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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.
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BMC Bioinformatics

ISSN: 1471-2105

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