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The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases.

Aravind L, Koonin EV - Genome Biol. (2001)

Bottom Line: Here we describe such predictions resulting from an analysis of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenases, a class of enzymes that are widespread in eukaryotes and bacteria and catalyze a variety of reactions typically involving the oxidation of an organic substrate using a dioxygen molecule.The EGL-9 protein from Caenorhabditis elegans is necessary for normal muscle function and its inactivation results in resistance against paralysis induced by the Pseudomonas aeruginosa toxin.This allows us to predict the catalytic activity for a wide range of biologically important, but biochemically uncharacterized proteins from eukaryotes and bacteria.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. aravind@ncbi.nlm.nih.gov

ABSTRACT

Background: Protein fold recognition using sequence profile searches frequently allows prediction of the structure and biochemical mechanisms of proteins with an important biological function but unknown biochemical activity. Here we describe such predictions resulting from an analysis of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenases, a class of enzymes that are widespread in eukaryotes and bacteria and catalyze a variety of reactions typically involving the oxidation of an organic substrate using a dioxygen molecule.

Results: We employ sequence profile analysis to show that the DNA repair protein AlkB, the extracellular matrix protein leprecan, the disease-resistance-related protein EGL-9 and several uncharacterized proteins define novel families of enzymes of the 2OG-Fe(II) oxygenase superfamily. The identification of AlkB as a member of the 2OG-Fe(II) oxygenase superfamily suggests that this protein catalyzes oxidative detoxification of alkylated bases. More distant homologs of AlkB were detected in eukaryotes and in plant RNA viruses, leading to the hypothesis that these proteins might be involved in RNA demethylation. The EGL-9 protein from Caenorhabditis elegans is necessary for normal muscle function and its inactivation results in resistance against paralysis induced by the Pseudomonas aeruginosa toxin. EGL-9 and leprecan are predicted to be novel protein hydroxylases that might be involved in the generation of substrates for protein glycosylation.

Conclusions: Here, using sequence profile searches, we show that several previously undetected protein families contain 2OG-Fe(II) oxygenase fold. This allows us to predict the catalytic activity for a wide range of biologically important, but biochemically uncharacterized proteins from eukaryotes and bacteria.

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Topological diagrams for three members of the 2OG-Fe(II) dioxygenase superfamily. The diagrams are based on the experimentally determined structures for E. nidulans isopenicillin N synthase (PDB: 1ips) and structural models of prolyl-4-hydroxylase and AlkB. The amino acid residues of the active site and the Fe(II) ion are shown as in Figure 2.
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Figure 3: Topological diagrams for three members of the 2OG-Fe(II) dioxygenase superfamily. The diagrams are based on the experimentally determined structures for E. nidulans isopenicillin N synthase (PDB: 1ips) and structural models of prolyl-4-hydroxylase and AlkB. The amino acid residues of the active site and the Fe(II) ion are shown as in Figure 2.

Mentions: The conserved portion of the 2OG-Fe(II) dioxygenase superfamily proteins comprises the core DSBH domain seen in the IPNS, DAOCS and CAS structures [8,9,10] and part of the amino-terminal α helix that showed considerable variability in both length and sequence between individual families (Figures 1,2). The DSBH region includes seven conserved strands that are common to all these proteins and are arranged in two sheets in a jelly-roll topology (Figures 2,3). However, different families have specific inserts in various positions between the conserved strands; some of these inserts contain additional secondary structures and show significant sequence conservation (Figures 1,3). For example, the insert between the fifth and sixth strand in AlkB is predicted to contain an extra strand, whereas in the small-molecule dioxygenase (IPNS/ethylene-forming enzyme (EFE)) family, the same region forms (or is predicted to form) a short helix (Figures 1,3). The clavaminic acid synthase, an outlier of this latter family, has its own characteristic inserts, including a giant (approximately 70 amino acids) insert between strands 4 and 5 [8], and some members of the AlkB family have smaller inserts in the same position (Figure 1). This reflects the relative resilience of the core DSBH to insertions, and accounts for difficulties in unification of this superfamilyby sequence-based methods. The multiple alignment contains at least three characteristic conserved motifs that center, respectively, at a HXD dyad near the amino terminus, a histidine towards the carboxyl terminus, and an arginine or lysine further downstream (Figure 1). The HXD dyad is located in a flexible loop that follows the first conserved strand and stacks with the sheet containing three of the core strands (Figures 2,3). The second conserved histidine is associated with the beginning of the sixth strand, whereas the conserved basic residue (R or K) is in the beginning of the seventh strand of the DSBH core (Figures 2,3). The sixth position after the conserved basic residue is invariably occupied by a bulky residue that is either arginine (in AlkB) or phenylalanine or tryptophan in all other members of this fold [8,9,10] (Figure 1).


The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases.

Aravind L, Koonin EV - Genome Biol. (2001)

Topological diagrams for three members of the 2OG-Fe(II) dioxygenase superfamily. The diagrams are based on the experimentally determined structures for E. nidulans isopenicillin N synthase (PDB: 1ips) and structural models of prolyl-4-hydroxylase and AlkB. The amino acid residues of the active site and the Fe(II) ion are shown as in Figure 2.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC30706&req=5

Figure 3: Topological diagrams for three members of the 2OG-Fe(II) dioxygenase superfamily. The diagrams are based on the experimentally determined structures for E. nidulans isopenicillin N synthase (PDB: 1ips) and structural models of prolyl-4-hydroxylase and AlkB. The amino acid residues of the active site and the Fe(II) ion are shown as in Figure 2.
Mentions: The conserved portion of the 2OG-Fe(II) dioxygenase superfamily proteins comprises the core DSBH domain seen in the IPNS, DAOCS and CAS structures [8,9,10] and part of the amino-terminal α helix that showed considerable variability in both length and sequence between individual families (Figures 1,2). The DSBH region includes seven conserved strands that are common to all these proteins and are arranged in two sheets in a jelly-roll topology (Figures 2,3). However, different families have specific inserts in various positions between the conserved strands; some of these inserts contain additional secondary structures and show significant sequence conservation (Figures 1,3). For example, the insert between the fifth and sixth strand in AlkB is predicted to contain an extra strand, whereas in the small-molecule dioxygenase (IPNS/ethylene-forming enzyme (EFE)) family, the same region forms (or is predicted to form) a short helix (Figures 1,3). The clavaminic acid synthase, an outlier of this latter family, has its own characteristic inserts, including a giant (approximately 70 amino acids) insert between strands 4 and 5 [8], and some members of the AlkB family have smaller inserts in the same position (Figure 1). This reflects the relative resilience of the core DSBH to insertions, and accounts for difficulties in unification of this superfamilyby sequence-based methods. The multiple alignment contains at least three characteristic conserved motifs that center, respectively, at a HXD dyad near the amino terminus, a histidine towards the carboxyl terminus, and an arginine or lysine further downstream (Figure 1). The HXD dyad is located in a flexible loop that follows the first conserved strand and stacks with the sheet containing three of the core strands (Figures 2,3). The second conserved histidine is associated with the beginning of the sixth strand, whereas the conserved basic residue (R or K) is in the beginning of the seventh strand of the DSBH core (Figures 2,3). The sixth position after the conserved basic residue is invariably occupied by a bulky residue that is either arginine (in AlkB) or phenylalanine or tryptophan in all other members of this fold [8,9,10] (Figure 1).

Bottom Line: Here we describe such predictions resulting from an analysis of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenases, a class of enzymes that are widespread in eukaryotes and bacteria and catalyze a variety of reactions typically involving the oxidation of an organic substrate using a dioxygen molecule.The EGL-9 protein from Caenorhabditis elegans is necessary for normal muscle function and its inactivation results in resistance against paralysis induced by the Pseudomonas aeruginosa toxin.This allows us to predict the catalytic activity for a wide range of biologically important, but biochemically uncharacterized proteins from eukaryotes and bacteria.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. aravind@ncbi.nlm.nih.gov

ABSTRACT

Background: Protein fold recognition using sequence profile searches frequently allows prediction of the structure and biochemical mechanisms of proteins with an important biological function but unknown biochemical activity. Here we describe such predictions resulting from an analysis of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenases, a class of enzymes that are widespread in eukaryotes and bacteria and catalyze a variety of reactions typically involving the oxidation of an organic substrate using a dioxygen molecule.

Results: We employ sequence profile analysis to show that the DNA repair protein AlkB, the extracellular matrix protein leprecan, the disease-resistance-related protein EGL-9 and several uncharacterized proteins define novel families of enzymes of the 2OG-Fe(II) oxygenase superfamily. The identification of AlkB as a member of the 2OG-Fe(II) oxygenase superfamily suggests that this protein catalyzes oxidative detoxification of alkylated bases. More distant homologs of AlkB were detected in eukaryotes and in plant RNA viruses, leading to the hypothesis that these proteins might be involved in RNA demethylation. The EGL-9 protein from Caenorhabditis elegans is necessary for normal muscle function and its inactivation results in resistance against paralysis induced by the Pseudomonas aeruginosa toxin. EGL-9 and leprecan are predicted to be novel protein hydroxylases that might be involved in the generation of substrates for protein glycosylation.

Conclusions: Here, using sequence profile searches, we show that several previously undetected protein families contain 2OG-Fe(II) oxygenase fold. This allows us to predict the catalytic activity for a wide range of biologically important, but biochemically uncharacterized proteins from eukaryotes and bacteria.

Show MeSH
Related in: MedlinePlus