7YCT

HYDROXYNITRILE LYASE FROM THE MILLIPEDE, Oxidus gracilis complexed with (R)-2-Chloromandelonitrile

PDB DOI: https://doi.org/10.2210/pdb7YCT/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 ?
R-Value Free: 0.200
R-Value Work: 0.171

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
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?? 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 83.48 kDa
Atom Count: 5,672
Modelled Residue Count: 650
Deposited Residue Count: 736
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2Z5XCT7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IJ5 (Subject of Investigation/LOI) Query on IJ5 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D]	E [auth A] F [auth A] I [auth B] M [auth C] N [auth C] E [auth A], F [auth A], I [auth B], M [auth C], N [auth C], Q [auth D]	(2~{R})-2-(2-chlorophenyl)-2-oxidanyl-ethanenitrile C₈ H₆ Cl N O ZECLJEYAWRQVIB-QMMMGPOBSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D]
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D]	H [auth A], L [auth B], O [auth C], P [auth C], T [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth D]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain R [auth D] SDF format, chain S [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D]	G [auth A], J [auth B], K [auth B], R [auth D], S [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain R [auth D] Focus chain S [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 ?
R-Value Free: 0.200
R-Value Work: 0.171
Space Group: P 6₃

Unit Cell:

Length ( ? )	Angle ( ? )
a = 123.79	α = 90
b = 123.79	β = 90
c = 129.5	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-01-24

Deposition Author(s):

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 (Full details and data files)

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

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Help and Resources

7YCT

HYDROXYNITRILE LYASE FROM THE MILLIPEDE, Oxidus gracilis complexed with (R)-2-Chloromandelonitrile

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)