1FLP

STRUCTURE OF THE SULFIDE-REACTIVE HEMOGLOBIN FROM THE CLAM LUCINA PECTINATA: CRYSTALLOGRAPHIC ANALYSIS AT 1.5 ANGSTROMS RESOLUTION

Summary for 1FLP

• Entry DOI: 10.2210/pdb1flp/pdb
• Descriptor: HEMOGLOBIN I (AQUO MET), PROTOPORPHYRIN IX CONTAINING FE (3 entities in total)
• Functional Keywords: oxygen transport
• Biological source: Lucina pectinata
• Cellular location: Cytoplasm: P41260
• Total number of polymer chains: 1
• Total formula weight: 15375.93

Authors

Rizzi, M.,Wittenberg, J.B.,Ascenzi, P.,Fasano, M.,Coda, A.,Bolognesi, M. (deposition date: 1994-05-16, release date: 1994-07-31, Last modification date: 2024-02-07)

Primary citation

Rizzi, M.,Wittenberg, J.B.,Coda, A.,Fasano, M.,Ascenzi, P.,Bolognesi, M.
Structure of the sulfide-reactive hemoglobin from the clam Lucina pectinata. Crystallographic analysis at 1.5 A resolution.
J.Mol.Biol., 244:86-99, 1994

PubMed 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 A 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 A 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.

PubMed: 7966324
DOI: 10.1006/jmbi.1994.1706

Experimental method

X-RAY DIFFRACTION (1.5 Å)