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Table 1 Inventory of the human genes that encode PLP-dependent enzymes

From: The B6 database: a tool for the description and classification of vitamin B6-dependent enzymatic activities and of the corresponding protein families

Activity Family Protein accession # E-value Isoforms Gene Chromosome
Glycine dehydrogenase NP_000161 0   GLDC 9
Glycine hydroxymethyltransferase NP_004160 2 e-294 NP_683718 SHMT1 17
Glycine hydroxymethyltransferase NP_005403 8 e-289   SHMT2 12
Glycine C-acetyltransferase NP_055106 4 e-225   GCAT 22
5-aminolevulinic acid synthase NP_954635 1 e-269 NP_000679 ALAS1 3
5-aminolevulinic acid synthase NP_000023 2 e-270 NP_001033057
Serine C-palmitoyltransferase NP_006406 6 e-240   SPTLC1(a) 14
Serine C-palmitoyltransferase NP_004854 6 e-299   SPTLC2 20
Serine C-palmitoyltransferase NP_060797 3 e-260   SPTLC3 20
Phosphorylase NP_002854 0   PYGL 14
Phosphorylase NP_005600 0   PYGM 11
Phosphorylase NP_002853 0   PYGB 20
Aspartate aminotransferase NP_002070 2 e-295   GOT1 10
Aspartate aminotransferase NP_689626 1 e-68   GOT1L1 8
Aspartate aminotransferase NP_002071 2 e-306   GOT2 16
Alanine aminotransferase NP_005300 6 e-262   GPT 8
Alanine aminotransferase NP_597700 3 e-267   GPT2 16
Tyrosine aminotransferase NP_000344 2 e-292   TAT 16
Kynurenine:oxoglutarate aminotransf. NP_004050 7 e-279   CCBL1 9
Kynurenine:oxoglutarate aminotransf. NP_001008662 4 e-266 NP_001008661 CCBL2 1
Ornithine:oxo-acid aminotransferase NP_000265 4 e-274   OAT 10
4-aminobutyrate aminotransferase NP_065737 0 NP_000654 ABAT 16
2-aminoadipate aminotransferase NP_872603 3 e-265 NP_057312 AADAT 4
Branched-chain aa aminotransferase NP_005495 3 e-191   BCAT1 12
Branched-chain aa aminotransferase NP_001181 1 e-181   BCAT2 19
Alanine:glyoxylate aminotransferase NP_114106 0   AGXT2 5
Alanine:glyoxylate aminotransferase NP_112569 1 e-114   AGXT2L1(b) 4
Alanine:glyoxylate aminotransferase NP_699204 8 e-100   AGXT2L2(b) 5
Serine:pyruvate aminotransferase NP_000021 7 e-269   AGXT 2
Phosphoserine aminotransferase NP_478059 8 e-235 NP_066977 PSAT1 9
Cysteine desulfurase NP_066923 5 e-290   NFS1 20
Cysteine desulfurase NP_060417 0   MOCOS 18
Kynureninase NP_003928 3 e-259   KYNU 2
Glutamate decarboxylase NP_000808 0   GAD1 2
Glutamate decarboxylase NP_000809 0   GAD2 10
Ornithine decarboxylase NP_002530 1 e-175   ODC1 2
Histidine decarboxylase NP_002103 1 e-285   HDC 15
Aromatic-L-amino-acid decarboxylase NP_000781 2 e-291 NP_001076440 DDC 7
Sulfinoalanine decarboxylase NP_997242 2 e-116   GADL1 3
Sulfinoalanine decarboxylase NP_057073 0   CSAD 12
Sphinganine-1-phosphate aldolase NP_003892 9 e-249   SGPL1 10
Cystathionine beta-synthase NP_000062 2 e-228   CBS 21
Threonine synthase NP_079114 7 e-91   THNSL1 10
Threonine synthase NP_060741 4 e-80   THNSL2(c) 2
L-serine ammonia-lyase NP_006834 5 e-209   SDS 12
L-serine ammonia-lyase NP_612441 2 e-205   SDSL 12
Cystathionine gamma-lyase NP_001893 7 e-296 NP_714964 CTH 1
1-ACC synthase NP_115981 1 e-81   ACCS(d) 11
1-ACC synthase NP_001027025 3 e-78   ACCSL 11
Selenocysteine lyase NP_057594 0   SCLY 2
Serine racemase NP_068766 8 e-243   SRR 17
Ornithine decarboxylase paralogue odcp NP_443724 8 e-197   ADC(e) 1
Ornithine decarboxylase paralogue odcp NP_056962 2 e-116 NP_680479 AZIN1(e) 8
L-phosphoseryl-tRNASer:seleno- phosphate seleniumtransferase sec.synthase NP_722547 0 NP_058651 SEPSECS 4
Unclassified activity Uncharact. family.prosc NP_009129 5 e-166   PROSC 8
Unassigned n/a NP_055842 9 e-8   PDXDC1 16
  1. The complete set of proteins from the NCBI 36 assembly of the human genome was searched as described in the text. The 'Family' column reports the name of the family whose HMM scored best when compared to the query. When possible, the family name is constituted by, or includes, the four-digits EC number of the corresponding activity. Note that the layout of the present table recapitulates the output provided by B6 database's site, with some modifications. In particular, the occurrence of protein isoforms derived from some genes was obtained by analysis of the crude program results. The official names of the genes corresponding to the transcripts and their chromosomal locations were obtained from NCBI.
  2. (a) This gene encodes the subunit LCB1 of human serine palmitoyltransferase. This subunit is not itself a PLP-dependent enzyme, but is homologous to a second subunit (LCB2) that is PLP-dependent [24].
  3. (b) The products of genes AGXT2L1 and AGXT2L2 are homologs of the mitochondrial alanine-glyoxylate aminotransferase (AGXT2), but were recently shown to lack this activity [25].
  4. (c) The murine homolog of this gene was shown to encode an enzyme with phospho-lyase activity [26].
  5. (d) This gene is homolog to the plant 1-aminocyclopropane-1-carboxylate (ACC) synthase, but the gene product was shown to lack this activity [27].
  6. (e) Genes ADC and AZIN1 encode ornithine decarboxylase antizyme inhibitors, i.e. proteins homologous to ornithine decarboxylase, but devoid of ornithine decarboxylase activity, that are involved in regulation of polyamine biosynthesis [28, 29]. The human ADC, contrary to its mouse ortholog, retains a conserved lysine at the active site.