Limits...
Analysis of proteins with the 'hot dog' fold: prediction of function and identification of catalytic residues of hypothetical proteins.

Pidugu LS, Maity K, Ramaswamy K, Surolia N, Suguna K - BMC Struct. Biol. (2009)

Bottom Line: The hot dog fold has been found in more than sixty proteins since the first report of its existence about a decade ago.This study reveals that though the basic architecture of the fold is well conserved in these proteins, significant differences exist in their sequence, nature of substrate and oligomerization.The analysis led to predictions regarding the functional classification and identification of possible catalytic residues of a number of hot dog fold-containing hypothetical proteins whose structures were determined in high throughput structural genomics projects.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India. plsmukhi@gmail.com

ABSTRACT

Background: The hot dog fold has been found in more than sixty proteins since the first report of its existence about a decade ago. The fold appears to have a strong association with fatty acid biosynthesis, its regulation and metabolism, as the proteins with this fold are predominantly coenzyme A-binding enzymes with a variety of substrates located at their active sites.

Results: We have analyzed the structural features and sequences of proteins having the hot dog fold. This study reveals that though the basic architecture of the fold is well conserved in these proteins, significant differences exist in their sequence, nature of substrate and oligomerization. Segments with certain conserved sequence motifs seem to play crucial structural and functional roles in various classes of these proteins.

Conclusion: The analysis led to predictions regarding the functional classification and identification of possible catalytic residues of a number of hot dog fold-containing hypothetical proteins whose structures were determined in high throughput structural genomics projects.

Show MeSH

Related in: MedlinePlus

Dimer of NodN-like hydratase from M. tuberculosis. The kink in the central α-helix shown by arrows (PDB code: 2C2I). Catalytic residues are shown in ball and stick representation.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2698920&req=5

Figure 7: Dimer of NodN-like hydratase from M. tuberculosis. The kink in the central α-helix shown by arrows (PDB code: 2C2I). Catalytic residues are shown in ball and stick representation.

Mentions: The crystal structure of a hypothetical protein from M. tuberculosis (PDB code: 2C2I) possesses the consensus sequence motif of the NodN-like subfamily, a subgroup of MaoC like hydratases [39]. This protein is a dimer with two overhanging segments which contain the catalytic residues Asp40 and His45. The N-terminus of each subunit has an additional short β-strand and a small α-helix. A proline residue Pro71 at the centre of the central helix causes a 25° kink in the long helix (Fig. 7), giving rise to a curved long tunnel similar to eukaryotic and human hydratase 2 enzymes which are specific to longer substrates.


Analysis of proteins with the 'hot dog' fold: prediction of function and identification of catalytic residues of hypothetical proteins.

Pidugu LS, Maity K, Ramaswamy K, Surolia N, Suguna K - BMC Struct. Biol. (2009)

Dimer of NodN-like hydratase from M. tuberculosis. The kink in the central α-helix shown by arrows (PDB code: 2C2I). Catalytic residues are shown in ball and stick representation.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2698920&req=5

Figure 7: Dimer of NodN-like hydratase from M. tuberculosis. The kink in the central α-helix shown by arrows (PDB code: 2C2I). Catalytic residues are shown in ball and stick representation.
Mentions: The crystal structure of a hypothetical protein from M. tuberculosis (PDB code: 2C2I) possesses the consensus sequence motif of the NodN-like subfamily, a subgroup of MaoC like hydratases [39]. This protein is a dimer with two overhanging segments which contain the catalytic residues Asp40 and His45. The N-terminus of each subunit has an additional short β-strand and a small α-helix. A proline residue Pro71 at the centre of the central helix causes a 25° kink in the long helix (Fig. 7), giving rise to a curved long tunnel similar to eukaryotic and human hydratase 2 enzymes which are specific to longer substrates.

Bottom Line: The hot dog fold has been found in more than sixty proteins since the first report of its existence about a decade ago.This study reveals that though the basic architecture of the fold is well conserved in these proteins, significant differences exist in their sequence, nature of substrate and oligomerization.The analysis led to predictions regarding the functional classification and identification of possible catalytic residues of a number of hot dog fold-containing hypothetical proteins whose structures were determined in high throughput structural genomics projects.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India. plsmukhi@gmail.com

ABSTRACT

Background: The hot dog fold has been found in more than sixty proteins since the first report of its existence about a decade ago. The fold appears to have a strong association with fatty acid biosynthesis, its regulation and metabolism, as the proteins with this fold are predominantly coenzyme A-binding enzymes with a variety of substrates located at their active sites.

Results: We have analyzed the structural features and sequences of proteins having the hot dog fold. This study reveals that though the basic architecture of the fold is well conserved in these proteins, significant differences exist in their sequence, nature of substrate and oligomerization. Segments with certain conserved sequence motifs seem to play crucial structural and functional roles in various classes of these proteins.

Conclusion: The analysis led to predictions regarding the functional classification and identification of possible catalytic residues of a number of hot dog fold-containing hypothetical proteins whose structures were determined in high throughput structural genomics projects.

Show MeSH
Related in: MedlinePlus