ISDA

Deposition Date 2022-07-01

Release Date 2024-01-24

Last Version Date 2024-11-13

Entry Detail

PDB ID:

7YCD

Keywords:

LYASE

Title:

HYDROXYNITRILE LYASE FROM THE MILLIPEDE, Oxidus gracilis bound with (R)-(+)-ALPHA-HYDROXYBENZENE-ACETONITRILE

Biological Source:

Source Organism:

Oxidus gracilis (Taxon ID: 291247)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.01 Å

R-Value Free:

0.23

R-Value Work:

0.20

Space Group:

P 63

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Hydroxynitrile lyase
Gene (Uniprot):OgraHNL
Chain IDs:A, B, C, D
Chain Length:184
Number of Molecules:4
Biological Source:Oxidus gracilis

UniProt ID:A0A2Z5XCT7

Ligand Molecules

MXN

SO4

Primary Citation

Structure-Based Site-Directed Mutagenesis of Hydroxynitrile Lyase from Cyanogenic Millipede, Oxidus gracilis for Hydrocyanation and Henry Reactions.

Chaikaew, S, Watanabe, Y, Zheng, D, Motojima, F, Yamaguchi, T, Asano, Y.Show

Chembiochem 25 e202400118 e202400118 (2024)

PMID: 38526556 DOI: 10.1002/cbic.202400118

Abstact

Hydroxynitrile lyase (HNL) from the cyanogenic millipede Oxidus gracillis (OgraHNL) is a crucial enzyme in the cyanogenesis pathway. Here, the crystal structures of OgraHNL complexed with sulfate, benzaldehyde (BA), (R)-mandelonitrile ((R)-Man), (R)-2-chloromandelonitrile ((R)-2-Cl-Man), and acetone cyanohydrin (ACN) were solved at 1.6, 1.7, 2.3, 2.1, and 2.0 Å resolutions, respectively. The structure of OgraHNL revealed that it belonged to the lipocalin superfamily. Based on this structure, positive variants were designed to further improve the catalytic activity and enantioselectivity of the enzyme for asymmetric hydrocyanation and Henry reactions.

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