5Y02

C-terminal peptide depleted mutant of hydroxynitrile lyase from Passiflora edulis (PeHNL) bound with (R)-mandelonitrile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

The crystal structure and catalytic mechanism of hydroxynitrile lyase from passion fruit, Passiflora edulis

Motojima, F.Nuylert, A.Asano, Y.

(2018) FEBS J 285: 313-324

  • DOI: https://doi.org/10.1111/febs.14339
  • Primary Citation of Related Structures:  
    5XZQ, 5XZT, 5Y02

  • PubMed Abstract: 

    Hydroxynitrile lyases (HNLs) are enzymes used in the synthesis of chiral cyanohydrins. The HNL from Passiflora edulis (PeHNL) is R-selective and is the smallest HNL known to date. The crystal structures of PeHNL and its C-terminal peptide depleted derivative were determined by molecular replacement method using the template structure of a heat stable protein, SP1, from Populus tremula at 2.8 and 1.8 Å resolution, respectively. PeHNL belongs to dimeric α+β barrel superfamily consisting of a central β-barrel in the middle of a dimer. The structure of PeHNL complexed with (R)-mandelonitrile ((R)-MAN) was also determined. The hydroxyl group of (R)-MAN forms hydrogen bonds with His8 and Tyr30 in the active site, whereas the nitrile group is oriented toward the carboxyl group of Glu54, unlike other HNLs, where it interacts with basic residues typically. The results of mutational analysis indicate that the catalytic dyad of His8-Asn101 is critical for the enzymatic reaction. The length of the hydrogen bond between His-Nδ1 and Asn101-Oδ1 is short in the PeHNL-(R)-MAN complex (~ 2.6 Å), which would increase the basicity of His8 to abstract a proton from the hydroxyl group of (R)-MAN. The cyanide ion released from the nitrile group abstracts a proton from the protonated His8 to generate a hydrogen cyanide. Thus, the His8 in the active site of PeHNL acts both as a general acid and a general base in the reaction. EC 4.1.2.10 DATABASE: Structural data are available in PDB database under the accession numbers 5XZQ, 5XZT, and 5Y02.


  • Organizational Affiliation

    Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hydroxynitrile lyase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
107Passiflora edulisMutation(s): 0 
Gene Names: PeHNL
UniProt
Find proteins for A0A1L7NZN4 (Passiflora edulis)
Explore A0A1L7NZN4 
Go to UniProtKB:  A0A1L7NZN4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1L7NZN4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MXN (Subject of Investigation/LOI)
Query on MXN

Download Ideal Coordinates CCD File 
M [auth A],
O [auth C],
S [auth F],
Y [auth K]
(2R)-hydroxy(phenyl)ethanenitrile
C8 H7 N O
NNICRUQPODTGRU-QMMMGPOBSA-N
HEZ
Query on HEZ

Download Ideal Coordinates CCD File 
AA [auth L]
N [auth B]
P [auth C]
Q [auth E]
R [auth E]
AA [auth L],
N [auth B],
P [auth C],
Q [auth E],
R [auth E],
T [auth G],
U [auth H],
W [auth I],
X [auth J]
HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
HBX
Query on HBX

Download Ideal Coordinates CCD File 
V [auth I],
Z [auth L]
benzaldehyde
C7 H6 O
HUMNYLRZRPPJDN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.811α = 90
b = 88.494β = 105.07
c = 104.454γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSTJapanJPMJER1102

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2017-11-29
    Changes: Database references
  • Version 1.2: 2017-12-13
    Changes: Database references
  • Version 1.3: 2018-02-07
    Changes: Database references
  • Version 1.4: 2018-05-16
    Changes: Data collection
  • Version 1.5: 2023-11-22
    Changes: Data collection, Database references, Refinement description