PDBsum entry 1s08

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protein metals Protein-protein interface(s) links
Transferase PDB id
Protein chains
411 a.a. *
_NA ×2
Waters ×402
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of the d147n mutant of 7,8- diaminopelargonic acid synthase
Structure: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase. Chain: a, b. Synonym: 7,8-diamino-pelargonic acid aminotransferase, dapa aminotransferase. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: bioa, b0774. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
2.10Å     R-factor:   0.203     R-free:   0.227
Authors: J.Sandmark,A.C.Eliot,K.Famm,G.Schneider,J.F.Kirsch
Key ref:
J.Sandmark et al. (2004). Conserved and nonconserved residues in the substrate binding site of 7,8-diaminopelargonic acid synthase from Escherichia coli are essential for catalysis. Biochemistry, 43, 1213-1222. PubMed id: 14756557 DOI: 10.1021/bi0358059
30-Dec-03     Release date:   23-Mar-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P12995  (BIOA_ECOLI) -  Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
429 a.a.
411 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Adenosylmethionine--8-amino-7-oxononanoate transaminase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: S-adenosyl-L-methionine + 8-amino-7-oxononanoate = S-adenosyl-4- methylthio-2-oxobutanoate + 7,8-diaminononanoate
+ 8-amino-7-oxononanoate
= S-adenosyl-4- methylthio-2-oxobutanoate
+ 7,8-diaminononanoate
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     biotin biosynthetic process   1 term 
  Biochemical function     catalytic activity     5 terms  


DOI no: 10.1021/bi0358059 Biochemistry 43:1213-1222 (2004)
PubMed id: 14756557  
Conserved and nonconserved residues in the substrate binding site of 7,8-diaminopelargonic acid synthase from Escherichia coli are essential for catalysis.
J.Sandmark, A.C.Eliot, K.Famm, G.Schneider, J.F.Kirsch.
The vitamin B(6)-dependent enzyme 7,8-diaminopelargonic acid (DAPA) synthase catalyzes the antepenultimate step in the synthesis of biotin, the transfer of the alpha-amino group of S-adenosyl-l-methionine (SAM) to 7-keto-8-aminopelargonic acid (KAPA) to form DAPA. The Y17F, Y144F, and D147N mutations in the active site were constructed independently. The k(max)/K(m)(app) values for the half-reaction with DAPA of the Y17F and Y144F mutants are reduced by 1300- and 2900-fold, respectively, compared to the WT enzyme. Crystallographic analyses of these mutants do not show significant changes in the structure of the active site. The kinetic deficiencies, together with a structural model of the enzyme-PLP/DAPA Michaelis complex, point to a role of these two residues in recognition of the DAPA/KAPA substrates and in catalysis. The k(max)/K(m)(app) values for the half-reaction with SAM are similar to that of the WT enzyme, showing that the two tyrosine residues are not involved in this half-reaction. Mutations of the conserved Arg253 uniquely affect the SAM kinetics, thus establishing this position as part of the SAM binding site. The D147N mutant is catalytically inactive in both half-reactions. The structure of this mutant exhibits significant changes in the active site, indicating that this residue plays an important structural role. Of the four residues examined, only Tyr144 and Arg253 are strictly conserved in the available amino acid sequences of DAPA synthases. This enzyme thus provides an illustrative example that active site residues essential for catalysis are not necessarily conserved, i.e., that during evolution alternative solutions for efficient catalysis by the same enzyme arose. Decarboxylated SAM [S-adenosyl-(5')-3-methylthiopropylamine] reacts nearly as well as SAM and cannot be eliminated as a putative in vivo amino donor.

Literature references that cite this PDB file's key reference

  PubMed id Reference
17898895 D.E.Scott, A.Ciulli, and C.Abell (2007).
Coenzyme biosynthesis: enzyme mechanism, structure and inhibition.
  Nat Prod Rep, 24, 1009-1026.  
17931411 H.Sandmark (2007).
Work and family: associations with long-term sick-listing in Swedish women - a case-control study.
  BMC Public Health, 7, 287.  
16676358 M.Seki (2006).
Biological significance and development of practical synthesis of biotin.
  Med Res Rev, 26, 434-482.  
16984394 S.Mann, and O.Ploux (2006).
7,8-Diaminoperlargonic acid aminotransferase from Mycobacterium tuberculosis, a potential therapeutic target. Characterization and inhibition studies.
  FEBS J, 273, 4778-4789.  
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