PDBsum entry 1ynu

Go to PDB code: 
protein ligands metals links
Lyase PDB id
Protein chain
417 a.a. *
_NI ×2
Waters ×122
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Crystal structure of apple acc synthase in complex with l-vi
Structure: 1-aminocyclopropane-1-carboxylate synthase. Chain: a. Synonym: acc synthase, s-adenosyl-l-methionine methylthioad lyase. Engineered: yes
Source: Malus x domestica. Organism_taxid: 3750. Strain: golden delicious. Tissue: fruit cortical tissue. Gene: acs-1. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.25Å     R-factor:   0.234     R-free:   0.289
Authors: G.Capitani,M.Tschopp,A.C.Eliot,J.F.Kirsch,M.G.Grutter
Key ref:
G.Capitani et al. (2005). Structure of ACC synthase inactivated by the mechanism-based inhibitor L-vinylglycine. FEBS Lett, 579, 2458-2462. PubMed id: 15848188 DOI: 10.1016/j.febslet.2005.03.048
25-Jan-05     Release date:   03-May-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P37821  (1A1C_MALDO) -  1-aminocyclopropane-1-carboxylate synthase
473 a.a.
417 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 1-aminocyclopropane-1-carboxylate synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Ethylene Biosynthesis
      Reaction: S-adenosyl-L-methionine = 1-aminocyclopropane-1-carboxylate + methylthioadenosine
Bound ligand (Het Group name = TRS)
matches with 66.67% similarity
+ methylthioadenosine
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PY4) matches with 65.22% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     biosynthetic process   4 terms 
  Biochemical function     catalytic activity     5 terms  


DOI no: 10.1016/j.febslet.2005.03.048 FEBS Lett 579:2458-2462 (2005)
PubMed id: 15848188  
Structure of ACC synthase inactivated by the mechanism-based inhibitor L-vinylglycine.
G.Capitani, M.Tschopp, A.C.Eliot, J.F.Kirsch, M.G.Grütter.
L-Vinylglycine (L-VG) is both a substrate for and a mechanism-based inhibitor of 1-aminocyclopropane-1-carboxylate (ACC) synthase. The ratio of the rate constants for catalytic conversion to alpha-ketobutyrate and ammonia to inactivation is 500/1. The crystal structure of the covalent adduct of the inactivated enzyme was determined at 2.25 Angstroms resolution. The active site contains an external aldimine of the adduct of L-VG with the pyridoxal 5'-phosphate cofactor. The side chain gamma-carbon of L-VG is covalently bound to the epsilon-amino group of Lys273. This species corresponds to one of the two alternatives proposed by Feng and Kirsch [Feng, L. and Kirsch, J.F. (2000) L-Vinylglycine is an alternative substrate as well as a mechanism-based inhibitor of 1-aminocyclopropane-1-carboxylate synthase. Biochemistry 39, and presumably results from Michael addition to a vinylglycine ketimine intermediate.
  Selected figure(s)  
Figure 1.
Fig. 1. Schematic summary of the reactions of ACC synthase with the inhibitors AVG and AMA. Prepared with ChemDraw.
Figure 2.
Fig. 2. Schematic summary of the ACC synthase-catalyzed reactions with the natural substrate, SAM and with l-VG. Prepared with ChemDraw.
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2005, 579, 2458-2462) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20108010 C.H.Küchenthal, J.Migenda, M.Polednia, and W.Maison (2010).
An improved protocol for the preparation of (S)-vinylglycine from (S)-methionine.
  Amino Acids, 39, 443-448.  
  19727327 D.B.Berkowitz, K.R.Karukurichi, la Salud-Bea, D.L.Nelson, and C.D.McCune (2008).
Use of Fluorinated Functionality in Enzyme Inhibitor Development: Mechanistic and Analytical Advantages.
  J Fluor Chem, 129, 731-742.  
16494487 D.B.Berkowitz, B.Wu, and H.Li (2006).
A formal [3,3]-sigmatropic rearrangement route to quaternary alpha-vinyl amino acids: use of allylic N-PMP trifluoroacetimidates.
  Org Lett, 8, 971-974.  
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.