3AQ6

Crystal structure of truncated hemoglobin from Tetrahymena pyriformis, Fe(III) form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A hydrogen-bonding network formed by the B10-E7-E11 residues of a truncated hemoglobin from Tetrahymena pyriformis is critical for stability of bound oxygen and nitric oxide detoxification.

Igarashi, J.Kobayashi, K.Matsuoka, A.

(2011) J Biol Inorg Chem 16: 599-609

  • DOI: https://doi.org/10.1007/s00775-011-0761-3
  • Primary Citation of Related Structures:  
    3AQ5, 3AQ6, 3AQ7, 3AQ8, 3AQ9

  • PubMed Abstract: 

    Truncated hemoglobins (trHbs) are distributed from bacteria to unicellular eukaryotes and have roles in oxygen transport and nitric oxide detoxification. It is known that trHbs exist in ciliates of the Tetrahymena group, but trHb structure and function remain poorly understood. To investigate trHb function with respect to stability of bound oxygen and protein structure, we measured the oxygen binding kinetics of Tetrahymena pyriformis trHb, and determined the crystal structure of the protein. The O(2) association and dissociation rate constants of T. pyriformis trHb were 5.5 μM(-1 )s(-1) and 0.18 s(-1), respectively. The autooxidation rate constant was 3.8 × 10(-3) h(-1). These values are similar to those of HbN from Mycobacterium tuberculosis. The three-dimensional structure of an Fe(II)-O(2) complex of T. pyriformis trHb was determined at 1.73-Å resolution. Tyr25 (B10) and Gln46 (E7) were hydrogen-bonded to a heme-bound O(2) molecule. Tyr25 donated a hydrogen bond to the terminal oxygen atom, whereas Gln46 hydrogen-bonded to the proximal oxygen atom. Furthermore, Tyr25 was hydrogen-bonded to the Gln46 and Gln50 (E11) residues. Mutations at Tyr25, Gln46, and Gln50 increased the O(2) dissociation and autooxidation rate constants. An Fe(III)-H(2)O complex of T. pyriformis trHb was formed following reaction of the Fe(II)-O(2) complex of T. pyriformis trHb, in a crystal state, with nitric oxide. This suggests that T. pyriformis trHb functions in nitric oxide detoxification.


  • Organizational Affiliation

    Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Japan. jotaro@tagen.tohoku.ac.jp


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Group 1 truncated hemoglobin
A, B
121Tetrahymena pyriformisMutation(s): 0 
UniProt
Find proteins for P17724 (Tetrahymena pyriformis)
Explore P17724 
Go to UniProtKB:  P17724
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17724
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.567α = 90
b = 69.567β = 90
c = 354.311γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description