PDBsum entry 1j0c

Lyase

PDB id: 1j0c

Contents

Protein chains

341 a.a. *

Ligands

PLP ×4

Waters ×373

* Residue conservation analysis

PDB id:

1j0c

Name:

Lyase

Title:

Acc deaminase mutated to catalytic residue

Structure:

1-aminocyclopropane-1-carboxylate deaminase. Chain: a, b, c, d. Synonym: accd, acc deaminase. Engineered: yes. Mutation: yes

Source:

Williopsis saturnus. Organism_taxid: 4906. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.75Å R-factor: 0.224 R-free: 0.299

Authors:

T.Ose,A.Fujino,M.Yao,M.Honma,I.Tanaka

Key ref:

T.Ose et al. (2003). Reaction intermediate structures of 1-aminocyclopropane-1-carboxylate deaminase: insight into PLP-dependent cyclopropane ring-opening reaction. J Biol Chem, 278, 41069-41076. PubMed id: 12882962 DOI: 10.1074/jbc.M305865200

Date:

12-Nov-02 Release date: 12-May-03

Protein chains

Q7M523  (1A1D_CYBSA) -  1-aminocyclopropane-1-carboxylate deaminase from Cyberlindnera saturnus

Seq: 341 a.a.

Struc: 341 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.5.99.7 - 1-aminocyclopropane-1-carboxylate deaminase.
• Reaction: 1-aminocyclopropane-1-carboxylate + H2O = 2-oxobutanoate + NH4⁺
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

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

reference

DOI no: 10.1074/jbc.M305865200

J Biol Chem 278:41069-41076 (2003)

PubMed id: 12882962

Reaction intermediate structures of 1-aminocyclopropane-1-carboxylate deaminase: insight into PLP-dependent cyclopropane ring-opening reaction.

T.Ose, A.Fujino, M.Yao, N.Watanabe, M.Honma, I.Tanaka.

ABSTRACT

The pyridoxal 5'-phosphate-dependent enzymes have been evolved to catalyze diverse substrates and to cause the reaction to vary. 1-Aminocyclopropane-1-carboxylate deaminase catalyzes the cyclopropane ring-opening reaction followed by deamination specifically. Since it was discovered in 1978, the enzyme has been widely investigated from the mechanistic and physiological viewpoints because the substrate is a precursor of the plant hormone ethylene and the enzymatic reaction includes a cyclopropane ring-opening. We have previously reported the crystal structure of the native enzyme. Here we report the crystal structures of the two reaction intermediates created by the mutagenesis complexed with the substrate. The substrate was validated in the active site of two forms: 1). covalent-bonded external aldimine with the coenzyme in the K51T form and 2). the non-covalent interaction around the coenzyme in the Y295F form. The orientations of the substrate in both structures were quite different form each other. In concert with other site-specific mutation experiments, this experiment revealed the ingenious and unique strategies that are used to achieve the specific activity. The substrate incorporated into the active site is reactivated by a two-phenol charge relay system to lead to the formation of a Schiff base with the coenzyme. The catalytic Lys51 residue may play a novel role to abstract the methylene proton from the substrate in cooperation with other factors, the carboxylate group of the substrate and the electron-adjusting apparatuses of the coenzyme.

Selected figure(s)

Figure 5.
FIG. 5. A view around active site of which is concerned with incorporated ACC. The charge relay system from two tyrosine residues and the modeling position of Lys51 are shown.

Figure 7.
FIG. 7. The putative total mechanism catalyzed by yACCD.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 41069-41076) copyright 2003.

Figures were selected by an automated process.