Structure of the sulfide-reactive hemoglobin from the clam Lucina pectinata

Crystallographic analysis at 1.5 Å resolution

Menico Rizzi, Jonathan B. Wittenberg, Alessandro Coda, Mauro Fasano, Paolo Ascenzi, Martino Bolognesi

Research output: Contribution to journalArticle

61 Citations (Scopus)

Abstract

The crystal structure of the aquo-met form of the sulfide-reactive hemoglobin (component I) from the gill of the symbiont-harboring mollusc, Lucina pectinata, has been solved and refined at 1.5 Å resolution, based on synchrotron radiation X-ray diffraction data, and employing molecular replacement techniques. The crystallographic R-factor, calculated for the data in the 15.0 to 1.5 Å resolution range, is 0.170, with highly regular stereochemical parameters for the protein model, and including 131 water molecules. The monomeric hemoglobin I chain consists of 142 amino acid residues, which have been partly identified on the basis of the crystallographic analysis. The molecule is characterized by an unusual distribution of aromatic residues, particularly in the region surrounding the distal site in the heme pocket. The heme distal residue is Gln(64)E7, while other notable amino acid substitutions include Trp(21)B2, Phe(29)B10, Leu(46)CD3, Phe(68)E11 and Trp(75)E18. An amino acid insertion (Ser44) is observed between sites CD1 and CD2. In the aquo-met protein, a water molecule is present at the sixth coordination position of the heme iron, and hydrogen bonded to Gln(64)E7. Simple model building shows that a dioxygen molecule, bound to ferrous protein, would contact with its free atom the ring edge of Phe(29)B10, being thus stabilized at the coordination site by an aromatic-electrostatic interaction. Similarly, the unique packing and organization of aromatic residues in the surroundings of the heme distal site is proposed as the molecular basis of the very high affinity of Lucina pectinata hemoglobin I for hydrogen sulfide, considered as one of the two physiological ligands of the protein.

Original languageEnglish
Pages (from-to)86-99
Number of pages14
JournalJournal of Molecular Biology
Volume244
Issue number1
Publication statusPublished - 1994

Fingerprint

Bivalvia
Sulfides
Heme
Hemoglobins
R388
Proteins
Amino Acids
Hydrogen Sulfide
Synchrotrons
Water
Mollusca
Amino Acid Substitution
Static Electricity
X-Ray Diffraction
Hydrogen
Iron
Radiation
Oxygen
Ligands

Keywords

  • Crystal structure
  • Heme protein
  • Monomeric molluse hemoglobin
  • Oxygen carrier
  • Sulfide carrier

ASJC Scopus subject areas

  • Virology

Cite this

Rizzi, M., Wittenberg, J. B., Coda, A., Fasano, M., Ascenzi, P., & Bolognesi, M. (1994). Structure of the sulfide-reactive hemoglobin from the clam Lucina pectinata: Crystallographic analysis at 1.5 Å resolution. Journal of Molecular Biology, 244(1), 86-99.

Structure of the sulfide-reactive hemoglobin from the clam Lucina pectinata : Crystallographic analysis at 1.5 Å resolution. / Rizzi, Menico; Wittenberg, Jonathan B.; Coda, Alessandro; Fasano, Mauro; Ascenzi, Paolo; Bolognesi, Martino.

In: Journal of Molecular Biology, Vol. 244, No. 1, 1994, p. 86-99.

Research output: Contribution to journalArticle

Rizzi, M, Wittenberg, JB, Coda, A, Fasano, M, Ascenzi, P & Bolognesi, M 1994, 'Structure of the sulfide-reactive hemoglobin from the clam Lucina pectinata: Crystallographic analysis at 1.5 Å resolution', Journal of Molecular Biology, vol. 244, no. 1, pp. 86-99.
Rizzi, Menico ; Wittenberg, Jonathan B. ; Coda, Alessandro ; Fasano, Mauro ; Ascenzi, Paolo ; Bolognesi, Martino. / Structure of the sulfide-reactive hemoglobin from the clam Lucina pectinata : Crystallographic analysis at 1.5 Å resolution. In: Journal of Molecular Biology. 1994 ; Vol. 244, No. 1. pp. 86-99.
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