1YNU

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

• PDB DOI: https://doi.org/10.2210/pdb1YNU/pdb

• Classification: LYASE
• Organism(s): Malus domestica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-01-25 Released: 2005-05-03 
• Deposition Author(s): Capitani, G., Tschopp, M., Eliot, A.C., Kirsch, J.F., Grutter, M.G.

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Experimental Data Snapshot

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

Starting Model: experimental

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

• PubMed: 15848188 
• DOI: https://doi.org/10.1016/j.febslet.2005.03.048
• Primary Citation of 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.

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Organizational Affiliation: 

Biochemisches Institut der Universität Zürich, Switzerland. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PQS (software)

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-aminocyclopropane-1-carboxylate synthase	A	473	Malus domestica	Mutation(s): 0  Gene Names: ACS-1 EC: 4.4.1.14
UniProt
Find proteins for P37821 (Malus domestica) Explore P37821  Go to UniProtKB:  P37821

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PY4	E [auth A]	2-[O-PHOSPHONOPYRIDOXYL]-AMINO- BUTYRIC ACID C12 H19 N2 O7 P VRMPGTOTVVJQMU-SNVBAGLBSA-N
TRS	F [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
NI	B [auth A], C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

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 = 103.3	α = 90
b = 59.36	β = 124.2
c = 79.05	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-03 
Deposition Author(s): Capitani, G., Tschopp, M., Eliot, A.C., Kirsch, J.F., Grutter, M.G.

Revision History  

• 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