1YNU | pdb_00001ynu

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 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.224 (DCC) 

Starting Model: experimental
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This is version 1.4 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: https://doi.org/10.1016/j.febslet.2005.03.048
  • Primary Citation Related Structures: 
    1YNU

  • 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. 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 Universität Zürich, Switzerland. capitani@bioc.unizh.ch

Macromolecule Content 

  • Total Structure Weight: 53.93 kDa 
  • Atom Count: 3,455 
  • Modeled Residue Count: 417 
  • Deposited Residue Count: 473 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
1-aminocyclopropane-1-carboxylate synthase473Malus domesticaMutation(s): 0 
Gene Names: ACS-1
EC: 4.4.1.14 (PDB Primary Data), 1.4 (UniProt)
UniProt
Find proteins for P37821 (Malus domestica)
Explore P37821 
Go to UniProtKB:  P37821
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37821
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.289 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.224 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.3α = 90
b = 59.36β = 124.2
c = 79.05γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-05-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary