Crystal structure of Mycobacterium tuberculosis trHbN TyrB10Phe mutant

Experimental Data Snapshot

  • Resolution: 1.73 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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Ligand interactions in the distal heme pocket of Mycobacterium tuberculosis truncated hemoglobin N: roles of TyrB10 and GlnE11 residues

Ouellet, Y.Milani, M.Couture, M.Bolognesi, M.Guertin, M.

(2006) Biochemistry 45: 8770-8781

  • DOI: https://doi.org/10.1021/bi060112o
  • Primary Citation of Related Structures:  
    2GKM, 2GKN, 2GL3, 2GLN

  • PubMed Abstract: 

    The crystallographic structure of oxygenated trHbN from Mycobacterium tuberculosis showed an extended heme distal site hydrogen-bonding network that includes Y(B10), Q(E11), and the bound O(2) (Milani, M., et al. (2001) EMBO J. 20, 3902-3909). In the present work, we analyze the effects that substitutions at the B10 and E11 positions exert on the heme and its coordinated ligands, using steady-state resonance Raman spectroscopy, absorption spectroscopy and X-ray crystallography. Our results show that (1) residues Y(B10) and Q(E11) control the binding and the ionization state of the heme-bound water molecules in ferric trHbN and are important in keeping the sixth coordination position vacant in deoxy trHbN; (2) residue Q(E11) plays a role in maintaining the integrity of the proximal Fe-His bond in deoxy trHbN; (3) in wild-type oxy-trHbN, the size and hydrogen-bonding capability of residue E11 is important to sustain proper interaction between Y(B10) and the heme-bound O(2); (4) CO-trHbN is in a conformational equilibrium, where either the Y(B10) or the Q(E11) residue interacts with the heme-bound CO; and (5) Y(B10) and Q(E11) residues control the conformation (and likely the dynamics) of the protein matrix tunnel gating residue F(E15). These findings suggest that the functional processes of ligand binding and diffusion are controlled in trHbN through the dynamic interaction of residues Y(B10), Q(E11), F(E15), and the heme ligand.

  • Organizational Affiliation

    Department of Biochemistry and Microbiology, Laval University, Quebec, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin-like protein HbN
A, B
136Mycobacterium tuberculosisMutation(s): 1 
Gene Names: glbN
Find proteins for P9WN25 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WN25 
Go to UniProtKB:  P9WN25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WN25
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.73 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.278α = 90
b = 61.932β = 90
c = 90.291γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-02-14
    Changes: Data collection