2PEG

Crystal structure of Trematomus bernacchii hemoglobin in a partial hemichrome state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural characterization of ferric hemoglobins from three antarctic fish species of the suborder notothenioidei.

Vergara, A.Franzese, M.Merlino, A.Vitagliano, L.Verde, C.di Prisco, G.Lee, H.C.Peisach, J.Mazzarella, L.

(2007) Biophys.J. 93: 2822-2829

  • DOI: 10.1529/biophysj.107.105700

  • PubMed Abstract: 
  • Spontaneous autoxidation of tetrameric Hbs leads to the formation of Fe (III) forms, whose physiological role is not fully understood. Here we report structural characterization by EPR of the oxidized states of tetrameric Hbs isolated from the Antarc ...

    Spontaneous autoxidation of tetrameric Hbs leads to the formation of Fe (III) forms, whose physiological role is not fully understood. Here we report structural characterization by EPR of the oxidized states of tetrameric Hbs isolated from the Antarctic fish species Trematomus bernacchii, Trematomus newnesi, and Gymnodraco acuticeps, as well as the x-ray crystal structure of oxidized Trematomus bernacchii Hb, redetermined at high resolution. The oxidation of these Hbs leads to formation of states that were not usually detected in previous analyses of tetrameric Hbs. In addition to the commonly found aquo-met and hydroxy-met species, EPR analyses show that two distinct hemichromes coexist at physiological pH, referred to as hemichromes I and II, respectively. Together with the high-resolution crystal structure (1.5 A) of T. bernacchii and a survey of data available for other heme proteins, hemichrome I was assigned by x-ray crystallography and by EPR as a bis-His complex with a distorted geometry, whereas hemichrome II is a less constrained (cytochrome b5-like) bis-His complex. In four of the five Antartic fish Hbs examined, hemichrome I is the major form. EPR shows that for HbCTn, the amount of hemichrome I is substantially reduced. In addition, the concomitant presence of a penta-coordinated high-spin Fe (III) species, to our knowledge never reported before for a wild-type tetrameric Hb, was detected. A molecular modeling investigation demonstrates that the presence of the bulkier Ile in position 67beta in HbCTn in place of Val as in the other four Hbs impairs the formation of hemichrome I, thus favoring the formation of the ferric penta-coordinated species. Altogether the data show that ferric states commonly associated with monomeric and dimeric Hbs are also found in tetrameric Hbs.


    Related Citations: 
    • 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
    • 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

    Department of Chemistry, University of Naples Federico II, Complesso Universitario Monte S. Angelo, I-80126 Naples, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit alpha
A
143Pseudotrematomus bernacchiiMutation(s): 0 
Gene Names: hba
Find proteins for P80043 (Pseudotrematomus bernacchii)
Go to UniProtKB:  P80043
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit beta
B
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
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
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 87.160α = 90.00
b = 87.740β = 97.66
c = 55.380γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
X-PLORrefinement
CNSrefinement
MAR345dtbdata collection
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-24
    Type: Initial release
  • Version 1.1: 2007-10-09
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description
  • Version 1.4: 2019-07-24
    Type: Data collection, Derived calculations, Refinement description