9FCG

Medicago truncatula 5'-ProFAR isomerase (HISN3) D57N mutant in complex with PrFAR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

Starting Model: in silico
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Ligand Structure Quality Assessment 


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Literature

Structural, kinetic, and evolutionary peculiarities of HISN3, a plant 5'-ProFAR isomerase.

Witek, W.Imiolczyk, B.Ruszkowski, M.

(2024) Plant Physiol Biochem 215: 109065-109065

  • DOI: https://doi.org/10.1016/j.plaphy.2024.109065
  • Primary Citation of Related Structures:  
    9FCF, 9FCG

  • PubMed Abstract: 

    Histidine biosynthesis is essential for the growth and development of plants, where it occurs within chloroplasts. The eleven reactions are catalyzed by eight enzymes, known as HISN1-8, each acting sequentially. Here, we present the crystal structures of a 5'-ProFAR isomerase (HISN3) from the model legume Medicago truncatula bound to its enzymatically synthesized substrate (ProFAR) and product (PrFAR). The active site of MtHISN3 contains a sodium cation that participates in ligand recognition, a feature not observed in bacterial and fungal structures of homologous enzymes. The steady-state kinetics of wild-type MtHISN3 revealed a slightly higher turnover rate compared to its bacterial homologs. Plant HISN3 sequences contain an unusually elongated Lys60-Ser91 fragment, while deletion of the 74-80 region resulted in a 30-fold loss in catalytic efficiency compared to the wild-type. Molecular dynamics simulations suggested that the fragment facilitates product release, thereby contributing to a higher k cat . Moreover, conservation analyses suggested a non-cyanobacterial origin for plant HISN3 enzymes, which is another instance of a non-cyanobacterial enzyme in the plant histidine biosynthetic pathway. Finally, a virtual screening campaign yielded five molecules, with the energy gains ranging between -13.6 and -13.1 kcal/mol, which provide new scaffolds for the future development of herbicides.


  • Organizational Affiliation

    Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase, chloroplastic274Medicago truncatulaMutation(s): 1 
Gene Names: 11441829MTR_2g015010MtrunA17_Chr2g0283151
EC: 5.3.1.16
UniProt
Find proteins for G7IFI7 (Medicago truncatula)
Explore G7IFI7 
Go to UniProtKB:  G7IFI7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG7IFI7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2ER (Subject of Investigation/LOI)
Query on 2ER

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
[(2R,3S,4R,5R)-5-[4-AMINOCARBONYL-5-[[(Z)-[(3R,4R)-3,4-DIHYDROXY-2-OXO-5-PHOSPHONOOXY-PENTYL]IMINOMETHYL]AMINO]IMIDAZOL-1-YL]-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE
C15 H25 N5 O15 P2
BLKFNHOCHNCLII-GHVQHMAVSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 4
  • Diffraction Data: https://doi.org/10.18150/LDLSBT
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.79α = 90
b = 87.79β = 90
c = 35.633γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
PHENIXrefinement
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePolandSonata 2018/31/D/NZ1/03630

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release