Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 14.03 kDa 
• Atom Count: 1096 
• Residue Count: 117 
• Unique protein chains: 1

5AB8

High resolution X-ray structure of the N-terminal truncated form (residues 1-11) of Mycobacterium tuberculosis HbN

• DOI: 10.2210/pdb5AB8/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-08-04 Released: 2015-11-04 
• Deposition Author(s): Pesce, A., Bustamante, J.P., Bidon-Chanal, A., Boechi, L., Estrin, D.A., Luque, F.J., Sebilo, A., Guertin, M., Bolognesi, M., Ascenzi, P., Nardini, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.209 
• R-Value Work: 0.140 
• R-Value Observed: 0.144 

Literature

The N-Terminal Pre-A Region of Mycobacterium Tuberculosis 2/2Hbn Promotes No-Dioxygenase Activity.

Pesce, A., Bustamante, J.P., Bidon-Chanal, A., Boechi, L., Estrin, D.A., Luque, F.J., Sebilo, A., Guertin, M., Bolognesi, M., Ascenzi, P., Nardini, M.

(2016) FEBS J 283: 305

• PubMed: 26499089 
• DOI: 10.1111/febs.13571
• Primary Citation of Related Structures:  
  5AB8


• PubMed Abstract: 
  

A unique defense mechanisms by which Mycobacterium tuberculosis protects itself from nitrosative stress is based on the O2 -dependent NO-dioxygenase (NOD) activity of truncated hemoglobin 2/2HbN (Mt2/2HbN). The NOD activity largely depends on the efficiency of ligand migration to the heme cavity through a two-tunnel (long and short) system; recently, it was also correlated with the presence at the Mt2/2HbN N-terminus of a short pre-A region, not conserved in most 2/2HbNs, whose deletion results in a drastic reduction of NO scavenging. In the present study, we report the crystal structure of Mt2/2HbN-ΔpreA, lacking the pre-A region, at a resolution of 1.53 Å. We show that removal of the pre-A region results in long range effects on the protein C-terminus, promoting the assembly of a stable dimer, both in the crystals and in solution. In the Mt2/2HbN-ΔpreA dimer, access of heme ligands to the short tunnel is hindered. Molecular dynamics simulations show that the long tunnel branch is the only accessible pathway for O2 -ligand migration to/from the heme, and that the gating residue Phe(62)E15 partly restricts the diameter of the tunnel. Accordingly, kinetic measurements indicate that the kon value for peroxynitrite isomerization by Mt2/2HbN-ΔpreA-Fe(III) is four-fold lower relative to the full-length protein, and that NO scavenging by Mt2/2HbN-ΔpreA-Fe(II)-O2 is reduced by 35-fold. Therefore, we speculate that Mt2/2HbN evolved to host the pre-A region as a mechanism for preventing dimerization, thus reinforcing the survival of the microorganism against the reactive nitrosative stress in macrophages.

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Organizational Affiliation: 

Department of Biosciences, University of Milan, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GROUP 1 TRUNCATED HEMOGLOBIN GLBN	A	125	Mycobacterium tuberculosis	Mutation(s): 0
Find proteins for P9WN25 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WN25  Go to UniProtKB:  P9WN25

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	A	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT	A	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.209 
• R-Value Work: 0.140 
• R-Value Observed: 0.144 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.16	α = 90
b = 43.16	β = 90
c = 212.9	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-08-04 
• Released Date: 2015-11-04 
Deposition Author(s): Pesce, A., Bustamante, J.P., Bidon-Chanal, A., Boechi, L., Estrin, D.A., Luque, F.J., Sebilo, A., Guertin, M., Bolognesi, M., Ascenzi, P., Nardini, M.

Revision History 

• Version 1.0: 2015-11-04
  Type: Initial release
  
• Version 1.1: 2016-03-09
  Changes: Database references
• Version 1.2: 2019-03-06
  Changes: Data collection, Experimental preparation, Other