4ESA

X-ray structure of carbonmonoxy hemoglobin of Eleginops maclovinus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

ATP regulation of the ligand-binding properties in temperate and cold-adapted haemoglobins. X-ray structure and ligand-binding kinetics in the sub-Antarctic fish Eleginops maclovinus.

Coppola, D.Abbruzzetti, S.Nicoletti, F.Merlino, A.Gambacurta, A.Giordano, D.Howes, B.D.De Sanctis, G.Vitagliano, L.Bruno, S.di Prisco, G.Mazzarella, L.Smulevich, G.Coletta, M.Viappiani, C.Vergara, A.Verde, C.

(2012) Mol Biosyst 8: 3295-3304

  • DOI: 10.1039/c2mb25210d

  • PubMed Abstract: 
  • The major haemoglobin of the sub-Antarctic fish Eleginops maclovinus was structurally and functionally characterised with the aim to compare molecular environmental adaptations in the O(2)-transport system of sub-Antarctic fishes of the suborder Noto ...

    The major haemoglobin of the sub-Antarctic fish Eleginops maclovinus was structurally and functionally characterised with the aim to compare molecular environmental adaptations in the O(2)-transport system of sub-Antarctic fishes of the suborder Notothenioidei with those of their high-latitude relatives. Ligand-binding kinetics of the major haemoglobin of E. maclovinus indicated strong stabilisation of the liganded quaternary T state, enhanced in the presence of the physiological allosteric effector ATP, compared to that of high-Antarctic Trematomus bernacchii. The activation enthalpy for O(2) dissociation was dramatically lower than that in T. bernacchii haemoglobin, suggesting remarkable differences in temperature sensitivity and structural changes associated with O(2) release and exit from the protein. The haemoglobin functional properties, together with the X-ray structure of the CO form at 1.49 Å resolution, the first of a temperate notothenioid, strongly support the hypothesis that in E. maclovinus, whose life-style varies according to changes in habitat, the mechanisms that regulate O(2) affinity and the ATP-induced Root effect differ from those of high-Antarctic Notothenioids.


    Related Citations: 
    • Combined crystallographic and spectroscopic analysis of Trematomus bernacchii hemoglobin highlights analogies and differences in the peculiar oxidation pathway of Antarctic fish hemoglobins.
      Merlino, A.,Vitagliano, L.,Howes, B.D.,Verde, C.,di Prisco, G.,Smulevich, G.,Sica, F.,Vergara, A.
      (2009) Biopolymers 91: 1117
    • Spectroscopic and crystallographic characterization of a tetrameric hemoglobin oxidation reveals structural features of the functional intermediate relaxed/tense state.
      Vitagliano, L.,Vergara, A.,Bonomi, G.,Merlino, A.,Verde, C.,di Prisco, G.,Howes, B.D.,Smulevich, G.,Mazzarella, L.
      (2008) J.Am.Chem.Soc. 130: 10527


    Organizational Affiliation

    Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, I-80131 Naples, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin alpha chain
A, C
143Eleginops maclovinusMutation(s): 0 
Gene Names: hba1
Find proteins for K7N5M5 (Eleginops maclovinus)
Go to UniProtKB:  K7N5M5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin beta chain
B, D
146Eleginops maclovinusMutation(s): 0 
Gene Names: hbb1
Find proteins for K7N5M6 (Eleginops maclovinus)
Go to UniProtKB:  K7N5M6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-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
CMO
Query on CMO

Download SDF File 
Download CCD File 
A, B, C, D
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 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: 1.45 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.175α = 90.00
b = 88.075β = 90.00
c = 123.194γ = 90.00
Software Package:
Software NamePurpose
SHELXLrefinement
HKL-2000data scaling
HKL-2000data collection
AMoREphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-07
    Type: Initial release
  • Version 1.1: 2013-01-02
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description