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PDBsum entry 2aa1
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protein ligands Protein-protein interface(s) links
Oxygen storage/transport PDB id
2aa1

 

 

 

 

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Contents
Protein chains
143 a.a. *
146 a.a. *
Ligands
HEM ×4
Waters ×369
* Residue conservation analysis
PDB id:
2aa1
Name: Oxygen storage/transport
Title: Crystal structure of the cathodic hemoglobin isolated from the antarctic fish trematomus newnesi
Structure: Hemoglobin alpha-1 chain. Chain: a, c. Hemoglobin beta-c chain. Chain: b, d
Source: Trematomus newnesi. Dusky notothen. Organism_taxid: 35730. Organism_taxid: 35730
Biol. unit: Tetramer (from PQS)
Resolution:
1.80Å     R-factor:   0.186     R-free:   0.220
Authors: L.Mazzarella,G.Bonomi,M.C.Lubrano,A.Merlino,A.Riccio,A.Vergara, L.Vitagliano,C.Verde,G.Di Prisco
Key ref:
L.Mazzarella et al. (2006). Minimal structural requirements for root effect: crystal structure of the cathodic hemoglobin isolated from the antarctic fish Trematomus newnesi. Proteins, 62, 316-321. PubMed id: 16299734 DOI: 10.1002/prot.20709
Date:
13-Jul-05     Release date:   02-Aug-05    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P45718  (HBA1_TRENE) -  Hemoglobin subunit alpha-1 from Trematomus newnesi
Seq:
Struc: 		142 a.a.
142 a.a.
Protein chains
Pfam   ArchSchema ?
P45721  (HBBC_TRENE) -  Hemoglobin subunit beta-C from Trematomus newnesi
Seq:
Struc: 		146 a.a.
146 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1002/prot.20709 Proteins 62:316-321 (2006)
PubMed id: 16299734  
 
 
Minimal structural requirements for root effect: crystal structure of the cathodic hemoglobin isolated from the antarctic fish Trematomus newnesi.
L.Mazzarella, G.Bonomi, M.C.Lubrano, A.Merlino, A.Riccio, A.Vergara, L.Vitagliano, C.Verde, G.di Prisco.
 
  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 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.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Fo-Fc electron density map of (A) the heme region, (B) the C-terminus of -chain, and (C) the [1] [2] interface at 3.5, 2.5, and 3.5 , respectively. 		Figure 2.
Figure 2. Stereo superimposition of the [1] [2] interface of the HbTb (black) and HbCTn (gray).
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 62, 316-321) copyright 2006.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21445848 L.Boechi, M.A.Martì, A.Vergara, F.Sica, L.Mazzarella, D.A.Estrin, and A.Merlino (2011).
Protonation of histidine 55 affects the oxygen access to heme in the alpha chain of the hemoglobin from the Antarctic fish Trematomus bernacchii.
  IUBMB Life, 63, 175-182.  
20210659 S.Campo, G.Nastasi, D.Fedeli, A.D'Ascola, G.M.Campo, A.Avenoso, A.Ferlazzo, A.Calatroni, and G.Falcioni (2010).
Molecular cloning and characterization of adult Sparus aurata hemoglobin genes.
  OMICS, 14, 187-200.  
19373928 A.Merlino, L.Vitagliano, B.D.Howes, C.Verde, G.di Prisco, G.Smulevich, F.Sica, and A.Vergara (2009).
Combined crystallographic and spectroscopic analysis of Trematomus bernacchii hemoglobin highlights analogies and differences in the peculiar oxidation pathway of Antarctic fish hemoglobins.
  Biopolymers, 91, 1117-1125.
PDB code: 3gkv
19651045 A.Vergara, M.Franzese, A.Merlino, G.Bonomi, C.Verde, D.Giordano, G.di Prisco, H.C.Lee, J.Peisach, and L.Mazzarella (2009).
Correlation between hemichrome stability and the root effect in tetrameric hemoglobins.
  Biophys J, 97, 866-874.
PDB code: 3gqg
19292863 D.Giordano, L.Boechi, A.Vergara, M.A.Martí, U.Samuni, D.Dantsker, L.Grassi, D.A.Estrin, J.M.Friedman, L.Mazzarella, G.di Prisco, and C.Verde (2009).
The hemoglobins of the sub-Antarctic fish Cottoperca gobio, a phyletically basal species--oxygen-binding equilibria, kinetics and molecular dynamics.
  FEBS J, 276, 2266-2277.  
19353640 E.Dodson, and G.Dodson (2009).
Movements at the hemoglobin A-hemes and their role in ligand binding, analyzed by X-ray crystallography.
  Biopolymers, 91, 1056-1063.  
17545238 A.Vergara, M.Franzese, A.Merlino, L.Vitagliano, C.Verde, G.di Prisco, H.C.Lee, J.Peisach, and L.Mazzarella (2007).
Structural characterization of ferric hemoglobins from three antarctic fish species of the suborder notothenioidei.
  Biophys J, 93, 2822-2829.
PDB code: 2peg
16717098 C.Verde, M.Balestrieri, D.de Pascale, D.Pagnozzi, G.Lecointre, and G.di Prisco (2006).
The oxygen transport system in three species of the boreal fish family Gadidae. Molecular phylogeny of hemoglobin.
  J Biol Chem, 281, 22073-22084.  
16909420 L.Mazzarella, A.Vergara, L.Vitagliano, A.Merlino, G.Bonomi, S.Scala, C.Verde, and G.di Prisco (2006).
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.
  Proteins, 65, 490-498.
PDB codes: 2h8d 2h8f
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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