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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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Predicted secondary structure of human "ancestral" TDH protein was determined using the Psi-Pred program and was aligned with that of the crystal structure of uridine diphosphogalactose-4-epimerase protein (GALE) from Escherichia coli[29,31] using 3D-PSSM. The labels are: human "ancestral" TDH protein predicted secondary structure, HsTDH_PSSM; human "ancestral" TDH protein sequence, HsTDH_seq; E. coli GALE protein sequence, EcGale_seq; E. coli GALE protein secondary structure, 1udc_SS; alpha-helix, H, highlighted in light blue; beta-sheet, E, highlighted in yellow; c = turn, coil or loop. Identical residues are shown and additionally, a ":" indicates positive equivalence.
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Figure 4: Predicted secondary structure of human "ancestral" TDH protein was determined using the Psi-Pred program and was aligned with that of the crystal structure of uridine diphosphogalactose-4-epimerase protein (GALE) from Escherichia coli[29,31] using 3D-PSSM. The labels are: human "ancestral" TDH protein predicted secondary structure, HsTDH_PSSM; human "ancestral" TDH protein sequence, HsTDH_seq; E. coli GALE protein sequence, EcGale_seq; E. coli GALE protein secondary structure, 1udc_SS; alpha-helix, H, highlighted in light blue; beta-sheet, E, highlighted in yellow; c = turn, coil or loop. Identical residues are shown and additionally, a ":" indicates positive equivalence.

Mentions: Using the translation of the human genomic sequence (with the stop codon replaced with the conserved arginine residue found in other TDH proteins) the predicted secondary structure of the likely "ancestral" TDH protein was determined using Psi-Pred [30] and aligned with the crystal structure of GALE from E. coli[29,31] (Fig. 4). The human ancestral TDH protein would have been a mixed alpha-helices/beta-sheet protein with a NAD+ binding Rossmann-fold and belongs to the tyrosine-dependent oxidoreductase protein family (also known as short-chain dehydrogenases). The characteristic Tyr-x-x-x-Lys couple (residues 191 and 195) found in all family members is important for catalysis with the conserved tyrosine serving as the active-site base [33]. Two domains were identified, with the larger amino-terminus domain (residues 53–234) having a NAD+ binding motif and the smaller carboxy-terminus domain (residues 218–329) likely to be involved in L-threonine binding. It is likely that the substrate is located in the cleft between the two domains.


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

Edgar AJ - BMC Genet. (2002)

Predicted secondary structure of human "ancestral" TDH protein was determined using the Psi-Pred program and was aligned with that of the crystal structure of uridine diphosphogalactose-4-epimerase protein (GALE) from Escherichia coli[29,31] using 3D-PSSM. The labels are: human "ancestral" TDH protein predicted secondary structure, HsTDH_PSSM; human "ancestral" TDH protein sequence, HsTDH_seq; E. coli GALE protein sequence, EcGale_seq; E. coli GALE protein secondary structure, 1udc_SS; alpha-helix, H, highlighted in light blue; beta-sheet, E, highlighted in yellow; c = turn, coil or loop. Identical residues are shown and additionally, a ":" indicates positive equivalence.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC131051&req=5

Figure 4: Predicted secondary structure of human "ancestral" TDH protein was determined using the Psi-Pred program and was aligned with that of the crystal structure of uridine diphosphogalactose-4-epimerase protein (GALE) from Escherichia coli[29,31] using 3D-PSSM. The labels are: human "ancestral" TDH protein predicted secondary structure, HsTDH_PSSM; human "ancestral" TDH protein sequence, HsTDH_seq; E. coli GALE protein sequence, EcGale_seq; E. coli GALE protein secondary structure, 1udc_SS; alpha-helix, H, highlighted in light blue; beta-sheet, E, highlighted in yellow; c = turn, coil or loop. Identical residues are shown and additionally, a ":" indicates positive equivalence.
Mentions: Using the translation of the human genomic sequence (with the stop codon replaced with the conserved arginine residue found in other TDH proteins) the predicted secondary structure of the likely "ancestral" TDH protein was determined using Psi-Pred [30] and aligned with the crystal structure of GALE from E. coli[29,31] (Fig. 4). The human ancestral TDH protein would have been a mixed alpha-helices/beta-sheet protein with a NAD+ binding Rossmann-fold and belongs to the tyrosine-dependent oxidoreductase protein family (also known as short-chain dehydrogenases). The characteristic Tyr-x-x-x-Lys couple (residues 191 and 195) found in all family members is important for catalysis with the conserved tyrosine serving as the active-site base [33]. Two domains were identified, with the larger amino-terminus domain (residues 53–234) having a NAD+ binding motif and the smaller carboxy-terminus domain (residues 218–329) likely to be involved in L-threonine binding. It is likely that the substrate is located in the cleft between the two domains.

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