3NFE

The crystal structure of hemoglobin I from trematomus newnesi in deoxygenated state

Summary for 3NFE

• Entry DOI: 10.2210/pdb3nfe/pdb
• Related: 1LA6 1T1N 2AA1 3D1K 3NG6
• Descriptor: Hemoglobin subunit alpha-1, Hemoglobin subunit beta-1/2, PROTOPORPHYRIN IX CONTAINING FE, ... (4 entities in total)
• Functional Keywords: root effect, fish hemoglobin, antarctic fish, oxygen transport
• Biological source: Trematomus newnesi (Dusky notothen); More
• Total number of polymer chains: 4
• Total formula weight: 66365.36

Authors

Vergara, A.,Vitagliano, L.,Merlino, A.,Sica, F.,Marino, K.,Mazzarella, L. (deposition date: 2010-06-10, release date: 2010-07-07, Last modification date: 2023-09-06)

Primary citation

Vergara, A.,Vitagliano, L.,Merlino, A.,Sica, F.,Marino, K.,Verde, C.,di Prisco, G.,Mazzarella, L.
An order-disorder transition plays a role in switching off the root effect in fish hemoglobins.
J.Biol.Chem., 285:32568-32575, 2010

PubMed Abstract: The Root effect is a widespread property among fish hemoglobins whose structural basis remains largely obscure. Here we report a crystallographic and spectroscopic characterization of the non-Root-effect hemoglobin isolated from the Antarctic fish Trematomus newnesi in the deoxygenated form. The crystal structure unveils that the T state of this hemoglobin is stabilized by a strong H-bond between the side chains of Asp95α and Asp101β at the α(1)β(2) and α(2)β(1) interfaces. This unexpected finding undermines the accepted paradigm that correlates the presence of this unusual H-bond with the occurrence of the Root effect. Surprisingly, the T state is characterized by an atypical flexibility of two α chains within the tetramer. Indeed, regions such as the CDα corner and the EFα pocket, which are normally well ordered in the T state of tetrameric hemoglobins, display high B-factors and non-continuous electron densities. This flexibility also leads to unusual distances between the heme iron and the proximal and distal His residues. These observations are in line with Raman micro-spectroscopy studies carried out both in solution and in the crystal state. The findings here presented suggest that in fish hemoglobins the Root effect may be switched off through a significant destabilization of the T state regardless of the presence of the inter-aspartic H-bond. Similar mechanisms may also operate for other non-Root effect hemoglobins. The implications of the flexibility of the CDα corner for the mechanism of the T-R transition in tetrameric hemoglobins are also discussed.

PubMed: 20610398
DOI: 10.1074/jbc.M110.143537

Experimental method

X-RAY DIFFRACTION (2.01 Å)