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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 1.4.4.2 NP_000161 0   GLDC 9
Glycine hydroxymethyltransferase 2.1.2.1 NP_004160 2 e-294 NP_683718 SHMT1 17
Glycine hydroxymethyltransferase 2.1.2.1 NP_005403 8 e-289   SHMT2 12
Glycine C-acetyltransferase 2.3.1.29 NP_055106 4 e-225   GCAT 22
5-aminolevulinic acid synthase 2.3.1.37 NP_954635 1 e-269 NP_000679 ALAS1 3
5-aminolevulinic acid synthase 2.3.1.37 NP_000023 2 e-270 NP_001033057
NP_001033058
NP_001033056
ALAS2 X
Serine C-palmitoyltransferase 2.3.1.50.a NP_006406 6 e-240   SPTLC1(a) 14
Serine C-palmitoyltransferase 2.3.1.50.b NP_004854 6 e-299   SPTLC2 20
Serine C-palmitoyltransferase 2.3.1.50.b NP_060797 3 e-260   SPTLC3 20
Phosphorylase 2.4.1.1 NP_002854 0   PYGL 14
Phosphorylase 2.4.1.1 NP_005600 0   PYGM 11
Phosphorylase 2.4.1.1 NP_002853 0   PYGB 20
Aspartate aminotransferase 2.6.1.1.a NP_002070 2 e-295   GOT1 10
Aspartate aminotransferase 2.6.1.1.a NP_689626 1 e-68   GOT1L1 8
Aspartate aminotransferase 2.6.1.1.a NP_002071 2 e-306   GOT2 16
Alanine aminotransferase 2.6.1.2.b NP_005300 6 e-262   GPT 8
Alanine aminotransferase 2.6.1.2.b NP_597700 3 e-267   GPT2 16
Tyrosine aminotransferase 2.6.1.5 NP_000344 2 e-292   TAT 16
Kynurenine:oxoglutarate aminotransf. 2.6.1.7 NP_004050 7 e-279   CCBL1 9
Kynurenine:oxoglutarate aminotransf. 2.6.1.7 NP_001008662 4 e-266 NP_001008661 CCBL2 1
Ornithine:oxo-acid aminotransferase 2.6.1.13 NP_000265 4 e-274   OAT 10
4-aminobutyrate aminotransferase 2.6.1.19.a NP_065737 0 NP_000654 ABAT 16
2-aminoadipate aminotransferase 2.6.1.39.a NP_872603 3 e-265 NP_057312 AADAT 4
Branched-chain aa aminotransferase 2.6.1.42 NP_005495 3 e-191   BCAT1 12
Branched-chain aa aminotransferase 2.6.1.42 NP_001181 1 e-181   BCAT2 19
Alanine:glyoxylate aminotransferase 2.6.1.44.a NP_114106 0   AGXT2 5
Alanine:glyoxylate aminotransferase 2.6.1.44.a NP_112569 1 e-114   AGXT2L1(b) 4
Alanine:glyoxylate aminotransferase 2.6.1.44.a NP_699204 8 e-100   AGXT2L2(b) 5
Serine:pyruvate aminotransferase 2.6.1.51 NP_000021 7 e-269   AGXT 2
Phosphoserine aminotransferase 2.6.1.52 NP_478059 8 e-235 NP_066977 PSAT1 9
Cysteine desulfurase 2.8.1.7.a NP_066923 5 e-290   NFS1 20
Cysteine desulfurase 2.8.1.7.b NP_060417 0   MOCOS 18
Kynureninase 3.7.1.3 NP_003928 3 e-259   KYNU 2
Glutamate decarboxylase 4.1.1.15.a NP_000808 0   GAD1 2
Glutamate decarboxylase 4.1.1.15.a NP_000809 0   GAD2 10
Ornithine decarboxylase 4.1.1.17.1 NP_002530 1 e-175   ODC1 2
Histidine decarboxylase 4.1.1.22.b NP_002103 1 e-285   HDC 15
Aromatic-L-amino-acid decarboxylase 4.1.1.28 NP_000781 2 e-291 NP_001076440 DDC 7
Sulfinoalanine decarboxylase 4.1.1.29 NP_997242 2 e-116   GADL1 3
Sulfinoalanine decarboxylase 4.1.1.29 NP_057073 0   CSAD 12
Sphinganine-1-phosphate aldolase 4.1.2.27 NP_003892 9 e-249   SGPL1 10
Cystathionine beta-synthase 4.2.1.22 NP_000062 2 e-228   CBS 21
Threonine synthase 4.2.3.1 NP_079114 7 e-91   THNSL1 10
Threonine synthase 4.2.3.1 NP_060741 4 e-80   THNSL2(c) 2
L-serine ammonia-lyase 4.3.1.17 NP_006834 5 e-209   SDS 12
L-serine ammonia-lyase 4.3.1.17 NP_612441 2 e-205   SDSL 12
Cystathionine gamma-lyase 4.4.1.1 NP_001893 7 e-296 NP_714964 CTH 1
1-ACC synthase 4.4.1.14 NP_115981 1 e-81   ACCS(d) 11
1-ACC synthase 4.4.1.14 NP_001027025 3 e-78   ACCSL 11
Selenocysteine lyase 4.4.1.16.b NP_057594 0   SCLY 2
Serine racemase 5.1.1.18 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.