2VEE

Structure of protoglobin from Methanosarcina acetivorans C2A

Summary for 2VEE

• Entry DOI: 10.2210/pdb2vee/pdb
• Related: 2VEB
• Descriptor: PROTOGLOBIN, PROTOPORPHYRIN IX CONTAINING FE (3 entities in total)
• Functional Keywords: hemoprotein structure, protein matrix tunnels, protoglobin, methanogenesis, archaea protein, transport protein
• Biological source: METHANOSARCINA ACETIVORANS
• Total number of polymer chains: 8
• Total formula weight: 189018.80

Authors

Nardini, M.,Pesce, A.,Thijs, L.,Saito, J.A.,Dewilde, S.,Alam, M.,Ascenzi, P.,Coletta, M.,Ciaccio, C.,Moens, L.,Bolognesi, M. (deposition date: 2007-10-22, release date: 2008-01-22, Last modification date: 2023-12-13)

Primary citation

Nardini, M.,Pesce, A.,Thijs, L.,Saito, J.A.,Dewilde, S.,Alam, M.,Ascenzi, P.,Coletta, M.,Ciaccio, C.,Moens, L.,Bolognesi, M.
Archaeal Protoglobin Structure Indicates New Ligand Diffusion Paths and Modulation of Haem-Reactivity.
Embo Rep., 9:157-, 2008

PubMed 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 A 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 protoglobin-specific 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.

PubMed: 18188182
DOI: 10.1038/SJ.EMBOR.7401153

Experimental method

X-RAY DIFFRACTION (2.6 Å)