3QZX

3D Structure of ferric methanosarcina acetivorans protoglobin Y61A mutant with unknown ligand

Summary for 3QZX

• Entry DOI: 10.2210/pdb3qzx/pdb
• Related: 2VEB 2VEE 3QZZ 3R0G
• Descriptor: Methanosarcina acetivorans protoglobin, PROTOPORPHYRIN IX CONTAINING FE, PHOSPHATE ION, ... (5 entities in total)
• Functional Keywords: globin fold, protoglobin, methanogenesis, archaea protein, oxygen binding, oxygen transport
• Biological source: Methanosarcina acetivorans
• Total number of polymer chains: 1
• Total formula weight: 23817.29

Authors

Pesce, A.,Tilleman, L.,Dewilde, S.,Ascenzi, P.,Coletta, M.,Ciaccio, C.,Bruno, S.,Moens, L.,Bolognesi, M.,Nardini, M. (deposition date: 2011-03-07, release date: 2011-06-08, Last modification date: 2024-02-21)

Primary citation

Pesce, A.,Tilleman, L.,Dewilde, S.,Ascenzi, P.,Coletta, M.,Ciaccio, C.,Bruno, S.,Moens, L.,Bolognesi, M.,Nardini, M.
Structural heterogeneity and ligand gating in ferric methanosarcina acetivorans protoglobin mutants.
Iubmb Life, 63:287-294, 2011

PubMed 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.

PubMed: 21618401
DOI: 10.1002/iub.484

Experimental method

X-RAY DIFFRACTION (1.3 Å)