8OVH | pdb_00008ovh

Crystal structure of O-acetyl-L-homoserine sulfhydrolase from Saccharomyces cerevisiae in complex with Pyridoxal-5'-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 
    0.238 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.176 (DCC) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Enzymatic Synthesis of l-Methionine Analogues and Application in a Methyltransferase Catalysed Alkylation Cascade.

Mohr, M.K.F.Saleem-Batcha, R.Cornelissen, N.V.Andexer, J.N.

(2023) Chemistry 29: e202301503-e202301503

  • DOI: https://doi.org/10.1002/chem.202301503
  • Primary Citation Related Structures: 
    8OVH

  • PubMed Abstract: 

    Chemical modification of small molecules is a key step for the development of pharmaceuticals. S-adenosyl-l-methionine (SAM) analogues are used by methyltransferases (MTs) to transfer alkyl, allyl and benzyl moieties chemo-, stereo- and regioselectively onto nucleophilic substrates, enabling an enzymatic way for specific derivatisation of a wide range of molecules. l-Methionine analogues are required for the synthesis of SAM analogues. Most of these are not commercially available. In nature, O-acetyl-l-homoserine sulfhydrolases (OAHS) catalyse the synthesis of l-methionine from O-acetyl-l-homoserine or l-homocysteine, and methyl mercaptan. Here, we investigated the substrate scope of ScOAHS from Saccharomyces cerevisiae for the production of l-methionine analogues from l-homocysteine and organic thiols. The promiscuous enzyme was used to synthesise nine different l-methionine analogues with modifications on the thioether residue up to a conversion of 75 %. ScOAHS was combined with an established MT dependent three-enzyme alkylation cascade, allowing transfer of in total seven moieties onto two MT substrates. For ethylation, conversion was nearly doubled with the new four-enzyme cascade, indicating a beneficial effect of the in situ production of l-methionine analogues with ScOAHS.


  • Organizational Affiliation
    • Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104, Freiburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 205 kDa 
  • Atom Count: 12,954 
  • Modeled Residue Count: 1,600 
  • Deposited Residue Count: 1,856 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Homocysteine/cysteine synthase
A, B, C, D
464Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MET17MET15MET25YLR303WL8003.1
EC: 2.5.1.47 (PDB Primary Data), 2.5.1.49 (PDB Primary Data)
UniProt
Find proteins for P06106 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P06106 
Go to UniProtKB:  P06106
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06106
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP
(Subject of Investigation/LOI)

Query on PLP



Download:Ideal Coordinates CCD File
E [auth A],
F [auth B],
I [auth C],
K [auth D]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
G [auth B],
H [auth C],
J [auth C],
L [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free:  0.238 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.176 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.579α = 90
b = 118.218β = 92.908
c = 131.381γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European UnionERC project 716966

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2023-08-30
    Changes: Data collection, Database references
  • Version 1.2: 2024-09-18
    Changes: Database references
  • Version 1.3: 2024-09-25
    Changes: Database references