1vdh
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| , resolution 2.00Å | |||||||
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Structure-based functional identification of a novel heme-binding protein from thermus thermophilus HB8
OverviewOverview
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.
About this StructureAbout this Structure
1VDH is a Protein complex structure of sequences from Thermus thermophilus. Full crystallographic information is available from OCA.
ReferenceReference
Structure-based functional identification of a novel heme-binding protein from Thermus thermophilus HB8., Ebihara A, Okamoto A, Kousumi Y, Yamamoto H, Masui R, Ueyama N, Yokoyama S, Kuramitsu S, J Struct Funct Genomics. 2005;6(1):21-32. PMID:15965735
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- Protein complex
- Thermus thermophilus
- Ebihara, A.
- Inoue, Y.
- Kousumi, Y.
- Kuramitsu, S.
- Masui, R.
- Okamoto, A.
- RSGI, RIKEN Structural Genomics/Proteomics Initiative.
- Shibata, T.
- Ueyama, N.
- Yamamoto, H.
- Yokoyama, S.
- Beta barrel
- Riken structural genomics/proteomics initiative
- Rsgi
- Structural genomic