Hemoglobin-binding protein HgbA in the outer membrane of Actinobacillus pleuropneumoniae: homology modelling reveals regions of potential interactions with hemoglobin and heme.
Analyses of the primary sequence of hemoglobin-binding protein HgbA from Actinobacillus pleuropneumoniae by comparative modelling and by a Hidden Markov Model identified its topological similarities to bacterial outer membrane receptors BtuB, FepA, FhuA, and FecA of Escherichia coli. The HgbA model has a globular N-terminal cork domain contained within a 22-stranded beta barrel domain, its folds being similar to the structures of outer membrane receptors that have been solved by X-ray crystallography. The barrel domain of the HgbA model superimposes onto the barrel domains of the four outer membrane receptors with rmsd values less than 1.0 A. This feature is consistent with a phylogenetic tree which indicated clustering of polypeptide sequences for three barrel domains. Furthermore, the HgbA model shares the highest structural similarity to BtuB, with the modelled HgbA barrel having approximately the same elliptical cross-section and height as that of BtuB. Extracellular loop regions of HgbA are predicted to be more extended than those of the E. coli outer membrane receptors, potentially facilitating a protein-protein interface with hemoglobin. Fold recognition modelling of the HgbA loop regions showed that 10 out of 11 predicted loops are highly homologous to known structures of protein loops that contribute to heme/iron or protein-protein interactions. Strikingly, HgbA loop 2 has structural homology to a loop in bovine endothelial nitric acid oxidase that is proximal to a heme-binding site; and HgbA loop 7 contains a histidine residue conserved in a motif that is involved in heme/hemoglobin interactions. These findings implicate HgbA loops 2 and 7 in recognition and binding of hemoglobin or the heme ligand.
Pawelek
Peter D
PD
Department of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, QC, Canada H3A 2B4.
Coulton
James W
JW
D016977:Actinobacillus pleuropneumoniae / Q000737:chemistry* / Q000235:genetics / Q000502:physiology; D000595:Amino Acid Sequence; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry* / Q000235:genetics / Q000502:physiology; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D002352:Carrier Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology; D006418:Heme / Q000378:metabolism*; D006454:Hemoglobins / Q000378:metabolism*; D008969:Molecular Sequence Data; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D040681:Structural Homology, Protein
D001425:Bacterial Outer Membrane Proteins; D001426:Bacterial Proteins; D002352:Carrier Proteins; D006454:Hemoglobins; C017206:hemoglobin-binding protein, bacteria; D006418:Heme