5AB8

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

Summary for 5AB8

• Entry DOI: 10.2210/pdb5ab8/pdb
• Descriptor: GROUP 1 TRUNCATED HEMOGLOBIN GLBN, PROTOPORPHYRIN IX CONTAINING FE, FORMIC ACID, ... (6 entities in total)
• Functional Keywords: oxygen transport, truncated hemoglobins, 2/2 hemoglobins, globin dynamics, bacterial globins, heme/ligand tunneling, no dioxygenase
• Biological source: MYCOBACTERIUM TUBERCULOSIS
• Total number of polymer chains: 1
• Total formula weight: 14025.58

Authors

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. (deposition date: 2015-08-04, release date: 2015-11-04, Last modification date: 2024-01-10)

Primary citation

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.
The N-Terminal Pre-A Region of Mycobacterium Tuberculosis 2/2Hbn Promotes No-Dioxygenase Activity.
FEBS J., 283:305-, 2016

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.

PubMed: 26499089
DOI: 10.1111/FEBS.13571

Experimental method

X-RAY DIFFRACTION (1.53 Å)