6R3W image
Entry Detail
PDB ID:
6R3W
Keywords:
Title:
M.tuberculosis nitrobindin with a water molecule coordinated to the heme iron atom
Biological Source:
PDB Version:
Deposition Date:
2019-03-21
Release Date:
2020-04-08
Method Details:
Experimental Method:
Resolution:
1.20 Å
R-Value Free:
0.17
R-Value Work:
0.13
R-Value Observed:
0.14
Space Group:
I 2 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:UPF0678 fatty acid-binding protein-like protein ERS007657_00996
Chain IDs:A
Chain Length:172
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
Ligand Molecules
Primary Citation
Mycobacterial and Human Nitrobindins: Structure and Function.
Antioxid.Redox Signal. 33 229 246 (2020)
PMID: 32295384 DOI: 10.1089/ars.2019.7874

Abstact

Aims: Nitrobindins (Nbs) are evolutionary conserved all-β-barrel heme-proteins displaying a highly solvent-exposed heme-Fe(III) atom. The physiological role(s) of Nbs is almost unknown. Here, the structural and functional properties of ferric Mycobacterium tuberculosis Nb (Mt-Nb(III)) and ferric Homo sapiens Nb (Hs-Nb(III)) have been investigated and compared with those of ferric Arabidopsis thaliana Nb (At-Nb(III), Rhodnius prolixus nitrophorins (Rp-NP(III)s), and mammalian myoglobins. Results: Data here reported demonstrate that Mt-Nb(III), At-Nb(III), and Hs-Nb(III) share with Rp-NP(III)s the capability to bind selectively nitric oxide, but display a very low reactivity, if any, toward histamine. Data obtained overexpressing Hs-Nb in human embryonic kidney 293 cells indicate that Hs-Nb localizes mainly in the cytoplasm and partially in the nucleus, thanks to a nuclear localization sequence encompassing residues Glu124-Leu154. Human Hs-Nb corresponds to the C-terminal domain of the human nuclear protein THAP4 suggesting that Nb may act as a sensor possibly modulating the THAP4 transcriptional activity residing in the N-terminal region. Finally, we provide strong evidence that both Mt-Nb(III) and Hs-Nb(III) are able to scavenge peroxynitrite and to protect free l-tyrosine against peroxynitrite-mediated nitration. Innovation: Data here reported suggest an evolutionarily conserved function of Nbs related to their role as nitric oxide sensors and components of antioxidant systems. Conclusion: Human THAP4 may act as a sensing protein that couples the heme-based Nb(III) reactivity with gene transcription. Mt-Nb(III) seems to be part of the pool of proteins required to scavenge reactive nitrogen and oxygen species produced by the host during the immunity response.

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