Structural characterization of a group II 2/2 hemoglobin from the plant pathogen Agrobacterium tumefaciens

• Published in: Biochimica et biophysica acta 2011-06, Vol.1814 (6), p.810-816
• Main Authors: Pesce, Alessandra, Nardini, Marco, LaBarre, Marie, Richard, Christian, Wittenberg, Jonathan B., Wittenberg, Beatrice A., Guertin, Michel, Bolognesi, Martino
• Format: Article
• Language: English
• Subjects: 2/2 Hemoglobin; Agrobacterium radiobacter; Agrobacterium tumefaciens - chemistry; Agrobacterium tumefaciens - metabolism; Amino Acid Sequence; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Binding Sites; crystal structure; Crystallography; Diatomic ligand recognition; Globin fold; heme; Heme - chemistry; Heme stabilization; hemoglobin; Hemoglobins - chemistry; Hemoglobins - metabolism; Hydrogen Bonding; Models, Molecular; Molecular Sequence Data; plant pathogenic bacteria; protein structure; Sequence Alignment; soil; Truncated hemoglobin
• ISSN: 1570-9639; 0006-3002; 1878-1454
• DOI: 10.1016/j.bbapap.2010.11.001

Within the 2/2 hemoglobin sub-family, no group II 2/2Hbs from proteobacteria have been so far studied. Here we present the first structural characterization of a group II 2/2Hb from the soil and phytopathogenic bacterium Agrobacterium tumefaciens ( At-2/2HbO). The crystal structure of ferric At-2/2HbO (reported at 2.1 Å resolution) shows the location of specific/unique heme distal site residues (e.g., His(42)CD1, a residue distinctive of proteobacteria group II 2/2Hbs) that surround a heme-liganded water molecule. A highly intertwined hydrogen-bonded network, involving residues Tyr(26)B10, His(42)CD1, Ser(49)E7, Trp(93)G8, and three distal site water molecules, stabilizes the heme-bound ligand. Such a structural organization suggests a path for diatomic ligand diffusion to/from the heme. Neither a similar distal site structuring effect nor the presence of distal site water molecules has been so far observed in group I and group III 2/2Hbs, thus adding new distinctive information to the complex picture of currently available 2/2Hb structural and functional data. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State. ► Agrobacterium tumefaciens 2/2 hemoglobin three-dimensional structure, aquo-met form. ► A hydrogen-bonded network of water molecules in the heme distal site cavity. ► Heme distal site residue variability among group I, II and III 2/2 hemoglobins. ► Diatomic ligand diffusion path to the heme in A. tumefaciens 2/2HbO. ► HisCD1 vs. the conserved PheCD1 residue in A. tumefaciens 2/2HbO.