-visible spectroscopy and X-ray crystallography the oxidation process, promoted by air or ferricyanide, of five hemoglobins extracted from Antarctic fishes (Notothenioidei). Spectroscopic analysis revealed that these hemoglobins share a common oxidation pathway, which shows striking differences from the oxidation processes of hemoglobins from other vertebrates. Indeed, simple exposure of these hemoglobins to air leads to the formation of a significant amount of the low-spin hexacoordinated form, denoted hemichrome. This hemichrome form, which is detected under a variety of experimental conditions, can be reversibly transformed to either carbomonoxy or deoxygenated forms with reducing agents. Interestingly, the spectra of the fully oxidized species, obtained by treating the protein with ferricyanide, show the simultaneous presence of peaks corresponding to different hexacoordinated states, the aquomet and the hemichrome. In order to assign the heme region state of the alpha and beta chains, the air-oxidized and ferricyanide-oxidized forms of Trematomus bernacchii hemoglobin were crystallized. Crystallographic analysis revealed that these forms correspond to an alpha(aquomet)-beta(bishistidyl-hemichrome) state. This demonstrates that the alpha and beta chains of Antarctic fish hemoglobins follow very different oxidation pathways. As found for Trematomus newnesi hemoglobin in a partial hemichrome state [Riccio, A., Vitagliano, L., di Prisco, G., Zagari, A. & Mazzarella, L. (2002) Proc. Natl Acad. Sci. USA99, 9801-9806], the quaternary structures of these alpha(aquomet)-beta(bishistidyl-hemichrome) forms are intermediate between the physiological R and T hemoglobin states. Together, these structures provide information on the general features of this intermediate state.


    Related Citations: 
    • The crystal structure of a tetrameric hemoglobin in a partial hemichrome state
      Riccio, A.,Vitagliano, L.,di Prisco, G.,Zagari, A.,Mazzarella, L.
      (2002) Proc.Natl.Acad.Sci.USA 99: 9801


    Organizational Affiliation

    Istituto di Biostrutture e Bioimmagini, CNR, Napoli, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin alpha chain
A, C
143Pseudotrematomus bernacchiiMutation(s): 0 
Gene Names: hba
Find proteins for P80043 (Pseudotrematomus bernacchii)
Go to UniProtKB:  P80043
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin beta chain
B, D
146Pseudotrematomus bernacchiiMutation(s): 0 
Gene Names: hbb
Find proteins for P80044 (Pseudotrematomus bernacchii)
Go to UniProtKB:  P80044
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A, C
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 55.993α = 77.06
b = 62.980β = 69.79
c = 63.502γ = 84.17
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
XPRESSdata collection
DENZOdata reduction
AMoREphasing
XPRESSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-04
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description