Hydroxide Rather Than Histidine Is Coordinated to the Heme in Five-coordinate Ferric Scapharca inaequivalvis Hemoglobin (original) (raw)
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Structure and Ligand Selection of Hemoglobin II from Lucina pectinata
Journal of Biological Chemistry, 2008
Lucina pectinata ctenidia harbor three heme proteins: sulfide-reactive hemoglobin I (HbI Lp ) and the oxygen transporting hemoglobins II and III (HbII Lp and HbIII Lp ) that remain unaffected by the presence of H 2 S. The mechanisms used by these three proteins for their function, including ligand control, remain unknown. The crystal structure of oxygen-bound HbII Lp shows a dimeric oxyHbII Lp where oxygen is tightly anchored to the heme through hydrogen bonds with Tyr 30 (B10) and Gln 65 (E7). The heme group is buried farther within HbII Lp than in HbI Lp . The proximal His 97 (F8) is hydrogen bonded to a water molecule, which interacts electrostatically with a propionate group, resulting in a Fe-His vibration at 211 cm ؊1 . The combined effects of the HbII Lp small heme pocket, the hydrogen bonding network, the His 97 trans-effect, and the orientation of the oxygen molecule confer stability to the oxy-HbII Lp complex. Oxidation of HbI Lp Phe(B10) 3 Tyr and HbII Lp only occurs when the pH is decreased from pH 7.5 to 5.0. Structural and resonance Raman spectroscopy studies suggest that HbII Lp oxygen binding and transport to the host bacteria may be regulated by the dynamic displacements of the Gln 65 (E7) and Tyr 30 (B10) pair toward the heme to protect it from changes in the heme oxidation state from Fe II to Fe III . by on August 1 0 , 2 0 0 9 www.jbc.org D ownloa de d from http://www.jbc.org/cgi/conte nt/full/M 7 0 5 0 2 6 2 0 0 /D C 1 S upplem e nta l M a te ria l ca n be found a t: L. pectinata HbII Structure APRIL 4, 2008 • VOLUME 283 • NUMBER 14 JOURNAL OF BIOLOGICAL CHEMISTRY 9415 by on August 1 0 , 2 0 0 9 www.jbc.org D ownloa de d from FIGURE 2. Multiple sequence alignment of the three types of hemoglobin from L. pectinata, the bivalve mollusk S. inaequivalvis, and domain one of the nematode A. suum hemoglobin. The corresponding helices as predicted by the program suite iMoltalk applying the STRIDE method are labeled (red squares). Conserved residues are shaded in cyan and residues at position B10 (Tyr 30 in L. pectinata), E7 (Gln 65 in L. pectinata), Lys 92 and Arg 100 (L. pectinata) are shaded in yellow. The gaps are labeled in green.
Archives of Biochemistry and Biophysics, 1997
permitted more marked movements of the heme than in the native protein. ᭧ 1997 Academic Press In the homodimeric hemoglobin from Scapharca, Key Words: cooperativity; dimeric hemoglobin (Sca-HbI, functional communication between the two pharca); unnatural heme derivatives. heme groups is based on their direct structural linkage across the subunit interface through the heme propionates. The heme -protein interactions have been altered in deutero-and meso-HbI by substitut-In the cooperative homodimeric hemoglobin, HbI, 3 ing the vinyl groups at positions 2 and 4 of protofrom the mollusk Scapharca inaequivalvis the hemeheme with hydrogen and ethyl groups, respectively.
Unusual Rocking Freedom of the Heme in the Hydrogen Sulfide-Binding Hemoglobin from Lucina pectinata
Journal of the American Chemical Society, 1998
Hemoglobin I (HbI) from the clam Lucina pectinata is, in its natural environment, a hydrogen sulfide (H 2 S)-transport heme protein. The resonance Raman (RR) spectrum of the metaquo and deoxyHbI species shows a very weak intensity peak at 370 cm-1 that corresponds to the normal mode of the heme propionates. This suggests the presence of a moderate hydrogen bonding between Arg99 and the heme-7propionate. However, the RR spectra of the metcyano, carbonmonoxy, and oxy HbI derivatives reveal the absence of the propionate vibrational frequency at 370 cm-1. The mode is insensitive to the oxidation state of the heme iron, but disappears when the HbI-ligand moiety is formed. These results propose the existence of flexible propionate groups which can result in a weaker hydrogen bond upon heme ligand binding. The longitudinal relaxation time (T 1) 1 H NMR data for the paramagnetic metcyano complex of HbI suggested that the 17.90 ppm signal belongs to the heme-6-propionate R′ protons (6-H R′). In relation to other myoglobins, the large difference in chemical shifts of this signal is attributed both to the lack of hydrogen bonds between the heme-6-propionate group and amino acid residues and to a flexible orientation of the side chain with respect to the heme plane. The data predict a model where the heme group of HbI is tightly bound to His96 (ν Fe-His at 218 cm-1), but due to the absence of strong hydrogen bonding interactions between the heme propionates and the nearby amino acids, the heme is not firmly anchored. Thus, relative to other heme proteins, the heme group of HbI from Lucina pectinata presents a rocking freedom that facilitates the binding between the heme and the incoming ligand.
Tertiary and Quaternary Allostery in Tetrameric Hemoglobin from Scapharca inaequivalvis
Biochemistry, 2013
The clam Scapharca inaequivalvis possesses two cooperative oxygen binding hemoglobins in its red cells: a homodimeric HbI and a heterotetrameric A2B2 HbII. Each AB dimeric half of HbII is assembled very similarly to that of the well studied HbI. This study presents crystal structures of HbII along with oxygen binding data both in the crystalline state and in wet nanoporous silica gels. Despite very similar ligand-linked structural transitions observed in HbI and HbII crystals, HbII in the crystal or encapsulated in silica gels apparently exhibits minimal cooperativity in oxygen binding, in contrast with the full cooperativity exhibited by HbI crystals. However, oxygen binding curves in the crystal indicate the presence of a significant functional inequivalence of A and B chains. When this inequivalence is taken into account, both crystal and R state gel functional data are consistent with the conservation of a tertiary contribution to cooperative oxygen binding, quantitatively similar to that measured for HbI, and are in keeping with the structural information. Furthermore, our results indicate that to fully express the cooperative ligand binding, HbII requires quaternary transitions hampered by crystal lattice and gel encapsulation, revealing greater complexity in cooperative function than the direct communication across a dimeric interface observed in HbI.