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)
3.90.1150.10 : Aspartate Aminotransferase, domain 1 D00085 D00092 D00101 D00102 D00103 D00104 D00107 D00108 D00255 D00257 D00258 D00265 D00269 D00515 M00031 D00279
3.40.640.10 : Aspartate Aminotransferase; domain 2 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
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).
P12995 BIOA_ECOLI S-adenosyl-L-methionine + 8-amino-7- oxononanoate = S-adenosyl-4-methylthio-2-oxobutanoate + 7,8- diaminononanoate. Homodimer. Cytoplasm. Pyridoxal phosphate.

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)
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
67040
15830
57532
8944
2247
PubChem 1051
34755
173
25244029
440336
652
1dtyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1dtyB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1mgvA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1mgvB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1mlyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1mlyB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1mlzA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1mlzB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Analogue:TZA Unbound
1qj3A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:KAP Unbound Unbound Unbound
1qj3B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:KAP Unbound Unbound Unbound
1qj5A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1qj5B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1s06A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1s06B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1s07A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1s07B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1s08A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1s08B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1s09A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1s09B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1s0aA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1s0aB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
3bv0A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
3bv0B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1dtyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound
1dtyB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound
1mgvA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound
1mgvB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound
1mlyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Intermediate-analogue:PLP-ACZ
1mlyB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Intermediate-analogue:PLP-ACZ
1mlzA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Intermediate-analogue:PLP-TZA
1mlzB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound
1qj3A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound
1qj3B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound
1qj5A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound
1qj5B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound
1s06A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:LLP Unbound Unbound Unbound Unbound Unbound
1s06B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:LLP Unbound Unbound Unbound Unbound Unbound
1s07A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound
1s07B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound
1s08A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:LLP Unbound Unbound Unbound Unbound Unbound
1s08B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:LLP Unbound Unbound Unbound Unbound Unbound
1s09A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:LLP Unbound Unbound Unbound Unbound Unbound
1s09B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:LLP Unbound Unbound Unbound Unbound Unbound
1s0aA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:LLP Unbound Unbound Unbound Unbound Unbound
1s0aB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:LLP Unbound Unbound Unbound Unbound Unbound
3bv0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound
3bv0B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
PDB;1qj3, 1qj5

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1dtyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dtyB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1mgvA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain mutant R391A
1mgvB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain mutant R391A
1mlyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1mlyB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1mlzA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1mlzB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qj3A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qj3B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qj5A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qj5B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1s06A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1s06B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1s07A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1s07B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1s08A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1s08B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1s09A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1s09B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1s0aA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain mutant Y17F
1s0aB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain mutant Y17F
3bv0A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3bv0B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dtyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 144;ASP 245;LYS 274 LYS 274(PLP binding)
1dtyB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 144;ASP 245;LYS 274 LYS 274(PLP binding)
1mgvA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 144;ASP 245;LYS 274 LYS 274(PLP binding)
1mgvB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 144;ASP 245;LYS 274 LYS 274(PLP binding)
1mlyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 144;ASP 245;LYS 274 LYS 274(PLP binding)
1mlyB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 144;ASP 245;LYS 274 LYS 274(PLP binding)
1mlzA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 144;ASP 245;LYS 274 LYS 274(PLP binding)
1mlzB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 144;ASP 245;LYS 274 LYS 274(PLP binding)
1qj3A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 144;ASP 245;LYS 274 LYS 274(PLP binding)
1qj3B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 144;ASP 245;LYS 274 LYS 274(PLP binding)
1qj5A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 144;ASP 245;LYS 274 LYS 274(PLP binding)
1qj5B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 144;ASP 245;LYS 274 LYS 274(PLP binding)
1s06A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 144;ASP 245; LLP 274(PLP binding) mutant R253K
1s06B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 144;ASP 245; LLP 274(PLP binding) mutant R253K
1s07A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 144;ASP 245;LYS 274 LYS 274(PLP binding) mutant R253A
1s07B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 144;ASP 245;LYS 274 LYS 274(PLP binding) mutant R253A
1s08A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 144;ASP 245; LLP 274(PLP binding) mutant D147N
1s08B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 144;ASP 245; LLP 274(PLP binding) mutant D147N
1s09A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 245; LLP 274(PLP binding) mutant Y144F
1s09B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 245; LLP 274(PLP binding) mutant Y144F
1s0aA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 144;ASP 245; LLP 274(PLP binding)
1s0aB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 144;ASP 245; LLP 274(PLP binding)
3bv0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 157;ASP 254;LYS 283 LYS 283(PLP binding)
3bv0B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 157;ASP 254;LYS 283 LYS 283(PLP binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
Fig.2
[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, evolution and action of vitamin B6-dependent enzymes.
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 [3] & [5].
According to the literature [4] & [6], this enzyme catalyzes the following reactions:
(A) Formation of external aldimine (with amine group of the first substrate, SAM).
(B) Isomerization (change in the position of double-bond).
(C) Schiff-base deforming (by hydration), releasing the first product, and PMP.
(D) Schiff-base forming (of PMP with carbonyl group of the second substrate, KAPA; by dehydration).
(E) Isomerization (change in the position of double-bond).
(F) Formation of internal aldimine, releasing the second product.

Created Updated
2004-03-18 2009-02-26