ISDA: 1VDH

Deposition Date 2004-03-22

Release Date 2004-09-22

Last Version Date 2023-12-27

Entry Detail

PDB ID:

1VDH

Keywords:

STRUCTURAL GENOMICS, UNKNOWN FUNCTION

Title:

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

Biological Source:

Source Organism(s):

Thermus thermophilus (Taxon ID: 274)

Expression System(s):

Escherichia coli bl21(de3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.00 Å

R-Value Free:

0.21

R-Value Work:

0.18

R-Value Observed:

0.18

Space Group:

P 21 21 21

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Macromolecular Entities

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:muconolactone isomerase-like
Gene (Uniprot):chdC
Mutagens:K182E
Chain IDs:A, B, C, D, E
Chain Length:249
Number of Molecules:5
Biological Source:Thermus thermophilus

UniProt ID:Q5SHL6 Pfam ID:PF06778

Primary Citation

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.Show

J. Struct. Funct. Genomics 6 21 32 (2005)

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

Abstact

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.

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Primary Citation of related structures

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