Structure-based functional identification of a novel heme-binding protein from Thermus thermophilus HB8.
The TT1485 gene from Thermus thermophilus HB8 encodes a hypothetical protein of unknown function with about 20 sequence homologs of bacterial or archaeal origin. Together they form a family of uncharacterized proteins, the cluster of orthologous group COG3253. Using a combination of amino acid sequence analysis, three-dimensional structural studies and biochemical assays, we identified TT1485 as a novel heme-binding protein. The crystal structure reveals that this protein is a pentamer and each monomer exhibits a beta-barrel fold. TT1485 is structurally similar to muconolactone isomerase, but this provided no functional clues. Amino acid sequence analysis revealed remote homology to a heme enzyme, chlorite dismutase. Strikingly, amino acid residues that are highly conserved in the homologous hypothetical proteins and chlorite dismutase cluster around a deep cavity on the surface of each monomer. Molecular modeling shows that the cavity can accommodate a heme group with a strictly conserved His as a heme ligand. TT1485 reconstituted with iron protoporphyrin IX chloride gave a low chlorite dismutase activity, indicating that TT1485 catalyzes a reaction other than chlorite degradation. The presence of a possible Fe-His-Asp triad in the heme proximal site suggests that TT1485 functions as a novel heme peroxidase to detoxify hydrogen peroxide within the cell.
Ebihara
Akio
A
RIKEN Harima Institute at SPring-8, Kouto, Mikazuki-cho, Sayo-gun, Hyogo, 679-5148, Japan.
Okamoto
Akihiro
A
Kousumi
Yukihide
Y
Yamamoto
Hitoshi
H
Masui
Ryoji
R
Ueyama
Norikazu
N
Yokoyama
Shigeyuki
S
Kuramitsu
Seiki
S
D000595:Amino Acid Sequence; D002352:Carrier Proteins / Q000737:chemistry* / Q000378:metabolism / Q000502:physiology; D018360:Crystallography, X-Ray; D019143:Evolution, Molecular; D019766:Genes, Archaeal; D005798:Genes, Bacterial; D000081062:Heme-Binding Proteins; D006420:Hemeproteins / Q000737:chemistry* / Q000378:metabolism / Q000502:physiology; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010088:Oxidoreductases / Q000737:chemistry / Q000235:genetics; D010544:Peroxidases / Q000737:chemistry* / Q000378:metabolism / Q000502:physiology; D017433:Protein Structure, Secondary; D017385:Sequence Homology; D016963:Thermus thermophilus / Q000737:chemistry* / Q000378:metabolism
D002352:Carrier Proteins; D000081062:Heme-Binding Proteins; D006420:Hemeproteins; D010088:Oxidoreductases; D010544:Peroxidases; C402794:chlorite dismutase