PDBsum entry 1ynu

Lyase

PDB id: 1ynu

Contents

Protein chain

417 a.a. *

Ligands

PY4

TRS

Metals

_NI ×2

__K

Waters ×122

* Residue conservation analysis

PDB id:

1ynu

Name:

Lyase

Title:

Crystal structure of apple acc synthase in complex with l-vinylglycine

Structure:

1-aminocyclopropane-1-carboxylate synthase. Chain: a. Synonym: acc synthase, s-adenosyl-l-methionine methylthioadenosine- 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.

Resolution:

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

Date:

25-Jan-05 Release date: 03-May-05

Protein chain

P37821  (1A1C_MALDO) -  1-aminocyclopropane-1-carboxylate synthase from Malus domestica

Seq: 473 a.a.

Struc: 417 a.a.

Enzyme reactions

• Enzyme class 1: E.C.1.4.-.-
• Enzyme class 2: E.C.4.4.1.14 - 1-aminocyclopropane-1-carboxylate synthase.

Pathway:

• Reaction: S-adenosyl-L-methionine = 1-aminocyclopropane-1-carboxylate + S-methyl- 5'-thioadenosine + H⁺
• Cofactor: Pyridoxal 5'-phosphate

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

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.

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, 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.