6QJZ

Identificationand Characterization of an Oxalylfrom Grass pea (Lathyrus sativusCoA-Synthetase L.)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The identification and characterization of an oxalyl-CoA synthetase from grass pea ( Lathyrus sativus L.).

Goldsmith, M.Barad, S.Peleg, Y.Albeck, S.Dym, O.Brandis, A.Mehlman, T.Reich, Z.

(2022) RSC Chem Biol 3: 320-333

  • DOI: https://doi.org/10.1039/d1cb00202c
  • Primary Citation of Related Structures:  
    6QJZ

  • PubMed Abstract: 

    Oxalic acid is a small metabolite found in many plants. It serves as protection from herbivores, a chelator of metal ions, a regulator of calcium levels, and additional tasks. However, it is also a strong di-carboxylic acid that can compromise plant viability by reducing cellular pH. Several metabolic pathways have evolved to control oxalate levels in plants by enzymatic degradation. Among them is the pathway that utilizes oxalyl-CoA synthetase (OCS, EC 6.2.1.8) and ATP to convert oxalate to oxalyl-CoA. Oxalyl-CoA can then be degraded to CO 2 or utilized as a precursor for the synthesis of other compounds. In grass pea ( Lathyrus sativus L.), a grain legume grown in Asia and Africa for human and animal consumption, the neurotoxic compound β- N -oxalyl-l-α,β-diaminopropionic acid (β-ODAP) is synthesized from oxalyl-CoA and l-α,β-diaminopropionic acid (l-DAPA). Here, we report on the identification and characterization of oxalyl CoA-synthetase from grass pea ( Ls OCS). The gene encoding Ls OCS was amplified from grass pea, and then expressed and purified from E. coli cells as an untagged, monomeric protein of 56 kDa. Its catalytic efficiency with oxalate, K oxalate M = 71.5 ± 13.3 μM, V max = 8.2 ± 0.8 μmole min -1 mg -1 , was similar to that of OCS homologs from Arabidopsis thaliana ( At AAE3) and Medicago truncatula ( Mt AAE3). The enzyme was crystalized in complex with AMP and is the first OCS whose structure was determined in the thioester-forming conformation. Finally, we propose that substituting Ls OCS with an oxalate oxidase or decarboxylase may reduce the levels of β-ODAP in grass pea.


  • Organizational Affiliation

    Dept. of Life Science Core Facilities, Weizmann Institute of Science Rehovot 7610001 Israel.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
oxalyl CoA-synthetase521Lathyrus sativusMutation(s): 0 
UniProt
Find proteins for A0A3G8GC37 (Lathyrus sativus)
Explore A0A3G8GC37 
Go to UniProtKB:  A0A3G8GC37
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3G8GC37
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP (Subject of Investigation/LOI)
Query on AMP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62α = 90
b = 74.26β = 90
c = 101.68γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2020-08-26 
  • Deposition Author(s): Dym, O.

Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael712884

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release
  • Version 1.1: 2022-04-13
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Refinement description