Structural heterogeneity and ligand gating in ferric methanosarcina acetivorans protoglobin mutants

Abstract

Protoglobin from Methanosarcina acetivorans C2A (MaPgb), a strictly anaerobic methanogenic Archaea, displays peculiar structural and functional properties within members of the hemoglobin superfamily. In fact, MaPgb‐specific loops and a N‐terminal extension (20 amino acid residues) completely bury the heme within the protein matrix. Therefore, the access of diatomic gaseous molecules to the heme is granted by two apolar tunnels reaching the heme distal site from locations at the B/G and B/E helix interfaces. The presence of two tunnels within the protein matrix could be partly responsible for the slightly biphasic ligand binding behavior. Unusually, MaPgb oxygenation is favored with respect to carbonylation. Here, the crucial role of Tyr(B10)61 and Ile(G11)149 residues, located in the heme distal site and lining the protein matrix tunnels 1 and 2, respectively, on ligand binding to the heme‐Fe‐atom and on distal site structural organization is reported. In particular, tunnel 1 accessibility is modulated by a complex reorganization of the Trp(B9)60 and Phe(E11)93 side‐chains, triggered by mutations of the Tyr(B10)61 and Ile(G11)149 residues, and affected by the presence and type of the distal heme‐bound ligand. © 2011 IUBMB IUBMB Life, 63(5): 287–294, 2011

Structural and Functional Characterization of the Globin-Coupled Sensors ofAzotobacter vinelandiiandBordetella pertussis

“…The overall fold of AvGReg-Gb and BpeGReg-Gb* conform to the modified globin fold typically found for GCS sensor domains (44,63,75) and protoglobin (40,45,46), consisting of 8 helices which, according to the classical globin nomenclature, have been named in alphabetical order from A to H, with a Z helix preceding the A at the N-terminus and the D helix absent (Figs. 5A,B).…”

Human nitrobindin: the first example of an all‐β‐barrel ferric heme‐protein that catalyzes peroxynitrite detoxification

“…ferric all-a-helical globins (i.e., Methanosarcina acetivorans protoglobin (Ma-Pgb), Mycobacterium tuberculosis truncated hemoglobin N (Mt-trHbN), Pseudoalteromonas haloplanktis truncated hemoglobin O (Ph-trHbO), horse heart Mb(III), sperm whale Mb (III), human Hb(III), human serum heme-albumin (human SA-heme), and Fusarium oxysporum cytochrome P450 NO reductase) and mixed b-barrel/ a-helical cardiolipin-bound and carboxymethylated cytochrome c (CL-cytc and CM-cytc, respectively) ( Table 2) ( [33,[36][37][38][39][40][41][42][43][44] and present study), suggesting that neither the very different structural organization [1,3,22,23,[50][51][52][53][54][55][56][57][58] nor the different solvent and ligand accessibility to the metal center ( Fig. 5, panel A) ( [1,3,22,23,[50][51][52][53][54][55][56][57][58] and present study) nor the Lewis acidity of the heme-Fe(III) atom [38] are at the root of the modulation of peroxynitrite isomerization. In fact, the reactivity of these heme-proteins appears to be limited by the out-to-in-plane movement of the heme-Fe(III) atom preceding ligand (i.e., peroxynitrite) binding ( Fig.…”

“…Of note, in ferric all-b-barrel human Nb and in most all-a-helical globins (e.g., sperm whale Mb and human Hb), the heme-Fe(III) atom is positioned~0.35 to~0.65 A out-of-plane on the proximal side with respect to the pyrrole nitrogen atoms of the porphyrin, respectively (Fig. 5, panel B) ( [1,3,22,23,[50][51][52][53][54]57,58] and present study). The high reactivity of ferric Campylobacter jejuni truncated hemoglobin P (Cj-trHbP) ( Table 2) reflects the high ligand accessibility to the heme center by the HisE7 path, the dynamic balance of hydrogen-bonding interactions at the heme distal site, and the penta-coordination of the heme-Fe atom; this suggested a role of Cj-trHbP in performing a peroxidase-like chemistry [46,[59][60][61].…”

Structure and Haem-Distal Site Plasticity in Methanosarcina acetivorans Protoglobin

“…The size and plasticity of the Ma Pgb*(III) distal site [25] suggest that the protein could bind haem ligands bigger than “classical” diatomic species. Therefore, a triatomic molecule such as azide was tested.…”