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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.

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Various quaternary associations of hot dog fold proteins. D – dimer (PDB code: 1MKA); dh – double hot dog (PDB code: 1C8U); H1 – hexamer with active site loops at interface (PDB code: 1Z6B); H2 – hexamer with N-terminal helices at interface (PDB code: 1YLI); H3 – hexamer with head-to-tail arrangement of dimers (PDB code: 2PFC); TA – tetramer with central helix interactions (PDB code: 1BVQ); TB – tetramer with back to back stacking of the β-sheets (PDB code: 1Q4T). DdhA (dimer of double hot dog with central helix interactions) is similar to TA while DdhB (dimer of double hot dogs with back to back interaction of the β-sheets) is similar to TB. Trdh (trimer of double hot dogs) is similar to H2.
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Figure 2: Various quaternary associations of hot dog fold proteins. D – dimer (PDB code: 1MKA); dh – double hot dog (PDB code: 1C8U); H1 – hexamer with active site loops at interface (PDB code: 1Z6B); H2 – hexamer with N-terminal helices at interface (PDB code: 1YLI); H3 – hexamer with head-to-tail arrangement of dimers (PDB code: 2PFC); TA – tetramer with central helix interactions (PDB code: 1BVQ); TB – tetramer with back to back stacking of the β-sheets (PDB code: 1Q4T). DdhA (dimer of double hot dog with central helix interactions) is similar to TA while DdhB (dimer of double hot dogs with back to back interaction of the β-sheets) is similar to TB. Trdh (trimer of double hot dogs) is similar to H2.

Mentions: Each subunit of a hot dog fold is made up of 5 or 6 highly curved antiparallel β-strands wrapped around a long α-helix. Our analysis indicated that the basic structural repeat unit of the hot dog fold proteins is either a homodimer of two such subunits or a double hot dog with a single polypeptide chain folding into two hot dog domains (Fig. 1). The dimer of hot dog folds is formed by the association of β-sheets from both the subunits to form a continuous anti-parallel β-sheet. The two helices run antiparallel to each other at the dimer interface. In the enzymes with the repeat unit as the dimer of hot dogs, the active sites comprise residues from both the subunits. In the case of double hot dogs, the two domains have an undetectable sequence similarity (~10% identity as derived from structure-based alignment). However, at the nucleotide level, the sequence identity between the two domains of the double hot dogs is around 50% [3]. Though these basic building blocks (homodimer or double hot dog) of various subfamilies are similar with root mean square deviations (rmsd) of 1.0–3.0 Å for the Cα atoms, they differ in their quaternary associations and are highly divergent in their sequences. The various quaternary associations observed are dimers (D); tetramers with central helix interactions at the tetramer interface (TA); tetramers with back to back stacking of the β-sheets of the repeating units (TB); hexamers with active site loops at the interface (H1); hexamers with N-terminal helices at the interface (H2); hexamers with head-to-tail arrangement of dimers (H3); dimers of double hot dogs with central helix interactions (DdhA); dimers of double hot dogs with back to back stacking of β-sheets (DdhB); and trimers of double hot dogs (Trdh) which appear like H2 (Fig. 2). The two domains of the double hot dogs are connected by long loops. Though they connect the second β-strand from the centre in the first subunit to the last β-strand of the second subunit in all the cases, the loops have considerable variation in length and conformation and also in the direction they follow to connect the subunits. This variation in the nature of the connecting loops appears to be linked with the quaternary association (DdhA, DdhB and Trdh) of the double hot dog fold proteins. The analysis of buried surface areas of various types of quaternary association has revealed that approximately 17–20%, 20–25%, 26–30%, 32–36%, 26–30% and 16% surface area per monomer gets buried upon the formation of D, TA, TB, H1, H2 and H3 types of quaternary associations, respectively.


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)

Various quaternary associations of hot dog fold proteins. D – dimer (PDB code: 1MKA); dh – double hot dog (PDB code: 1C8U); H1 – hexamer with active site loops at interface (PDB code: 1Z6B); H2 – hexamer with N-terminal helices at interface (PDB code: 1YLI); H3 – hexamer with head-to-tail arrangement of dimers (PDB code: 2PFC); TA – tetramer with central helix interactions (PDB code: 1BVQ); TB – tetramer with back to back stacking of the β-sheets (PDB code: 1Q4T). DdhA (dimer of double hot dog with central helix interactions) is similar to TA while DdhB (dimer of double hot dogs with back to back interaction of the β-sheets) is similar to TB. Trdh (trimer of double hot dogs) is similar to H2.
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Figure 2: Various quaternary associations of hot dog fold proteins. D – dimer (PDB code: 1MKA); dh – double hot dog (PDB code: 1C8U); H1 – hexamer with active site loops at interface (PDB code: 1Z6B); H2 – hexamer with N-terminal helices at interface (PDB code: 1YLI); H3 – hexamer with head-to-tail arrangement of dimers (PDB code: 2PFC); TA – tetramer with central helix interactions (PDB code: 1BVQ); TB – tetramer with back to back stacking of the β-sheets (PDB code: 1Q4T). DdhA (dimer of double hot dog with central helix interactions) is similar to TA while DdhB (dimer of double hot dogs with back to back interaction of the β-sheets) is similar to TB. Trdh (trimer of double hot dogs) is similar to H2.
Mentions: Each subunit of a hot dog fold is made up of 5 or 6 highly curved antiparallel β-strands wrapped around a long α-helix. Our analysis indicated that the basic structural repeat unit of the hot dog fold proteins is either a homodimer of two such subunits or a double hot dog with a single polypeptide chain folding into two hot dog domains (Fig. 1). The dimer of hot dog folds is formed by the association of β-sheets from both the subunits to form a continuous anti-parallel β-sheet. The two helices run antiparallel to each other at the dimer interface. In the enzymes with the repeat unit as the dimer of hot dogs, the active sites comprise residues from both the subunits. In the case of double hot dogs, the two domains have an undetectable sequence similarity (~10% identity as derived from structure-based alignment). However, at the nucleotide level, the sequence identity between the two domains of the double hot dogs is around 50% [3]. Though these basic building blocks (homodimer or double hot dog) of various subfamilies are similar with root mean square deviations (rmsd) of 1.0–3.0 Å for the Cα atoms, they differ in their quaternary associations and are highly divergent in their sequences. The various quaternary associations observed are dimers (D); tetramers with central helix interactions at the tetramer interface (TA); tetramers with back to back stacking of the β-sheets of the repeating units (TB); hexamers with active site loops at the interface (H1); hexamers with N-terminal helices at the interface (H2); hexamers with head-to-tail arrangement of dimers (H3); dimers of double hot dogs with central helix interactions (DdhA); dimers of double hot dogs with back to back stacking of β-sheets (DdhB); and trimers of double hot dogs (Trdh) which appear like H2 (Fig. 2). The two domains of the double hot dogs are connected by long loops. Though they connect the second β-strand from the centre in the first subunit to the last β-strand of the second subunit in all the cases, the loops have considerable variation in length and conformation and also in the direction they follow to connect the subunits. This variation in the nature of the connecting loops appears to be linked with the quaternary association (DdhA, DdhB and Trdh) of the double hot dog fold proteins. The analysis of buried surface areas of various types of quaternary association has revealed that approximately 17–20%, 20–25%, 26–30%, 32–36%, 26–30% and 16% surface area per monomer gets buried upon the formation of D, TA, TB, H1, H2 and H3 types of quaternary associations, respectively.

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