2H8D

Crystal structure of deoxy hemoglobin from Trematomus bernacchii at pH 8.4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.180 

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
  • Primary Citation of Related Structures:  
  • Also Cited By: 3D1K

  • 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: 
    • 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
    • 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


    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: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin alpha subunit
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 subunit
B, D
146Pseudotrematomus bernacchiiMutation(s): 0 
Gene Names: hbb
Find proteins for P80044 (Pseudotrematomus bernacchii)
Go to UniProtKB:  P80044
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
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: 1.78 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.800α = 90.00
b = 94.630β = 90.19
c = 61.860γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORmodel building
X-PLORphasing
SCALEPACKdata scaling
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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