2AA1

Crystal structure of the cathodic hemoglobin isolated from the Antarctic fish Trematomus Newnesi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 316-321

  • DOI: 10.1002/prot.20709
  • Also Cited By: 3D1K, 2H8F, 2H8D

  • PubMed Abstract: 
  • The cathodic hemoglobin component of the Antarctic fish Trematomus newnesi (HbCTn) is a Root-effect protein. The interpretation of its functional properties in relation to its sequence is puzzling. Indeed, HbCTn sequence is characterized by an extrem ...

    The cathodic hemoglobin component of the Antarctic fish Trematomus newnesi (HbCTn) is a Root-effect protein. The interpretation of its functional properties in relation to its sequence is puzzling. Indeed, HbCTn sequence is characterized by an extremely low histidyl content, and in particular by the lack of His146beta and His69beta, which are believed to be important in Bohr and Root effects, respectively. Furthermore, previous analyses suggested that the local environment of Asp95alpha, Asp99beta, and Asp101beta should not be appropriate for the formation of Asp-Asp interactions, which are important for the Root effect. Here, we report the high-resolution crystal structure of the deoxy form of HbCTn. Our data provide a structural interpretation for the very low oxygen affinity of the protein and insights into the structural determinants of the Root effect protein. The structure demonstrates that the presence of Ile41alpha and Ser97alpha at the alpha1beta2 interface does not prevent the formation of the inter-Asp interactions in HbCTn, as previous studies had suggested. The present data indicate that the hydrogen bond formed between Asp95alpha and Asp101beta, which is stabilized by Asp99beta, is per se sufficient to generate the Root effect, and it is the minimal structural requirement needed for the design of Root-effect Hbs.


    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


    Organizational Affiliation

    Dipartimento di Chimica, Universit√° degli Studi di Napoli Federico II, Naples, Italy. mazzarella@chemistry.unina.it




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin alpha-1 chain
A, C
143Trematomus newnesiMutation(s): 0 
Gene Names: hba1
Find proteins for P45718 (Trematomus newnesi)
Go to UniProtKB:  P45718
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin beta-C chain
B, D
146Trematomus newnesiMutation(s): 0 
Find proteins for P45721 (Trematomus newnesi)
Go to UniProtKB:  P45721
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: 1.8 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.186 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 58.097α = 80.73
b = 60.801β = 81.36
c = 61.232γ = 62.01
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance