PDBsum entry 1j0a

Lyase

PDB id: 1j0a

Contents

Protein chains

325 a.a. *

Ligands

SO4 ×3

PLP ×3

IPA

Waters ×94

* Residue conservation analysis

PDB id:

1j0a

Name:

Lyase

Title:

Crystal structure analysis of the acc deaminase homologue

Structure:

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

Source:

Pyrococcus horikoshii. Organism_taxid: 70601. Strain: ot3. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.50Å R-factor: 0.201 R-free: 0.270

Authors:

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

Key ref:

A.Fujino et al. (2004). Structural and enzymatic properties of 1-aminocyclopropane-1-carboxylate deaminase homologue from Pyrococcus horikoshii. J Mol Biol, 341, 999. PubMed id: 15328614 DOI: 10.1016/j.jmb.2004.06.062

Date:

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

Protein chains

O57809  (1A1D_PYRHO) -  Putative 1-aminocyclopropane-1-carboxylate deaminase from Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

Seq: 325 a.a.

Struc: 325 a.a.

Enzyme reactions

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

1-aminocyclopropane-1-carboxylate + H2O = 2-oxobutanoate (Bound ligand (Het Group name = IPA) matches with 57.14% similarity) + 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: 10.1016/j.jmb.2004.06.062

J Mol Biol 341:999 (2004)

PubMed id: 15328614

Structural and enzymatic properties of 1-aminocyclopropane-1-carboxylate deaminase homologue from Pyrococcus horikoshii.

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

ABSTRACT

1-Aminocyclopropane-l-carboxylate deaminase (ACCD) is a pyridoxal 5/-phosphate dependent enzyme that shows deaminase activity toward ACC, a precursor of plant hormone ethylene. ACCD from some soil bacteria has been reported to be able to break the cyclopropane ring of ACC to yield a-ketobutyrate and ammonia. We reported the crystal structure of ACCD from the yeast Hansenula saturnus in the absence/presence of substrate ACC, and proposed its ingenious reaction mechanisms. In order to study the enzyme further, we overexpressed the ACCD homologue protein (phAHP) from the fully decoded hyperthermophilic archearon, Pyrococcus horikoshii OT3. However, phAHP does not show ACCD activity at high temperature as well as at room temperature, though it has significant sequence similarity. Instead of ACCD activity, the GC-MS analysis and enzymatic method show that phAHP has deaminase activity toward L and D-serine. Here, we present the crystal structures of the native and ACC-complexed phAHP. The overall topology of the phAHP structure is very similar to that of ACCD; however, critical differences were observed around the active site. Here, the differences of enzymatic activity between phAHP and ACCD are discussed based on the structural differences of these two proteins. We suggest that the catalytic disagreement between these two enzymes comes from the difference of the residues near the pyridine ring of pyridoxal 5'-phosphate (PLP), not the difference of the catalytic residues themselves. We also propose a condition necessary in the primary sequence to have ACCD activity.

Selected figure(s)

Figure 5.
Figure 5. Ribbon representation of the two dimers. The crystallographic dimer (AA dimer) is shown in red, the non-crystallographic (NCS) dimer (BC dimer) in blue and green. The PLP is shown in yellow using the ball-and-stick model. The Figure is a view from the NCS 2-fold axis.

Figure 10.
Figure 10. Comparison of active sites between phAHP and hACCD. (a) Superimposition of ACC complexed phAHP (yellow) and ACC complexed hACCD (K51T, green). (b) Stereo view showing the active site of phAHP. The main chain is colored blue and the side-chains that form the pathway from the solvent region are colored gray. PLP is shown in yellow ball-and-stick model. The black arrow indicates the plausible substrate pathway. (c) Stereo view showing the active site of hACCD. The main-chain is colored green and the side-chains that form the cavity from the solvent region are colored gray. PLP is shown in yellow ball-and-stick model. The orientation is the same as that in (b).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 341, 999-0) copyright 2004.

Figures were selected by an automated process.