8AP0 | pdb_00008ap0

ForT Mutant T138V


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.203 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.157 (Depositor), 0.160 (DCC) 

Starting Model: experimental
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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

Experimental and computational snapshots of C-C bond formation in a C-nucleoside synthase.

Li, W.Girt, G.C.Radadiya, A.Stewart, J.J.P.Richards, N.G.J.Naismith, J.H.

(2023) Open Biol 13: 220287-220287

  • DOI: https://doi.org/10.1098/rsob.220287
  • Primary Citation Related Structures: 
    8AOZ, 8AP0

  • PubMed Abstract: 

    The biosynthetic enzyme, ForT, catalyses the formation of a C-C bond between 4-amino-1 H -pyrazoledicarboxylic acid and MgPRPP to produce a C-nucleoside precursor of formycin A. The transformation catalysed by ForT is of chemical interest because it is one of only a few examples in which C-C bond formation takes place via an electrophilic substitution of a small, aromatic heterocycle. In addition, ForT is capable of discriminating between the aminopyrazoledicarboxylic acid and an analogue in which the amine is replaced by a hydroxyl group; a remarkable feat given the steric and electronic similarities of the two molecules. Here we report biophysical measurements, structural biology and quantum chemical calculations that provide a detailed molecular picture of ForT-catalysed C-C bond formation and the conformational changes that are coupled to catalysis. Our findings set the scene for employing engineered ForT variants in the biocatalytic production of novel, anti-viral C-nucleoside and C-nucleotide analogues.


  • Organizational Affiliation
    • Structural Biology, The Rosalind Franklin Institute, Didcot OX11 0QS, UK.

Macromolecule Content 

  • Total Structure Weight: 37.43 kDa 
  • Atom Count: 2,910 
  • Modeled Residue Count: 332 
  • Deposited Residue Count: 341 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-ribofuranosylaminobenzene 5'-phosphate synthaseA [auth AAA]341Streptomyces kaniharaensisMutation(s): 1 
Gene Names: cof6F7Q99_03185
UniProt
Find proteins for A0A5S9CYM0 (Streptomyces kaniharaensis)
Explore A0A5S9CYM0 
Go to UniProtKB:  A0A5S9CYM0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5S9CYM0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PRP

Query on PRP



Download:Ideal Coordinates CCD File
B [auth AAA]1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose
C5 H13 O14 P3
PQGCEDQWHSBAJP-TXICZTDVSA-N
MYO
(Subject of Investigation/LOI)

Query on MYO



Download:Ideal Coordinates CCD File
C [auth AAA]4-azanyl-1~{H}-pyrazole-3,5-dicarboxylic acid
C5 H5 N3 O4
IGUCGPRNZVGVNO-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth AAA],
E [auth AAA]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
F [auth AAA]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
G [auth AAA]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.203 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.157 (Depositor), 0.160 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.23α = 90
b = 139.042β = 90
c = 109.651γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB_T006161_1

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-07
    Type: Initial release
  • Version 1.1: 2022-09-21
    Changes: Data collection
  • Version 1.2: 2023-03-22
    Changes: Database references
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description