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The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

Edgar AJ - BMC Genet. (2002)

Bottom Line: These truncated proteins are the result of 3 mutations within the gene.There is a SNP, A to G, present in the genomic DNA sequence of some individuals which results in the loss of the acceptor splice site preceding exon 4.The acceptor splice site preceding exon 6 was lost in all 23 individuals genotyped and there is an in-frame stop codon in exon 6 (CGA to TGA) resulting in arginine-214 being replaced by a stop codon.

View Article: PubMed Central - HTML - PubMed

Affiliation: Tissue Engineering & Regenerative Medicine Centre, Division of Investigative Science, Faculty of Medicine, Imperial College of Science, Technology and Medicine, Chelsea & Westminster Hospital, London, United Kingdom. alasdair.edgar@ic.ac.uk

ABSTRACT

Background: L-threonine is an indispensable amino acid. One of the major L-threonine degradation pathways is the conversion of L-threonine via 2-amino-3-ketobutyrate to glycine. L-threonine dehydrogenase (EC 1.1.1.103) is the first enzyme in the pathway and catalyses the reaction: L-threonine + NAD+ = 2-amino-3-ketobutyrate + NADH. The murine and porcine L-threonine dehydrogenase genes (TDH) have been identified previously, but the human gene has not been identified.

Results: The human TDH gene is located at 8p23-22 and has 8 exons spanning 10 kb that would have been expected to encode a 369 residue ORF. However, 2 cDNA TDH transcripts encode truncated proteins of 157 and 230 residues. These truncated proteins are the result of 3 mutations within the gene. There is a SNP, A to G, present in the genomic DNA sequence of some individuals which results in the loss of the acceptor splice site preceding exon 4. The acceptor splice site preceding exon 6 was lost in all 23 individuals genotyped and there is an in-frame stop codon in exon 6 (CGA to TGA) resulting in arginine-214 being replaced by a stop codon. These truncated proteins would be non-functional since they have lost part of the NAD+ binding motif and the COOH terminal domain that is thought to be involved in binding L-threonine. TDH mRNA was present in all tissues examined.

Conclusions: The human L-threonine 3-dehydrogenase gene is an expressed pseudogene having lost the splice acceptor site preceding exon 6 and codon arginine-214 (CGA) is mutated to a stop codon (TGA).

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Clustal alignment of the predicted human protein with other eukaryotic L-threonine dehydrogenase (TDH) protein sequences and 2 UDP-galactose 4-epimerase sequences (GALE). The species and the derivation of the sequences are as follows: Homo sapiens, HsTDH, genomic DNA (accession No. AC011959); HsGALE, cDNA (NP_000394); Sus scrofa, (pig), Ss, cDNA (AY095535); Mus musculus, mouse, Mm, cDNA (AY116662); Danio rerio (zebrafish), Dr, ESTs (electronic contigous sequence); Takifugu rubripes (puffer fish), Tr, genomic DNA, (AF411956); Ciona intestinalis (a tunicate), Ci, ESTs; Drosophila melanogaster, Dm, genomic DNA gene CG5955 and ESTs; Caenorhabditis elegans, Ce, genomic DNA (U64847) and ESTs; Escherichia coli, EcTDH (P07913) and EcGALE (AAC73846). The locations of the exon/exon boundaries are shown on the translated protein as underlined residues. Conserved residues are indicated by a (*), strongly similar residues by a (:) and weakly similar residues by a (.). Residues that are common to at least two protein sequences are shown in bold. The in-frame stop codon in the human sequence is indicated by a red (#). Gale protein residues in contact with the ligand nicotinamide-adenine-dinucleotide are highlighted in green and those residues in contact with the sugar ligands, uridine-5'-diphosphate-mannose and uridine-5'-diphosphate-4-deoxy-4-fluoro-alpha-d-galactose are highlighted in yellow. Those residues that have been shown to contact both NAD and sugar are highlighted in light blue [26-29].
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Figure 3: Clustal alignment of the predicted human protein with other eukaryotic L-threonine dehydrogenase (TDH) protein sequences and 2 UDP-galactose 4-epimerase sequences (GALE). The species and the derivation of the sequences are as follows: Homo sapiens, HsTDH, genomic DNA (accession No. AC011959); HsGALE, cDNA (NP_000394); Sus scrofa, (pig), Ss, cDNA (AY095535); Mus musculus, mouse, Mm, cDNA (AY116662); Danio rerio (zebrafish), Dr, ESTs (electronic contigous sequence); Takifugu rubripes (puffer fish), Tr, genomic DNA, (AF411956); Ciona intestinalis (a tunicate), Ci, ESTs; Drosophila melanogaster, Dm, genomic DNA gene CG5955 and ESTs; Caenorhabditis elegans, Ce, genomic DNA (U64847) and ESTs; Escherichia coli, EcTDH (P07913) and EcGALE (AAC73846). The locations of the exon/exon boundaries are shown on the translated protein as underlined residues. Conserved residues are indicated by a (*), strongly similar residues by a (:) and weakly similar residues by a (.). Residues that are common to at least two protein sequences are shown in bold. The in-frame stop codon in the human sequence is indicated by a red (#). Gale protein residues in contact with the ligand nicotinamide-adenine-dinucleotide are highlighted in green and those residues in contact with the sugar ligands, uridine-5'-diphosphate-mannose and uridine-5'-diphosphate-4-deoxy-4-fluoro-alpha-d-galactose are highlighted in yellow. Those residues that have been shown to contact both NAD and sugar are highlighted in light blue [26-29].

Mentions: The predicted human TDH protein possesses very weak similarity to the human uridine diphosphogalactose-4-epimerase protein (GALE). GALE catalyses the interconversion of UDP-galactose and UDP-glucose in the metabolic pathway that converts galactose into glucose1-phosphate, and also catalyses the interconversion of UDP-GalNAc and UDP-GlcNAc. An alignment of the human TDH protein with other eukaryotic TDH protein sequences and GALE proteins from Homo sapiens and Escherichia coli identified conserved residues likely to contact the nicotinamide-adenine-dinucleotide cofactor (NAD+) (Fig. 3) [25]. They are Gly-58, Gly-61, Gly-64, Asp-84, Asp-102, Ile-103, Leu-104, His-123, Leu-127, Val-142, Asn-143, Ser-165, Tyr-191, Lys-195 and Tyr-218 [26-29]. In view of the different substrates utilised by the 2 enzymes, of those 22 residues that contact the sugar substrate in GALE only one, Asp-325, is conserved (excluding those residues involved in contact with both sugar and NAD+).


The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

Edgar AJ - BMC Genet. (2002)

Clustal alignment of the predicted human protein with other eukaryotic L-threonine dehydrogenase (TDH) protein sequences and 2 UDP-galactose 4-epimerase sequences (GALE). The species and the derivation of the sequences are as follows: Homo sapiens, HsTDH, genomic DNA (accession No. AC011959); HsGALE, cDNA (NP_000394); Sus scrofa, (pig), Ss, cDNA (AY095535); Mus musculus, mouse, Mm, cDNA (AY116662); Danio rerio (zebrafish), Dr, ESTs (electronic contigous sequence); Takifugu rubripes (puffer fish), Tr, genomic DNA, (AF411956); Ciona intestinalis (a tunicate), Ci, ESTs; Drosophila melanogaster, Dm, genomic DNA gene CG5955 and ESTs; Caenorhabditis elegans, Ce, genomic DNA (U64847) and ESTs; Escherichia coli, EcTDH (P07913) and EcGALE (AAC73846). The locations of the exon/exon boundaries are shown on the translated protein as underlined residues. Conserved residues are indicated by a (*), strongly similar residues by a (:) and weakly similar residues by a (.). Residues that are common to at least two protein sequences are shown in bold. The in-frame stop codon in the human sequence is indicated by a red (#). Gale protein residues in contact with the ligand nicotinamide-adenine-dinucleotide are highlighted in green and those residues in contact with the sugar ligands, uridine-5'-diphosphate-mannose and uridine-5'-diphosphate-4-deoxy-4-fluoro-alpha-d-galactose are highlighted in yellow. Those residues that have been shown to contact both NAD and sugar are highlighted in light blue [26-29].
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC131051&req=5

Figure 3: Clustal alignment of the predicted human protein with other eukaryotic L-threonine dehydrogenase (TDH) protein sequences and 2 UDP-galactose 4-epimerase sequences (GALE). The species and the derivation of the sequences are as follows: Homo sapiens, HsTDH, genomic DNA (accession No. AC011959); HsGALE, cDNA (NP_000394); Sus scrofa, (pig), Ss, cDNA (AY095535); Mus musculus, mouse, Mm, cDNA (AY116662); Danio rerio (zebrafish), Dr, ESTs (electronic contigous sequence); Takifugu rubripes (puffer fish), Tr, genomic DNA, (AF411956); Ciona intestinalis (a tunicate), Ci, ESTs; Drosophila melanogaster, Dm, genomic DNA gene CG5955 and ESTs; Caenorhabditis elegans, Ce, genomic DNA (U64847) and ESTs; Escherichia coli, EcTDH (P07913) and EcGALE (AAC73846). The locations of the exon/exon boundaries are shown on the translated protein as underlined residues. Conserved residues are indicated by a (*), strongly similar residues by a (:) and weakly similar residues by a (.). Residues that are common to at least two protein sequences are shown in bold. The in-frame stop codon in the human sequence is indicated by a red (#). Gale protein residues in contact with the ligand nicotinamide-adenine-dinucleotide are highlighted in green and those residues in contact with the sugar ligands, uridine-5'-diphosphate-mannose and uridine-5'-diphosphate-4-deoxy-4-fluoro-alpha-d-galactose are highlighted in yellow. Those residues that have been shown to contact both NAD and sugar are highlighted in light blue [26-29].
Mentions: The predicted human TDH protein possesses very weak similarity to the human uridine diphosphogalactose-4-epimerase protein (GALE). GALE catalyses the interconversion of UDP-galactose and UDP-glucose in the metabolic pathway that converts galactose into glucose1-phosphate, and also catalyses the interconversion of UDP-GalNAc and UDP-GlcNAc. An alignment of the human TDH protein with other eukaryotic TDH protein sequences and GALE proteins from Homo sapiens and Escherichia coli identified conserved residues likely to contact the nicotinamide-adenine-dinucleotide cofactor (NAD+) (Fig. 3) [25]. They are Gly-58, Gly-61, Gly-64, Asp-84, Asp-102, Ile-103, Leu-104, His-123, Leu-127, Val-142, Asn-143, Ser-165, Tyr-191, Lys-195 and Tyr-218 [26-29]. In view of the different substrates utilised by the 2 enzymes, of those 22 residues that contact the sugar substrate in GALE only one, Asp-325, is conserved (excluding those residues involved in contact with both sugar and NAD+).

Bottom Line: These truncated proteins are the result of 3 mutations within the gene.There is a SNP, A to G, present in the genomic DNA sequence of some individuals which results in the loss of the acceptor splice site preceding exon 4.The acceptor splice site preceding exon 6 was lost in all 23 individuals genotyped and there is an in-frame stop codon in exon 6 (CGA to TGA) resulting in arginine-214 being replaced by a stop codon.

View Article: PubMed Central - HTML - PubMed

Affiliation: Tissue Engineering & Regenerative Medicine Centre, Division of Investigative Science, Faculty of Medicine, Imperial College of Science, Technology and Medicine, Chelsea & Westminster Hospital, London, United Kingdom. alasdair.edgar@ic.ac.uk

ABSTRACT

Background: L-threonine is an indispensable amino acid. One of the major L-threonine degradation pathways is the conversion of L-threonine via 2-amino-3-ketobutyrate to glycine. L-threonine dehydrogenase (EC 1.1.1.103) is the first enzyme in the pathway and catalyses the reaction: L-threonine + NAD+ = 2-amino-3-ketobutyrate + NADH. The murine and porcine L-threonine dehydrogenase genes (TDH) have been identified previously, but the human gene has not been identified.

Results: The human TDH gene is located at 8p23-22 and has 8 exons spanning 10 kb that would have been expected to encode a 369 residue ORF. However, 2 cDNA TDH transcripts encode truncated proteins of 157 and 230 residues. These truncated proteins are the result of 3 mutations within the gene. There is a SNP, A to G, present in the genomic DNA sequence of some individuals which results in the loss of the acceptor splice site preceding exon 4. The acceptor splice site preceding exon 6 was lost in all 23 individuals genotyped and there is an in-frame stop codon in exon 6 (CGA to TGA) resulting in arginine-214 being replaced by a stop codon. These truncated proteins would be non-functional since they have lost part of the NAD+ binding motif and the COOH terminal domain that is thought to be involved in binding L-threonine. TDH mRNA was present in all tissues examined.

Conclusions: The human L-threonine 3-dehydrogenase gene is an expressed pseudogene having lost the splice acceptor site preceding exon 6 and codon arginine-214 (CGA) is mutated to a stop codon (TGA).

Show MeSH
Related in: MedlinePlus