6OTY

Crystallographic Structure of (HbII-HbIII)-O2 from Lucina pectinata at pH 4.0

Summary for 6OTY

• Entry DOI: 10.2210/pdb6oty/pdb
• Descriptor: Hemoglobin II, Hemoglobin III, PROTOPORPHYRIN IX CONTAINING FE, ... (4 entities in total)
• Functional Keywords: hemeprotein, oxygen transport
• Biological source: Phacoides pectinatus (Thick lucine); More
• Total number of polymer chains: 2
• Total formula weight: 35830.60

Authors

Marchany-Rivera, D.,Smith, C.A.,Rodriguez-Perez, J.D.,Lopez-Garriga, J. (deposition date: 2019-05-03, release date: 2020-04-01, Last modification date: 2023-10-11)

Primary citation

Marchany-Rivera, D.,Smith, C.A.,Rodriguez-Perez, J.D.,Lopez-Garriga, J.
Lucina pectinata oxyhemoglobin (II-III) heterodimer pH susceptibility.
J.Inorg.Biochem., 207:111055-111055, 2020

PubMed Abstract: Lucina pectinata live in high concentrations of hydrogen sulfide (HS) and contains one hemoglobin, Hemoglobin I (HbI), transporting HS and two hemoglobins, Hemoglobin II (HbII) and Hemoglobin (HbIII), transferring dioxygen to symbionts. HbII and HbIII contain B10 tyrosine (Tyr) and E7 glutamine (Gln) in the heme pocket generating an efficient hydrogen bonding network with the (HbII-HbIII)-O species, leading to very low ligand dissociation rates. The results indicate that the oxy-hemeprotein is susceptible to pH from 4 to 9, at acidic conditions, and as a function of the potassium ferricyanide concentration, 100% of the met-aquo derivative is produced. Without a strong oxidant, pH 5 generates a small concentration of the met-aquo complex. The process is accelerated by the presence of salts, as indicated by the crystallization structures and UV-Vis spectra. The results suggest that acidic pH generates conformational changes associated with B10 and E7 heme pocket amino acids, weakening the (HbII-HbIII)-O hydrogen bond network. The observation is supported by X-ray crystallography, since at pH 4 and 5, the heme-Fe tends to oxidize, while at pH 7, the oxy-heterodimer is present. Conformational changes also are observed at higher pH by the presence of a 605 nm transition associated with the iron heme-Tyr interaction. Therefore, pH is one crucial factor regulating the (HbII-HbIII)-O complex hydrogen-bonding network. Thus, it can be proposed that the hydrogen bonding adjustments between the heme bound O and the Tyr and Gln amino acids contribute to oxygen dissociation from the (HbII-HbIII)-O system.

PubMed: 32217352
DOI: 10.1016/j.jinorgbio.2020.111055

Experimental method

X-RAY DIFFRACTION (2.598 Å)