DB code: D00109
| CATH domain | 3.90.1150.10 : Aspartate Aminotransferase, domain 1 | |
|---|---|---|
| 3.40.640.10 : Aspartate Aminotransferase; domain 2 | Catalytic domain | |
| E.C. | 2.6.1.62 | |
| CSA | ||
| M-CSA | ||
| MACiE | M0249 | |
| CATH domain | Related DB codes (homologues) |
|---|---|
| 3.40.640.10 : Aspartate Aminotransferase; domain 2 | D00085 D00092 D00101 D00102 D00103 D00104 D00107 D00108 D00255 D00257 D00258 D00265 D00269 D00515 M00031 D00279 |
| 3.90.1150.10 : Aspartate Aminotransferase, domain 1 | D00085 D00092 D00101 D00102 D00103 D00104 D00107 D00108 D00255 D00257 D00258 D00265 D00269 D00515 M00031 D00279 |
| Uniprot Enzyme Name | UniprotKB | Protein name | Synonyms | RefSeq | Pfam |
|---|---|---|---|---|
| P12995 |
Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
|
EC
2.6.1.62
7,8-diamino-pelargonic acid aminotransferase DAPA AT DAPA aminotransferase 7,8-diaminononanoate synthase DANS Diaminopelargonic acid synthase |
NP_415295.1
(Protein)
NC_000913.2 (DNA/RNA sequence) YP_489047.1 (Protein) NC_007779.1 (DNA/RNA sequence) |
PF00202
(Aminotran_3)
[Graphical View] |
| P0A4X6 |
Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
|
EC
2.6.1.62
7,8-diamino-pelargonic acid aminotransferase DAPA AT DAPA aminotransferase 7,8-diaminononanoate synthase DANS Diaminopelargonic acid synthase |
NP_216084.1
(Protein)
NC_000962.3 (DNA/RNA sequence) NP_336072.1 (Protein) NC_002755.2 (DNA/RNA sequence) YP_006514957.1 (Protein) NC_018143.1 (DNA/RNA sequence) |
PF00202
(Aminotran_3)
[Graphical View] |
| KEGG enzyme name |
|---|
|
adenosylmethionine---8-amino-7-oxononanoate transaminase
7,8-diaminonanoate transaminase 7,8-diaminononanoate transaminase DAPA transaminase 7,8-diaminopelargonic acid aminotransferase DAPA aminotransferase 7-keto-8-aminopelargonic acid diaminopelargonate synthase 7-keto-8-aminopelargonic acid aminotransferase |
| UniprotKB: Accession Number | Entry name | Activity | Subunit | Subcellular location | Cofactor |
|---|---|---|---|---|---|
| P12995 | BIOA_ECOLI | S-adenosyl-L-methionine + 8-amino-7- oxononanoate = S-adenosyl-4-methylthio-2-oxobutanoate + 7,8- diaminononanoate. | Homodimer. | Cytoplasm. | Pyridoxal phosphate. |
| P0A4X6 | BIOA_MYCTU | S-adenosyl-L-methionine + 8-amino-7- oxononanoate = S-adenosyl-4-methylthio-2-oxobutanoate + 7,8- diaminononanoate. | Homodimer (By similarity). | Pyridoxal phosphate (By similarity). |
| KEGG Pathways | Map code | Pathways | E.C. |
|---|---|---|
| MAP00780 | Biotin metabolism |
| Compound table | ||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Cofactors | Substrates | Products | Intermediates | |||||||||||||||
| KEGG-id | C00018 | C00019 | C01092 | C04425 | C01037 | I00037 | I00038 | I00039 | C00647 | I00040 | I00041 | I00042 | ||||||
| E.C. |
(carbinolabine)
|
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| Compound | Pyridoxal phosphate | S-Adenosyl-L-methionine | 8-Amino-7-oxononanoate | S-Adenosyl-4-methylthio-2-oxobutanoate | 7,8-Diaminononanoate | External aldimine intermediate (initial stage:PLP-SAM) | Quinonoid Intermediate-1 (PLP-SAM) | Ketimine intermediate-1 (PLP-SAM) | Tetrahedral intermediate from ketimine to PMP | Pyridoxamine phosphate (PMP) | Ketimine intermediate-2 (PLP-Diaminononanoate) | Quinonoid Intermediate-2 (PLP-Diaminononanoate) | External aldimine intermediate (final stage:PLP-Diaminononanoate) | |||||
| Type | aromatic ring (with nitrogen atoms),phosphate group/phosphate ion | amino acids,amine group,nucleoside,sulfonium ion | amino acids,carbohydrate,fatty acid | amide group,carbohydrate,carboxyl group,nucleoside,sulfonium ion | amino acids,amine group,fatty acid | |||||||||||||
| ChEBI |
18405 18405 |
67040 67040 |
15830 57532 15830 57532 |
8944 8944 |
2247 2247 |
|||||||||||||
| PubChem |
1051 1051 |
34755 34755 |
173 25244029 173 25244029 |
440336 440336 |
652 652 |
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| 1dtyA01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1dtyB01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1mgvA01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1mgvB01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1mlyA01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1mlyB01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1mlzA01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1mlzB01 |
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Unbound | Unbound | Unbound | Unbound | Analogue:TZA | Unbound | |||||||
| 1qj3A01 |
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Unbound | Unbound | Bound:KAP | Unbound | Unbound | Unbound | |||||||
| 1qj3B01 |
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Unbound | Unbound | Bound:KAP | Unbound | Unbound | Unbound | |||||||
| 1qj5A01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1qj5B01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1s06A01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1s06B01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1s07A01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1s07B01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1s08A01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1s08B01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1s09A01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1s09B01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1s0aA01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1s0aB01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 3bv0A01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 3bv0B01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1dtyA02 |
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Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1dtyB02 |
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Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1mgvA02 |
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Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1mgvB02 |
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Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1mlyA02 |
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Bound:PLP | Unbound | Unbound | Unbound | Unbound | Intermediate-analogue:PLP-ACZ | |||||||
| 1mlyB02 |
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Bound:PLP | Unbound | Unbound | Unbound | Unbound | Intermediate-analogue:PLP-ACZ | |||||||
| 1mlzA02 |
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Bound:PLP | Unbound | Unbound | Unbound | Unbound | Intermediate-analogue:PLP-TZA | |||||||
| 1mlzB02 |
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Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1qj3A02 |
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Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1qj3B02 |
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Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1qj5A02 |
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Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1qj5B02 |
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Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1s06A02 |
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Bound:LLP | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1s06B02 |
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Bound:LLP | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1s07A02 |
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Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1s07B02 |
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Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1s08A02 |
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Bound:LLP | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1s08B02 |
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Bound:LLP | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1s09A02 |
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Bound:LLP | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1s09B02 |
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Bound:LLP | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1s0aA02 |
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Bound:LLP | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 1s0aB02 |
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Bound:LLP | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 3bv0A02 |
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Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| 3bv0B02 |
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Bound:PLP | Unbound | Unbound | Unbound | Unbound | Unbound | |||||||
| Reference for Active-site residues | ||
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| resource | references | E.C. |
| PDB;1qj3, 1qj5 | ||
| Active-site residues | ||||||||||
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| PDB | Catalytic residues | Cofactor-binding residues | Modified residues | Main-chain involved in catalysis | Comment | |||||
| 1dtyA01 |
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| 1dtyB01 |
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| 1mgvA01 |
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mutant R391A | ||||
| 1mgvB01 |
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mutant R391A | ||||
| 1mlyA01 |
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| 1mlyB01 |
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| 1mlzA01 |
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| 1mlzB01 |
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| 1qj3A01 |
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| 1qj3B01 |
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| 1qj5A01 |
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| 1qj5B01 |
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| 1s06A01 |
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| 1s06B01 |
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| 1s07A01 |
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| 1s07B01 |
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| 1s08A01 |
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| 1s08B01 |
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| 1s09A01 |
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| 1s09B01 |
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| 1s0aA01 |
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mutant Y17F | ||||
| 1s0aB01 |
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mutant Y17F | ||||
| 3bv0A01 |
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| 3bv0B01 |
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| 1dtyA02 |
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TYR 144;ASP 245;LYS 274 | LYS 274(PLP binding) | |||
| 1dtyB02 |
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TYR 144;ASP 245;LYS 274 | LYS 274(PLP binding) | |||
| 1mgvA02 |
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TYR 144;ASP 245;LYS 274 | LYS 274(PLP binding) | |||
| 1mgvB02 |
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TYR 144;ASP 245;LYS 274 | LYS 274(PLP binding) | |||
| 1mlyA02 |
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TYR 144;ASP 245;LYS 274 | LYS 274(PLP binding) | |||
| 1mlyB02 |
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TYR 144;ASP 245;LYS 274 | LYS 274(PLP binding) | |||
| 1mlzA02 |
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TYR 144;ASP 245;LYS 274 | LYS 274(PLP binding) | |||
| 1mlzB02 |
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TYR 144;ASP 245;LYS 274 | LYS 274(PLP binding) | |||
| 1qj3A02 |
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TYR 144;ASP 245;LYS 274 | LYS 274(PLP binding) | |||
| 1qj3B02 |
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TYR 144;ASP 245;LYS 274 | LYS 274(PLP binding) | |||
| 1qj5A02 |
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TYR 144;ASP 245;LYS 274 | LYS 274(PLP binding) | |||
| 1qj5B02 |
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TYR 144;ASP 245;LYS 274 | LYS 274(PLP binding) | |||
| 1s06A02 |
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TYR 144;ASP 245; | LLP 274(PLP binding) | mutant R253K | ||
| 1s06B02 |
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TYR 144;ASP 245; | LLP 274(PLP binding) | mutant R253K | ||
| 1s07A02 |
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TYR 144;ASP 245;LYS 274 | LYS 274(PLP binding) | mutant R253A | ||
| 1s07B02 |
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TYR 144;ASP 245;LYS 274 | LYS 274(PLP binding) | mutant R253A | ||
| 1s08A02 |
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TYR 144;ASP 245; | LLP 274(PLP binding) | mutant D147N | ||
| 1s08B02 |
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TYR 144;ASP 245; | LLP 274(PLP binding) | mutant D147N | ||
| 1s09A02 |
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;ASP 245; | LLP 274(PLP binding) | mutant Y144F | ||
| 1s09B02 |
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;ASP 245; | LLP 274(PLP binding) | mutant Y144F | ||
| 1s0aA02 |
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TYR 144;ASP 245; | LLP 274(PLP binding) | |||
| 1s0aB02 |
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TYR 144;ASP 245; | LLP 274(PLP binding) | |||
| 3bv0A02 |
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TYR 157;ASP 254;LYS 283 | LYS 283(PLP binding) | |||
| 3bv0B02 |
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TYR 157;ASP 254;LYS 283 | LYS 283(PLP binding) | |||
| References for Catalytic Mechanism | ||
|---|---|---|
| References | Sections | No. of steps in catalysis |
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[4]
|
Fig.2 | |
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[6]
|
Scheme 2 | |
| References | |
|---|---|
| [1] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 374976 |
| Journal | Methods Enzymol |
| Year | 1979 |
| Volume | 62 |
| Pages | 342-7 |
| Authors | Eisenberg MA, Stoner GL |
| Title | 7,8-Diaminopelargonic acid aminotransferase. |
| Related PDB | |
| Related UniProtKB | |
| [2] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 10089517 |
| Journal | Acta Crystallogr D Biol Crystallogr |
| Year | 1998 |
| Volume | 54 |
| Pages | 1397-8 |
| Authors | Kack H, Gibson KJ, Gatenby AA, Schneider G, Lindqvist Y |
| Title | Purification and preliminary X-ray crystallographic studies of recombinant 7,8-diaminopelargonic acid synthase from Escherichia coli. |
| Related PDB | |
| Related UniProtKB | |
| [3] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 9914259 |
| Journal | Curr Opin Struct Biol |
| Year | 1998 |
| Volume | 8 |
| Pages | 759-69 |
| Authors | Jansonius JN |
| Title |
Structure, |
| Related PDB | |
| Related UniProtKB | |
| [4] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) |
| Medline ID | 99384134 |
| PubMed ID | 10452893 |
| Journal | J Mol Biol |
| Year | 1999 |
| Volume | 291 |
| Pages | 857-76 |
| Authors | Kack H, Sandmark J, Gibson K, Schneider G, Lindqvist Y |
| Title | Crystal structure of diaminopelargonic acid synthase: evolutionary relationships between pyridoxal-5'-phosphate-dependent enzymes. |
| Related PDB | 1qj3 1qj5 |
| Related UniProtKB | P12995 |
| [5] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 10673430 |
| Journal | Structure Fold Des |
| Year | 2000 |
| Volume | 8 |
| Pages | R1-6 |
| Authors | Schneider G, Kack H, Lindqvist Y |
| Title | The manifold of vitamin B6 dependent enzymes. |
| Related PDB | |
| Related UniProtKB | |
| [6] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 12379100 |
| Journal | Biochemistry |
| Year | 2002 |
| Volume | 41 |
| Pages | 12582-9 |
| Authors | Eliot AC, Sandmark J, Schneider G, Kirsch JF |
| Title | The dual-specific active site of 7,8-diaminopelargonic acid synthase and the effect of the R391A mutation. |
| Related PDB | 1mgv |
| Related UniProtKB | |
| [7] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 12218056 |
| Journal | J Biol Chem |
| Year | 2002 |
| Volume | 277 |
| Pages | 43352-8 |
| Authors | Sandmark J, Mann S, Marquet A, Schneider G |
| Title | Structural basis for the inhibition of the biosynthesis of biotin by the antibiotic amiclenomycin. |
| Related PDB | 1mly 1mlz |
| Related UniProtKB | |
| [8] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 14599009 |
| Journal | Org Biomol Chem |
| Year | 2003 |
| Volume | 1 |
| Pages | 3498-9 |
| Authors | Breen RS, Campopiano DJ, Webster S, Brunton M, Watt R, Baxter RL |
| Title | The mechanism of 7,8-diaminopelargonate synthase; the role of S-adenosylmethionine as the amino donor. |
| Related PDB | |
| Related UniProtKB | |
| [9] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 14756557 |
| Journal | Biochemistry |
| Year | 2004 |
| Volume | 43 |
| Pages | 1213-22 |
| Authors | Sandmark J, Eliot AC, Famm K, Schneider G, Kirsch JF |
| Title | Conserved and nonconserved residues in the substrate binding site of 7,8-diaminopelargonic acid synthase from Escherichia coli are essential for catalysis. |
| Related PDB | 1s06 1s07 1s08 1s09 1s0a |
| Related UniProtKB | |
| Comments |
|---|
|
This enzyme belongs to the type-I PLP-dependent enzyme superfamily (or Aspartate aminotransferase family), According to the literature [4] & [6], (A) Formation of external aldimine (with amine group of the first substrate, (B) Isomerization (change in the position of double-bond). (C) Schiff-base deforming (by hydration), (D) Schiff-base forming (of PMP with carbonyl group of the second substrate, (E) Isomerization (change in the position of double-bond). (F) Formation of internal aldimine, |
| Created | Updated |
|---|---|
| 2004-03-18 | 2009-02-26 |