3ZJQ

M.acetivorans protoglobin in complex with nicotinamide

Summary for 3ZJQ

• Entry DOI: 10.2210/pdb3zjq/pdb
• Related: 3ZJH 3ZJI 3ZJJ 3ZJL 3ZJM 3ZJN 3ZJO 3ZJP
• Descriptor: PROTOGLOBIN, PROTOPORPHYRIN IX CONTAINING FE, NICOTINAMIDE, ... (5 entities in total)
• Functional Keywords: iron-binding protein
• Biological source: METHANOSARCINA ACETIVORANS
• Total number of polymer chains: 2
• Total formula weight: 47591.04

Authors

Pesce, A.,Tilleman, L.,Donne, J.,Aste, E.,Ascenzi, P.,Ciaccio, C.,Coletta, M.,Moens, L.,Viappiani, C.,Dewilde, S.,Bolognesi, M.,Nardini, M. (deposition date: 2013-01-18, release date: 2013-06-26, Last modification date: 2023-12-20)

Primary citation

Pesce, A.,Tilleman, L.,Donne, J.,Aste, E.,Ascenzi, P.,Ciaccio, C.,Coletta, M.,Moens, L.,Viappiani, C.,Dewilde, S.,Bolognesi, M.,Nardini, M.
Structure and Haem-Distal Site Plasticity in Methanosarcina Acetivorans Protoglobin.
Plos One, 8:66144-, 2013

PubMed Abstract: Protoglobin from Methanosarcina acetivorans C2A (MaPgb), a strictly anaerobic methanogenic Archaea, is a dimeric haem-protein whose biological role is still unknown. As other globins, protoglobin can bind O2, CO and NO reversibly in vitro, but it displays specific functional and structural properties within members of the hemoglobin superfamily. CO binding to and dissociation from the haem occurs through biphasic kinetics, which arise from binding to (and dissociation from) two distinct tertiary states in a ligation-dependent equilibrium. From the structural viewpoint, protoglobin-specific loops and a N-terminal extension of 20 residues completely bury the haem within the protein matrix. Thus, access of small ligand molecules to the haem is granted by two apolar tunnels, not common to other globins, which reach the haem distal site from locations at the B/G and B/E helix interfaces. Here, the roles played by residues Trp(60)B9, Tyr(61)B10 and Phe(93)E11 in ligand recognition and stabilization are analyzed, through crystallographic investigations on the ferric protein and on selected mutants. Specifically, protein structures are reported for protoglobin complexes with cyanide, with azide (also in the presence of Xenon), and with more bulky ligands, such as imidazole and nicotinamide. Values of the rate constant for cyanide dissociation from ferric MaPgb-cyanide complexes have been correlated to hydrogen bonds provided by Trp(60)B9 and Tyr(61)B10 that stabilize the haem-Fe(III)-bound cyanide. We show that protoglobin can strikingly reshape, in a ligand-dependent way, the haem distal site, where Phe(93)E11 acts as ligand sensor and controls accessibility to the haem through the tunnel system by modifying the conformation of Trp(60)B9.

PubMed: 23776624
DOI: 10.1371/JOURNAL.PONE.0066144

Experimental method

X-RAY DIFFRACTION (1.9 Å)