1YNU

Crystal structure of apple ACC synthase in complex with L-vinylglycine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of ACC synthase inactivated by the mechanism-based inhibitor L-vinylglycine.

Capitani, G.Tschopp, M.Eliot, A.C.Kirsch, J.F.Grutter, M.G.

(2005) Febs Lett. 579: 2458-2462

  • DOI: 10.1016/j.febslet.2005.03.048

  • PubMed Abstract: 
  • 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. Th ...

    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, 2436-2444] and presumably results from Michael addition to a vinylglycine ketimine intermediate.


    Organizational Affiliation

    Biochemisches Institut der Universit├Ąt Z├╝rich, Switzerland. capitani@bioc.unizh.ch




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1-aminocyclopropane-1-carboxylate synthase
A
473Malus domesticaMutation(s): 0 
Gene Names: ACS-1
EC: 1.4.-.-, 4.4.1.14
Find proteins for P37821 (Malus domestica)
Go to UniProtKB:  P37821
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PY4
Query on PY4

Download SDF File 
Download CCD File 
A
2-[O-PHOSPHONOPYRIDOXYL]-AMINO- BUTYRIC ACID
VITAMIN B6 COMPLEXED WITH 2-AMINO-BUTYRIC ACID
C12 H19 N2 O7 P
VRMPGTOTVVJQMU-SNVBAGLBSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.234 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 103.300α = 90.00
b = 59.360β = 124.20
c = 79.050γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance