7YCD

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

• PDB DOI: https://doi.org/10.2210/pdb7YCD/pdb

• Classification: LYASE
• Organism(s): Oxidus gracilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-07-01 Released: 2024-01-24 
• Deposition Author(s): Chaikaew, S., Watanabe, Y., Zheng, D., Motojima, F., Asano, Y.
• Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.233 
• R-Value Work: 0.202 

Literature

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.

(2024) Chembiochem 25: e202400118-e202400118

• PubMed: 38526556 
• DOI: https://doi.org/10.1002/cbic.202400118
• Primary Citation of Related Structures:  
  7YAX, 7YCB, 7YCD, 7YCF, 7YCT


• PubMed Abstract: 
  

  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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Organizational Affiliation: 

Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

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

Macromolecule Content

• Total Structure Weight: 83.18 kDa 
• Atom Count: 5,547 
• Modelled Residue Count: 651 
• Deposited Residue Count: 736 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxynitrile lyase	A, B, C, D	184	Oxidus gracilis	Mutation(s): 0  Gene Names: OgraHNL
UniProt
Find proteins for A0A2Z5XCT7 (Oxidus gracilis) Explore A0A2Z5XCT7  Go to UniProtKB:  A0A2Z5XCT7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MXN (Subject of Investigation/LOI)	E [auth A], F [auth A], I [auth B], J [auth B], M [auth C], N [auth C], P [auth D], Q [auth D]	(2R)-hydroxy(phenyl)ethanenitrile C8 H7 N O NNICRUQPODTGRU-QMMMGPOBSA-N
SO4 (Subject of Investigation/LOI)	G [auth A], H [auth A], K [auth B], L [auth B], O [auth C], R [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.233 
• R-Value Work: 0.202 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.43	α = 90
b = 123.43	β = 90
c = 129.87	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-24 
Deposition Author(s): Chaikaew, S., Watanabe, Y., Zheng, D., Motojima, F., Asano, Y.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJER1102
Japan Society for the Promotion of Science (JSPS)	Japan	17H06169
Japan Society for the Promotion of Science (JSPS)	Japan	22H00361

Revision History  

• Version 1.0: 2024-01-24
  Type: Initial release
  
• Version 1.1: 2024-06-19
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Structure summary