2H8F

Crystal structure of deoxy hemoglobin from Trematomus bernacchii at pH 6.2

Summary for 2H8F

• Entry DOI: 10.2210/pdb2h8f/pdb
• Related: 2aa1 2h8d
• Descriptor: Hemoglobin alpha subunit, Hemoglobin beta subunit, PROTOPORPHYRIN IX CONTAINING FE, ... (4 entities in total)
• Functional Keywords: root effect, ph, cooperativity, hemoglobin, allostery, high resolution, transport protein
• Biological source: Trematomus bernacchii (emerald rockcod); More
• Total number of polymer chains: 4
• Total formula weight: 66139.23

Authors

Mazzarella, L.,Vergara, A.,Vitagliano, L.,Merlino, A.,Bonomi, G.,Scala, S.,Verde, C.,di Prisco, G. (deposition date: 2006-06-07, release date: 2006-08-29, Last modification date: 2011-07-13)

Primary citation

Mazzarella, L.,Vergara, A.,Vitagliano, L.,Merlino, A.,Bonomi, G.,Scala, S.,Verde, C.,di Prisco, G.
High resolution crystal structure of deoxy hemoglobin from Trematomus bernacchii at different pH values: The role of histidine residues in modulating the strength of the root effect.
Proteins, 65:490-498, 2006

PubMed Abstract: The Root effect is a widespread property in fish hemoglobins (Hbs) that produces a drastic reduction of cooperativity and oxygen-binding ability at acidic pH. Here, we report the high-resolution structure of the deoxy form of Hb isolated from the Antarctic fish Trematomus bernacchii (HbTb) crystallized at pH 6.2 and 8.4. The structure at acidic pH has been previously determined at a moderate resolution (Ito et al., J Mol Biol 1995;250:648-658). Our results provide a clear picture of the events occurring upon the pH increase from 6.2 to 8.4, observed within a practically unchanged crystal environment. In particular, at pH 8.4, the interaspartic hydrogen bond at the alpha(1)beta(2) interface is partially broken, suggesting a pK(a) close to 8.4 for Asp95alpha. In addition, a detailed survey of the histidine modifications, caused by the change in pH, also indicates that at least three hot regions of the molecule are modified (Ebeta helix, Cbeta-tail, CDalpha corner) and can be considered to be involved at various levels in the release of the Root protons. Most importantly, at the CDalpha corner, the break of the salt bridge Asp48alpha-His55alpha allows us to describe a detailed mechanism that transmits the modification from the CDalpha corner far to the alpha heme. More generally, the results shed light on the role played by the histidine residues in modulating the strength of the Root effect and also support the emerging idea that the structural determinants, at least for a part of the Root effect, are specific of each Hb endowed with this property.

PubMed: 16909420
DOI: 10.1002/prot.21114

Experimental method

X-RAY DIFFRACTION (1.3 Å)