1LA6

The crystal structure of Trematomus newnesi hemoglobin in a partial hemichrome state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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This is version 1.2 of the entry. See complete history


Literature

The crystal structure of a tetrameric hemoglobin in a partial hemichrome state

Riccio, A.Vitagliano, L.di Prisco, G.Zagari, A.Mazzarella, L.

(2002) Proc Natl Acad Sci U S A 99: 9801-9806

  • DOI: 10.1073/pnas.132182099
  • Primary Citation of Related Structures:  
    1LA6

  • PubMed Abstract: 
  • Tetrameric hemoglobins are the most widely used systems in studying protein cooperativity. Allosteric effects in hemoglobins arise from the switch between a relaxed (R) state and a tense (T) state occurring upon oxygen release. Here we report the 2.0-A crystal structure of the main hemoglobin component of the Antarctic fish Trematomus newnesi, in a partial hemichrome form ...

    Tetrameric hemoglobins are the most widely used systems in studying protein cooperativity. Allosteric effects in hemoglobins arise from the switch between a relaxed (R) state and a tense (T) state occurring upon oxygen release. Here we report the 2.0-A crystal structure of the main hemoglobin component of the Antarctic fish Trematomus newnesi, in a partial hemichrome form. The two alpha-subunit iron atoms are bound to a CO molecule, whereas in the beta subunits the distal histidine residue is the sixth ligand of the heme iron. This structure, a tetrameric hemoglobin in the hemichrome state, demonstrates that the iron coordination by the distal histidine, usually associated with denaturing states, may be tolerated in a native-like hemoglobin structure. In addition, several features of the tertiary and quaternary organization of this structure are intermediate between the R and T states and agree well with the R --> T transition state properties obtained by spectroscopic and kinetic techniques. The analysis of this structure provides a detailed pathway of heme-heme communication and it indicates that the plasticity of the beta heme pocket plays a role in the R --> T transition of tetrameric hemoglobins.


    Related Citations: 
    • Liganded and unliganded forms of Antarctic fish haemoglobins in polyethylene glycol: crystallization of an R-state haemichrome intermediate
      Riccio, A., Vitagliano, L., di Prisco, G., Zagari, A., Mazzarella, L.
      (2001) Acta Crystallogr 57: 1144
    • 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

    Istituto di Biochimica delle Proteine ed Enzimologia, Consiglio Nazionale delle Ricerche, I-80125 Naples, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin alpha-1 chain A143Trematomus newnesiMutation(s): 0 
Gene Names: hba1
Find proteins for P45718 (Trematomus newnesi)
Explore P45718 
Go to UniProtKB:  P45718
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin beta-1/2 chain B146Trematomus newnesiMutation(s): 0 
Find proteins for P45720 (Trematomus newnesi)
Explore P45720 
Go to UniProtKB:  P45720
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CMO
Query on CMO

Download Ideal Coordinates CCD File 
A
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.853α = 90
b = 88.19β = 97.79
c = 55.142γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-31
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance