Archaeal protoglobin structure indicates new ligand diffusion paths and modulation of haem‐reactivity

Abstract

The structural adaptability of the globin fold has been highlighted by the recent discovery of the 2-on-2 haemoglobins, of neuroglobin and cytoglobin. Protoglobin from Methanosarcina acetivorans C2A-a strictly anaerobic methanogenic Archaea-is, to the best of our knowledge, the latest entry adding new variability and functional complexity to the haemoglobin (Hb) superfamily. Here, we report the 1.3 Å crystal structure of oxygenated M. acetivorans protoglobin, together with the first insight into its ligand-binding properties. We show that, contrary to all known globins, protoglobin-specific loops and an amino-terminal extension completely bury the haem within the protein matrix. Access of O 2 , CO and NO to the haem is granted by the protoglobinspecific apolar tunnels reaching the haem distal site from locations at the B/G and B/E helix interfaces. Functionally, M. acetivorans dimeric protoglobin shows a selectivity ratio for O 2 /CO binding to the haem that favours O 2 ligation and anticooperativity in ligand binding. Both properties are exceptional within the Hb superfamily.

Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park

“…Specifically, the NAG1 contains the most deeply rooted protoglobin known to date (Supplementary Figure S8), and appears to provide an evolutionary linkage to higher globins such as hemoglobin that are thought to have evolved from an ancestral protoglobin (Moens et al, 1996;Freitas et al, 2005;Nardini et al, 2008). Protoglobins from the obligately aerobic hyperthermophile A. pernix and the strictly anaerobic methanogen Methanosarcina acetivorans have been found to bind molecular oxygen, nitric oxide and CO, potentially protecting the organisms from nitrosative and oxidative stress (Freitas et al, 2004).…”

Structural heterogeneity and ligand gating in ferric methanosarcina acetivorans protoglobin mutants

“…2B and 4A). It is worth noting that Phe(E11)93 mobility has been already observed in MaPgbO 2 , where the residue side-chain is affected by conformational disorder (6). On the contrary, Phe(E11)93 adopts a defined conformation in the ligand-free ferric MaPgb (6), where the fixed conformation of Phe(E11)93 triggers a rotation of about 458 of the Tyr(B10)61 side-chain relative to MaPgbO 2 , giving rise to a wider distal site cavity.…”

“…Tunnel 2 ($5 Å in diameter, and $10 Å in length) is a straight opening to the heme distal cavity nestled among residues Tyr(B10)61, Leu(B13)64, Gly(B14)65, Leu(C5)71, Phe(CD1)74, and Leu(E4)86. All residues lining the MaPgb tunnels are conserved in known Pgbs, suggesting functional implications for ligand diffusion to/from the heme cavity, for multiligand storage and/or for (pseudo-)enzymatic actions (6). The presence of two tunnels within the protein matrix could be partly responsible for the slightly biphasic behavior of CO binding of the Here, the role of the Tyr(B10)61 and Ile(G11)149 residues, located in the heme distal site and lining tunnels 1 and 2, respectively, is reported.…”

“…Homodimeric MaPgb displays unusual functional and structural properties, as O 2 and CO binding are slightly anticooperative processes (6). Moreover, the heme is completely buried in the Pgb protein matrix and the diatomic ligand diffusion path to the heme pocket through the E7-gate is precluded.…”

“…So far, two archaeal Pgbs have been characterized, namely, one from the obligate aerobic hyperthermophile Aeropyrum pernix (2) and one from the strictly anaerobic methanogen Methanosarcina acetivorans [protoglobin from Methanosarcina acetivorans C2A (MaPgb)] (6). Although functional issues are still unclear, these two archaeal Pgbs have been proposed to facilitate O 2 detoxification and/or to act as CO sensor/supplier in methanogenesis (2,6).…”