3D1K

R/T intermediate quaternary structure of an antarctic fish hemoglobin in an alpha(CO)-beta(pentacoordinate) state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10527-10535

  • DOI: 10.1021/ja803363p
  • Also Cited By: 4ESA, 3GKV

  • PubMed Abstract: 
  • Tetrameric hemoglobins represent the most commonly used model for the description of the basic concepts of protein allostery. The classical stereochemical model assumes a concerted transition of the protein, upon oxygen release, from the relaxed (R) ...

    Tetrameric hemoglobins represent the most commonly used model for the description of the basic concepts of protein allostery. The classical stereochemical model assumes a concerted transition of the protein, upon oxygen release, from the relaxed (R) to the tense (T) state. Despite the large amount of data accumulated on the end-points of the transition, scarce structural information is available on the intermediate species along the pathway. Here we report a spectroscopic characterization of the autoxidation process of the Trematomus newnesi major Hb component and the atomic resolution structure (1.25 A) of an intermediate form along the pathway characterized by a different binding and oxidation state of the alpha and beta chains. In contrast to the alpha-heme iron, which binds a CO molecule, the beta iron displays a pentacoordinated oxidized state, which is rare in tetrameric hemoglobins. Interestingly, the information provided by the present analysis is not limited to the characterization of the peculiar oxidation process of Antarctic fish hemoglobins. Indeed, this structure represents the most detailed snapshot of hemoglobin allosteric transition hitherto achieved. Upon ligand release at the beta heme, a cascade of structural events is observed. Notably, several structural features of the tertiary structure of the alpha and beta chains closely resemble those typically observed in the deoxygenated state. The overall quaternary structure also becomes intermediate between the R and the T state. The analysis of the alterations induced by the ligand release provides a clear picture of the temporal sequence of the events associated with the transition. The implications of the present findings have also been discussed in the wider context of tetrameric Hbs.


    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
    • 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


    Organizational Affiliation

    Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit alpha-1
A
142Trematomus newnesiMutation(s): 0 
Gene Names: hba1
Find proteins for P45718 (Trematomus newnesi)
Go to UniProtKB:  P45718
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit beta-1/2
B
146Trematomus newnesiMutation(s): 0 
Find proteins for P45720 (Trematomus newnesi)
Go to UniProtKB:  P45720
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
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
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
ACE
Query on ACE

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Download CCD File 
A
ACETYL GROUP
C2 H4 O
IKHGUXGNUITLKF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.167 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 88.458α = 90.00
b = 87.664β = 99.16
c = 55.502γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
AMoREphasing
SHELXL-97refinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

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