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PDBsum entry 1mgv

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
1mgv
Jmol
Contents
Protein chains
428 a.a. *
Ligands
PLP ×2
IPA ×4
Metals
_NA ×2
Waters ×342
* Residue conservation analysis
PDB id:
1mgv
Name: Transferase
Title: Crystal structure of the r391a mutant of 7,8-diaminopelargon synthase
Structure: 7,8-diamino-pelargonic acid aminotransferase. Chain: a, b. Synonym: adenosylmethionine-8-amino-7-oxononanoate aminotra dapa aminotransferase. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: bioa. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.10Å     R-factor:   0.203     R-free:   0.233
Authors: A.C.Eliot,J.Sandmark,G.Schneider,J.F.Kirsch
Key ref:
A.C.Eliot et al. (2002). The dual-specific active site of 7,8-diaminopelargonic acid synthase and the effect of the R391A mutation. Biochemistry, 41, 12582-12589. PubMed id: 12379100 DOI: 10.1021/bi026339a
Date:
16-Aug-02     Release date:   27-Nov-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P12995  (BIOA_ECOLI) -  Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Seq:
Struc:
429 a.a.
428 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.2.6.1.62  - 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
S-adenosyl-L-methionine
+ 8-amino-7-oxononanoate
= S-adenosyl-4- methylthio-2-oxobutanoate
+ 7,8-diaminononanoate
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PLP) matches with 93.75% similarity
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  

 

 
    reference    
 
 
DOI no: 10.1021/bi026339a Biochemistry 41:12582-12589 (2002)
PubMed id: 12379100  
 
 
The dual-specific active site of 7,8-diaminopelargonic acid synthase and the effect of the R391A mutation.
A.C.Eliot, J.Sandmark, G.Schneider, J.F.Kirsch.
 
  ABSTRACT  
 
7,8-diaminopelargonic acid (DAPA) synthase (EC 2.6.1.62) is a pyridoxal phosphate (PLP)-dependent transaminase that catalyzes the transfer of the alpha-amino group from S-adenosyl-L-methionine (SAM) to 7-keto-8-aminopelargonic acid (KAPA) to form DAPA in the antepenultimate step in the biosynthesis of biotin. The wild-type enzyme has a steady-state kcat value of 0.013 s(-1), and the K(m) values for SAM and KAPA are 150 and <2 microM, respectively. The k(max) and apparent K(m) values for the half-reaction of the PLP form of the enzyme with SAM are 0.016 s(-1) and 300 microM, respectively, while those for the reaction with DAPA are 0.79 s(-1) and 1 microM. The R391A mutant enzyme exhibits near wild-type kinetic parameters in the reaction with SAM, while the apparent K(m) for DAPA is increased 180-fold. The 2.1 A crystal structure of the R391A mutant enzyme shows that the mutation does not significantly alter the structure. These results indicate that the conserved arginine residue is not required for binding the alpha-amino acid SAM, but it is important for recognition of DAPA.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
17680656 B.K.Cho, H.Y.Park, J.H.Seo, J.Kim, T.J.Kang, B.S.Lee, and B.G.Kim (2008).
Redesigning the substrate specificity of omega-aminotransferase for the kinetic resolution of aliphatic chiral amines.
  Biotechnol Bioeng, 99, 275-284.  
17898895 D.E.Scott, A.Ciulli, and C.Abell (2007).
Coenzyme biosynthesis: enzyme mechanism, structure and inhibition.
  Nat Prod Rep, 24, 1009-1026.  
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.  
15880481 S.W.Van Arsdell, J.B.Perkins, R.R.Yocum, L.Luan, C.L.Howitt, N.P.Chatterjee, and J.G.Pero (2005).
Removing a bottleneck in the Bacillus subtilis biotin pathway: bioA utilizes lysine rather than S-adenosylmethionine as the amino donor in the KAPA-to-DAPA reaction.
  Biotechnol Bioeng, 91, 75-83.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.