| Literature DB >> 30524950 |
Giovanna De Simone1, Alessandra di Masi1, Fabio Polticelli1,2, Paolo Ascenzi3.
Abstract
Nitrobindins (Nbs), constituting a heme-protein family spanning from bacteria to Homo sapiens, display an all-β-barrel structural organization. Human Nb has been described as a domain of the nuclear protein named THAP4, whose physiological function is still unknown. We report the first evidence of the heme-Fe(III)-based detoxification of peroxynitrite by the all-β-barrel C-terminal Nb-like domain of THAP4. Ferric human Nb (Nb(III)) catalyzes the conversion of peroxynitrite to NO 3 - and impairs the nitration of free l-tyrosine. The rate of human Nb(III)-mediated scavenging of peroxynitrite is similar to those of all-α-helical horse heart and sperm whale myoglobin and human hemoglobin, generally taken as the prototypes of all-α-helical heme-proteins. The heme-Fe(III) reactivity of all-β-barrel human Nb(III) and all-α-helical prototypical heme-proteins possibly reflects the out-to-in-plane transition of the heme-Fe(III)-atom preceding peroxynitrite binding. Human Nb(III) not only catalyzes the detoxification of peroxynitrite but also binds NO, possibly representing a target of reactive nitrogen species.Entities:
Keywords: human nitrobindin; kinetics; peroxynitrite scavenging; protection of l‐tyrosine nitration
Year: 2018 PMID: 30524950 PMCID: PMC6275384 DOI: 10.1002/2211-5463.12534
Source DB: PubMed Journal: FEBS Open Bio ISSN: 2211-5463 Impact factor: 2.693
Figure 1Peroxynitrite isomerization in the absence and presence of human Nb(III).
Figure 2Effect of human Nb(III) on peroxynitrite isomerization (k obs), at 25.0 °C. (A) Averaged time courses of the human Nb(III)‐mediated isomerization of peroxynitrite at pH 7.1. Data analysis according to Eqn (1) allowed us to determine the following values of k obs: 4.9 × 10−1 s−1 (trace a) and 1.4 s−1 (trace b). The human Nb(III) concentration was 5.0 × 10−6 m (trace a) and 3.5 × 10−5 m (trace b). The peroxynitrite concentration was 2.0 × 10−4 m. (B) Dependence of k obs on the human Nb(III) concentration, at pH 6.1 (open circles), 7.1 (open triangles), and 7.7 (open diamonds). Kinetics were analyzed according to Eqn (2) with values of k obs and k 0 given in Table 1. (C) Dependence of k obs on the human apo‐Nb concentration, at pH 7.1. The symbol on the ordinate axis indicates the value of k 0 (=(2.6 ± 0.3) × 10−1 s−1). The average value of k obs is (2.7 ± 0.4) × 10−1 s−1. The peroxynitrite concentration was 2.0 × 10−4 m. Where not shown, the standard deviation is smaller than the symbol.
Values of k on and k 0 values for peroxynitrite isomerization by human Nb(III), at 25.0 °C
| pH |
|
|
|---|---|---|
| 6.1 | (1.1 ± 0.1) × 105 | (6.2 ± 0.7) × 10−1 |
| 6.3 | (9.8 ± 1.1) × 104 | (4.9 ± 0.5) × 10−1 |
| 6.6 | (8.1 ± 0.8) × 104 | (4.1 ± 0.4) × 10−1 |
| 7.1 | (3.4 ± 0.4) × 104 | (2.6 ± 0.3) × 10−1 |
| 7.4 | (1.8 ± 0.2) × 104 | (1.3 ± 0.1) × 10−1 |
| 7.7 | (1.3 ± 0.2) × 104 | (6.3 ± 0.8) × 10−2 |
Figure 3Effect of pH on human Nb(III)‐mediated peroxynitrite isomerization, at 25.0 °C. (A) Effect of pH on values of k on. The continuous line was calculated according to Eqn (3) with p a = 6.7 ± 0.2 and k lim = (1.4 ± 0.1) × 105 m −1·s−1. (B) Effect of pH on values of k 0. The continuous line was calculated according to Eqn (3) with p a = 6.8 ± 0.2 and k lim = (7.1 ± 0.5) × 10−1 s−1. Where not shown, the standard deviation is smaller than the symbol.
Figure 4Protective role of Nb on peroxynitrite‐mediated nitrosylation of free L‐tyrosine, at pH 7.1 and 25.0 °C. Effect of human Nb(III) (open triangles) and apo‐Nb (filled triangles) concentration on the relative yield of nitro‐l‐tyrosine formed by the reaction of peroxynitrite with free l‐tyrosine. The symbol on the ordinate axis (open triangle) indicates the relative yield of nitro‐l‐tyrosine obtained in the absence of human Nb(III) and apo‐Nb. The free l‐tyrosine concentration was 1.0 × 10−4 m. The peroxynitrite concentration was 2.0 × 10−4 m. Relative nitro‐l‐tyrosine yield (%) = (yield with added human Nb(III) or apo‐Nb/yield with no human Nb(III) or apo‐Nb) × 100. Where not shown, the standard deviation is smaller than the symbol.
Peroxynitrite scavenging by ferric heme‐proteins and heme‐model compounds. n.d., not determined
| Heme‐protein |
|
|
|---|---|---|
|
| 3.8 × 104 | 2.8 × 10−1 |
|
| 6.2 × 104 | 2.7 × 10−1 |
|
| 2.9 × 104 | 2.8 × 10−1 |
|
| 9.6 × 105 | 3.0 × 10−1 |
| Horse heart Mb | 2.9 × 104 | 3.5 × 10−1 |
| Sperm whale Mb | 1.6 × 104 | n.d. |
| Human Hb | 1.2 × 104 | 3.0 × 10−1 |
| Human Nb | 3.4 × 104 | 2.6 × 10−1 |
| Human SA‐heme | 4.1 × 105 | 2.6 × 10−1 |
| CL‐cyt | 3.2 × 105 | 2.9 × 10−1 |
| CM‐cyt | 6.8 × 104 | 2.8 × 10−1 |
|
| ~ 5 × 105 | 9.0 × 10−2 |
| Fe(TMPS) | 6.0 × 104 | 5.5 × 10−1 |
| Fe(TMPS) | 3.0 × 105 | 1.35 |
| Fe(TPPS) | 8.6 × 105 | 1.35 |
| Fe(TMPyP) | 1.6 × 106 | 1.35 |
| MP11 | 4.1 × 104 | 2.8 × 10−1 |
pH 7.4 and 20.0 °C. From 44.
pH 7.0 and 20.0 °C. From 42.
pH 7.0 and 20.0 °C. From 43.
pH 7.3 and 25.0 °C. From 46.
pH 7.0 and 20.0 °C. From 36.
pH 7.5 and 20.0 °C. From 38.
pH 7.1 and 25.0 °C. Present study.
pH 7.2 and 22.0 °C. From 39.
pH 7.0 and 20.0 °C. CL was 1.6 × 10−4 m. From 40.
pH 7.0 and 20.0 °C. From 41.
pH 8.0 and 12.0 °C. From 33.
pH 7.6 and 25.0 °C. From 34.
pH 7.4 and 37.0 °C. From 35.
pH 7.2 and 20.0 °C. From 45.
Figure 5Structural aspects of the heme site of human Nb(III) (PDB code: 3IA8) 23 and sperm whale Mb(III) (PDB code: 5MBN) 50. (A) Solvent accessible surface of the heme distal site of human Nb(III) and sperm whale Mb(III). The heme distal plane is much more solvent accessible in human Nb(III) than in sperm whale Mb(III). (B) Schematic representation of the heme coordination in human Nb(III) and sperm whale Mb(III). The heme proximal residues of human Nb and sperm whale Mb are His155 and His93, respectively. In human Nb(III) and sperm whale Mb(III), the heme‐Fe(III) atom is positioned ~ 0.35 to ~ 0.65 Å out‐of‐plane on the proximal side with respect to the pyrrole nitrogen atoms of the porphyrin, respectively. The pictures have been drawn with UCSF‐Chimera package 64.