2H8F

Crystal structure of deoxy hemoglobin from Trematomus bernacchii at pH 6.2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

High resolution crystal structure of deoxy hemoglobin from Trematomus bernacchii at different pH values: The role of histidine residues in modulating the strength of the root effect.

Mazzarella, L.Vergara, A.Vitagliano, L.Merlino, A.Bonomi, G.Scala, S.Verde, C.di Prisco, G.

(2006) Proteins 65: 490-498

  • DOI: 10.1002/prot.21114
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The Root effect is a widespread property in fish hemoglobins (Hbs) that produces a drastic reduction of cooperativity and oxygen-binding ability at acidic pH. Here, we report the high-resolution structure of the deoxy form of Hb isolated from the Ant ...

    The Root effect is a widespread property in fish hemoglobins (Hbs) that produces a drastic reduction of cooperativity and oxygen-binding ability at acidic pH. Here, we report the high-resolution structure of the deoxy form of Hb isolated from the Antarctic fish Trematomus bernacchii (HbTb) crystallized at pH 6.2 and 8.4. The structure at acidic pH has been previously determined at a moderate resolution (Ito et al., J Mol Biol 1995;250:648-658). Our results provide a clear picture of the events occurring upon the pH increase from 6.2 to 8.4, observed within a practically unchanged crystal environment. In particular, at pH 8.4, the interaspartic hydrogen bond at the alpha(1)beta(2) interface is partially broken, suggesting a pK(a) close to 8.4 for Asp95alpha. In addition, a detailed survey of the histidine modifications, caused by the change in pH, also indicates that at least three hot regions of the molecule are modified (Ebeta helix, Cbeta-tail, CDalpha corner) and can be considered to be involved at various levels in the release of the Root protons. Most importantly, at the CDalpha corner, the break of the salt bridge Asp48alpha-His55alpha allows us to describe a detailed mechanism that transmits the modification from the CDalpha corner far to the alpha heme. More generally, the results shed light on the role played by the histidine residues in modulating the strength of the Root effect and also support the emerging idea that the structural determinants, at least for a part of the Root effect, are specific of each Hb endowed with this property.


    Related Citations: 
    • Minimal structural requirements for root effect: crystal structure of the cathodic hemoglobin isolated from the antarctic fish Trematomus newnesi
      Mazzarella, L., Bonomi, G., Lubrano, M.C., Merlino, A., Riccio, A., Vergara, A., Vitagliano, L., Verde, C., di Prisco, G.
      (2006) Proteins 62: 316
    • Crystal structure of Trematomus newnesi haemoglobin re-opens the root effect question
      Mazzarella, L., D'Avino, R., di Prisco, G., Savino, C., Vitagliano, L., Moody, P.C.E., Zagari, A.
      (1999) J Mol Biol 287: 897

    Organizational Affiliation

    Dipartimento di Chimica, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte S. Angelo, via Cinthia, I-80126 Naples, Italy. lelio.mazzarella@unina.it



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin beta subunitB, D146Trematomus bernacchiiMutation(s): 0 
Gene Names: hbb
Find proteins for P80044 (Pseudotrematomus bernacchii)
Explore P80044 
Go to UniProtKB:  P80044
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin alpha subunitA, C143Trematomus bernacchiiMutation(s): 0 
Gene Names: hba
Find proteins for P80043 (Pseudotrematomus bernacchii)
Explore P80043 
Go to UniProtKB:  P80043
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.151 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.85α = 90
b = 95.042β = 90.19
c = 61.824γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORmodel building
SHELXL-97refinement
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance