EzCatDB: D00109
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DB codeD00109
CATH domainDomain 13.90.1150.10 : Aspartate Aminotransferase, domain 1
Domain 23.40.640.10 : Aspartate Aminotransferase; domain 2Catalytic domain
E.C.2.6.1.62
MACiEM0249

CATH domainRelated DB codes (homologues)
3.40.640.10 : Aspartate Aminotransferase; domain 2D00085,D00092,D00101,D00102,D00103,D00104,D00107,D00108,D00255,D00257,D00258,D00265,D00269,D00515,M00031,D00279
3.90.1150.10 : Aspartate Aminotransferase, domain 1D00085,D00092,D00101,D00102,D00103,D00104,D00107,D00108,D00255,D00257,D00258,D00265,D00269,D00515,M00031,D00279

Enzyme Name
UniProtKBKEGG

P12995P0A4X6
Protein nameAdenosylmethionine-8-amino-7-oxononanoate aminotransferaseAdenosylmethionine-8-amino-7-oxononanoate aminotransferaseadenosylmethionine---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
SynonymsEC 2.6.1.62
7,8-diamino-pelargonic acid aminotransferase
DAPA AT
DAPA aminotransferase
7,8-diaminononanoate synthase
DANS
Diaminopelargonic acid synthase
EC 2.6.1.62
7,8-diamino-pelargonic acid aminotransferase
DAPA AT
DAPA aminotransferase
7,8-diaminononanoate synthase
DANS
Diaminopelargonic acid synthase
RefSeqNP_415295.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_489047.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
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)
PfamPF00202 (Aminotran_3)
[Graphical view]
PF00202 (Aminotran_3)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00780Biotin metabolism

UniProtKB:Accession NumberP12995P0A4X6
Entry nameBIOA_ECOLIBIOA_MYCTU
ActivityS-adenosyl-L-methionine + 8-amino-7- oxononanoate = S-adenosyl-4-methylthio-2-oxobutanoate + 7,8- diaminononanoate.S-adenosyl-L-methionine + 8-amino-7- oxononanoate = S-adenosyl-4-methylthio-2-oxobutanoate + 7,8- diaminononanoate.
SubunitHomodimer.Homodimer (By similarity).
Subcellular locationCytoplasm.
CofactorPyridoxal phosphate.Pyridoxal phosphate (By similarity).

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProductsintermediates
KEGG-idC00018C00019C01092C04425C01037I00037I00038I00039
C00647I00040I00041I00042
CompoundPyridoxal phosphateS-Adenosyl-L-methionine8-Amino-7-oxononanoateS-Adenosyl-4-methylthio-2-oxobutanoate7,8-DiaminononanoateExternal 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)
Typearomatic ring (with nitrogen atoms),phosphate group/phosphate ionamino acids,amine group,nucleoside,sulfonium ionamino acids,carbohydrate,fatty acidamide group,carbohydrate,carboxyl group,nucleoside,sulfonium ionamino acids,amine group,fatty acid







ChEBI18405
67040
15830
57532
8944
2247








PubChem1051
34755
25244029
173
440336
652








                     
1dtyA01UnboundUnboundUnboundUnboundUnbound     Unbound  
1dtyB01UnboundUnboundUnboundUnboundUnbound     Unbound  
1mgvA01UnboundUnboundUnboundUnboundUnbound     Unbound  
1mgvB01UnboundUnboundUnboundUnboundUnbound     Unbound  
1mlyA01UnboundUnboundUnboundUnboundUnbound     Unbound  
1mlyB01UnboundUnboundUnboundUnboundUnbound     Unbound  
1mlzA01UnboundUnboundUnboundUnboundUnbound     Unbound  
1mlzB01UnboundUnboundUnboundUnboundAnalogue:TZA     Unbound  
1qj3A01UnboundUnboundBound:KAPUnboundUnbound     Unbound  
1qj3B01UnboundUnboundBound:KAPUnboundUnbound     Unbound  
1qj5A01UnboundUnboundUnboundUnboundUnbound     Unbound  
1qj5B01UnboundUnboundUnboundUnboundUnbound     Unbound  
1s06A01UnboundUnboundUnboundUnboundUnbound     Unbound  
1s06B01UnboundUnboundUnboundUnboundUnbound     Unbound  
1s07A01UnboundUnboundUnboundUnboundUnbound     Unbound  
1s07B01UnboundUnboundUnboundUnboundUnbound     Unbound  
1s08A01UnboundUnboundUnboundUnboundUnbound     Unbound  
1s08B01UnboundUnboundUnboundUnboundUnbound     Unbound  
1s09A01UnboundUnboundUnboundUnboundUnbound     Unbound  
1s09B01UnboundUnboundUnboundUnboundUnbound     Unbound  
1s0aA01UnboundUnboundUnboundUnboundUnbound     Unbound  
1s0aB01UnboundUnboundUnboundUnboundUnbound     Unbound  
3bv0A01UnboundUnboundUnboundUnboundUnbound     Unbound  
3bv0B01UnboundUnboundUnboundUnboundUnbound     Unbound  
1dtyA02Bound:PLPUnboundUnboundUnboundUnbound     Unbound  
1dtyB02Bound:PLPUnboundUnboundUnboundUnbound     Unbound  
1mgvA02Bound:PLPUnboundUnboundUnboundUnbound     Unbound  
1mgvB02Bound:PLPUnboundUnboundUnboundUnbound     Unbound  
1mlyA02Bound:PLPUnboundUnboundUnboundUnbound     Intermediate-analogue:PLP-ACZ  
1mlyB02Bound:PLPUnboundUnboundUnboundUnbound     Intermediate-analogue:PLP-ACZ  
1mlzA02Bound:PLPUnboundUnboundUnboundUnbound     Intermediate-analogue:PLP-TZA  
1mlzB02Bound:PLPUnboundUnboundUnboundUnbound     Unbound  
1qj3A02Bound:PLPUnboundUnboundUnboundUnbound     Unbound  
1qj3B02Bound:PLPUnboundUnboundUnboundUnbound     Unbound  
1qj5A02Bound:PLPUnboundUnboundUnboundUnbound     Unbound  
1qj5B02Bound:PLPUnboundUnboundUnboundUnbound     Unbound  
1s06A02Bound:LLPUnboundUnboundUnboundUnbound     Unbound  
1s06B02Bound:LLPUnboundUnboundUnboundUnbound     Unbound  
1s07A02Bound:PLPUnboundUnboundUnboundUnbound     Unbound  
1s07B02Bound:PLPUnboundUnboundUnboundUnbound     Unbound  
1s08A02Bound:LLPUnboundUnboundUnboundUnbound     Unbound  
1s08B02Bound:LLPUnboundUnboundUnboundUnbound     Unbound  
1s09A02Bound:LLPUnboundUnboundUnboundUnbound     Unbound  
1s09B02Bound:LLPUnboundUnboundUnboundUnbound     Unbound  
1s0aA02Bound:LLPUnboundUnboundUnboundUnbound     Unbound  
1s0aB02Bound:LLPUnboundUnboundUnboundUnbound     Unbound  
3bv0A02Bound:PLPUnboundUnboundUnboundUnbound     Unbound  
3bv0B02Bound:PLPUnboundUnboundUnboundUnbound     Unbound  

Active-site residues
resource
PDB;1qj3, 1qj5
pdbCatalytic residuesCofactor-binding residuesModified residuescomment
            
1dtyA01 
 
 
 
1dtyB01 
 
 
 
1mgvA01 
 
 
mutant R391A
1mgvB01 
 
 
mutant R391A
1mlyA01 
 
 
 
1mlyB01 
 
 
 
1mlzA01 
 
 
 
1mlzB01 
 
 
 
1qj3A01 
 
 
 
1qj3B01 
 
 
 
1qj5A01 
 
 
 
1qj5B01 
 
 
 
1s06A01 
 
 
 
1s06B01 
 
 
 
1s07A01 
 
 
 
1s07B01 
 
 
 
1s08A01 
 
 
 
1s08B01 
 
 
 
1s09A01 
 
 
 
1s09B01 
 
 
 
1s0aA01 
 
 
mutant Y17F
1s0aB01 
 
 
mutant Y17F
3bv0A01 
 
 
 
3bv0B01 
 
 
 
1dtyA02TYR 144;ASP 245;LYS 274
LYS 274(PLP binding)
                    
 
1dtyB02TYR 144;ASP 245;LYS 274
LYS 274(PLP binding)
                    
 
1mgvA02TYR 144;ASP 245;LYS 274
LYS 274(PLP binding)
                    
 
1mgvB02TYR 144;ASP 245;LYS 274
LYS 274(PLP binding)
                    
 
1mlyA02TYR 144;ASP 245;LYS 274
LYS 274(PLP binding)
                    
 
1mlyB02TYR 144;ASP 245;LYS 274
LYS 274(PLP binding)
                    
 
1mlzA02TYR 144;ASP 245;LYS 274
LYS 274(PLP binding)
                    
 
1mlzB02TYR 144;ASP 245;LYS 274
LYS 274(PLP binding)
                    
 
1qj3A02TYR 144;ASP 245;LYS 274
LYS 274(PLP binding)
                    
 
1qj3B02TYR 144;ASP 245;LYS 274
LYS 274(PLP binding)
                    
 
1qj5A02TYR 144;ASP 245;LYS 274
LYS 274(PLP binding)
                    
 
1qj5B02TYR 144;ASP 245;LYS 274
LYS 274(PLP binding)
                    
 
1s06A02TYR 144;ASP 245;       
                    
LLP 274(PLP binding)
mutant R253K
1s06B02TYR 144;ASP 245;       
                    
LLP 274(PLP binding)
mutant R253K
1s07A02TYR 144;ASP 245;LYS 274
LYS 274(PLP binding)
                    
mutant R253A
1s07B02TYR 144;ASP 245;LYS 274
LYS 274(PLP binding)
                    
mutant R253A
1s08A02TYR 144;ASP 245;       
                    
LLP 274(PLP binding)
mutant D147N
1s08B02TYR 144;ASP 245;       
                    
LLP 274(PLP binding)
mutant D147N
1s09A02       ;ASP 245;       
                    
LLP 274(PLP binding)
mutant Y144F
1s09B02       ;ASP 245;       
                    
LLP 274(PLP binding)
mutant Y144F
1s0aA02TYR 144;ASP 245;       
                    
LLP 274(PLP binding)
 
1s0aB02TYR 144;ASP 245;       
                    
LLP 274(PLP binding)
 
3bv0A02TYR 157;ASP 254;LYS 283
LYS 283(PLP binding)
                    
 
3bv0B02TYR 157;ASP 254;LYS 283
LYS 283(PLP binding)
                    
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]Fig.2
[6]Scheme 2

references
[1]
PubMed ID374976
JournalMethods Enzymol
Year1979
Volume62
Pages342-7
AuthorsEisenberg MA, Stoner GL
Title7,8-Diaminopelargonic acid aminotransferase.
[2]
PubMed ID10089517
JournalActa Crystallogr D Biol Crystallogr
Year1998
Volume54
Pages1397-8
AuthorsKack H, Gibson KJ, Gatenby AA, Schneider G, Lindqvist Y
TitlePurification and preliminary X-ray crystallographic studies of recombinant 7,8-diaminopelargonic acid synthase from Escherichia coli.
[3]
PubMed ID9914259
JournalCurr Opin Struct Biol
Year1998
Volume8
Pages759-69
AuthorsJansonius JN
TitleStructure, evolution and action of vitamin B6-dependent enzymes.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS)
Medline ID99384134
PubMed ID10452893
JournalJ Mol Biol
Year1999
Volume291
Pages857-76
AuthorsKack H, Sandmark J, Gibson K, Schneider G, Lindqvist Y
TitleCrystal structure of diaminopelargonic acid synthase: evolutionary relationships between pyridoxal-5'-phosphate-dependent enzymes.
Related PDB1qj3,1qj5
Related UniProtKBP12995
[5]
PubMed ID10673430
JournalStructure Fold Des
Year2000
Volume8
PagesR1-6
AuthorsSchneider G, Kack H, Lindqvist Y
TitleThe manifold of vitamin B6 dependent enzymes.
[6]
PubMed ID12379100
JournalBiochemistry
Year2002
Volume41
Pages12582-9
AuthorsEliot AC, Sandmark J, Schneider G, Kirsch JF
TitleThe dual-specific active site of 7,8-diaminopelargonic acid synthase and the effect of the R391A mutation.
Related PDB1mgv
[7]
PubMed ID12218056
JournalJ Biol Chem
Year2002
Volume277
Pages43352-8
AuthorsSandmark J, Mann S, Marquet A, Schneider G
TitleStructural basis for the inhibition of the biosynthesis of biotin by the antibiotic amiclenomycin.
Related PDB1mly,1mlz
[8]
PubMed ID14599009
JournalOrg Biomol Chem
Year2003
Volume1
Pages3498-9
AuthorsBreen RS, Campopiano DJ, Webster S, Brunton M, Watt R, Baxter RL
TitleThe mechanism of 7,8-diaminopelargonate synthase; the role of S-adenosylmethionine as the amino donor.
[9]
PubMed ID14756557
JournalBiochemistry
Year2004
Volume43
Pages1213-22
AuthorsSandmark J, Eliot AC, Famm K, Schneider G, Kirsch JF
TitleConserved and nonconserved residues in the substrate binding site of 7,8-diaminopelargonic acid synthase from Escherichia coli are essential for catalysis.
Related PDB1s06,1s07,1s08,1s09,1s0a

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.

createdupdated
2004-03-182009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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