3GKV

X-ray structure of an intermediate along the oxidation pathway of Trematomus bernacchii hemoglobin

Summary for 3GKV

• Entry DOI: 10.2210/pdb3gkv/pdb
• Descriptor: Hemoglobin subunit alpha, Hemoglobin subunit beta, PROTOPORPHYRIN IX CONTAINING FE, ... (5 entities in total)
• Functional Keywords: hemoglobin, intermediate quaternary structure, acetylation, heme, iron, metal-binding, oxygen transport, transport
• Biological source: Trematomus bernacchii (Emerald rockcod); More
• Total number of polymer chains: 2
• Total formula weight: 33125.63

Authors

Merlino, A.,Vitagliano, L.,Sica, F.,Vergara, A.,Mazzarella, L. (deposition date: 2009-03-11, release date: 2009-05-05, Last modification date: 2024-10-16)

Primary citation

Merlino, A.,Vitagliano, L.,Howes, B.D.,Verde, C.,di Prisco, G.,Smulevich, G.,Sica, F.,Vergara, A.
Combined crystallographic and spectroscopic analysis of Trematomus bernacchii hemoglobin highlights analogies and differences in the peculiar oxidation pathway of Antarctic fish hemoglobins
Biopolymers, 91:1117-1125, 2009

PubMed Abstract: Recent studies have demonstrated that hemoglobins isolated from Antarctic fish undergo peculiar oxidation processes. Here we show, by combining crystallographic and spectroscopic data, that the oxidation pathway of Trematomus bernacchii hemoglobin (HbTb) is distinct from that observed for the major component of Trematomus newnesi (Hb1Tn), despite the high sequence identity of the two proteins and structural similarity of their ferrous and fully oxidized states. Resonance Raman analysis of HbTb autoxidation upon air-exposure reveals the absence of the oxidized pentacoordinated state that was observed for Hb1Tn. The HbTb oxidation pathway is characterized by two ferric species: an aquo hexacoordinated high spin state and a bis-histidyl hexacoordinated low spin form, which appear in the early stages of the oxidation process. The high resolution structure of an intermediate along the oxidation pathway has been determined at 1.4 A resolution. The analysis of the electron density of the heme pocket shows, for both the alpha and the beta iron, the coexistence of multiple binding states. In this partially oxidized form, HbTb exhibits significant deviations from the canonical R state both at the local and global level. The analysis of these modifications highlights the structural correlation between key functional regions of the protein.

PubMed: 19373928
DOI: 10.1002/bip.21206

Experimental method

X-RAY DIFFRACTION (1.4 Å)