1VDH

Structure-based functional identification of a novel heme-binding protein from thermus thermophilus HB8

Summary for 1VDH

• Entry DOI: 10.2210/pdb1vdh/pdb
• Descriptor: muconolactone isomerase-like protein (2 entities in total)
• Functional Keywords: beta barrel, structural genomics, riken structural genomics/proteomics initiative, rsgi, unknown function
• Biological source: Thermus thermophilus
• Total number of polymer chains: 5
• Total formula weight: 144723.79

Authors

Ebihara, A.,Okamoto, A.,Kousumi, Y.,Yamamoto, H.,Masui, R.,Ueyama, N.,Shibata, T.,Inoue, Y.,Yokoyama, S.,Kuramitsu, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2004-03-22, release date: 2004-09-22, Last modification date: 2023-12-27)

Primary citation

Ebihara, A.,Okamoto, A.,Kousumi, Y.,Yamamoto, H.,Masui, R.,Ueyama, N.,Yokoyama, S.,Kuramitsu, S.
Structure-based functional identification of a novel heme-binding protein from Thermus thermophilus HB8.
J.STRUCT.FUNCT.GENOM., 6:21-32, 2005

PubMed Abstract: 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.

PubMed: 15965735
DOI: 10.1007/s10969-005-1103-x

Experimental method

X-RAY DIFFRACTION (2 Å)