6YQQ

ForT-PRPP complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

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This is version 1.4 of the entry. See complete history. 


Literature

Uncovering the chemistry of C-C bond formation in C-nucleoside biosynthesis: crystal structure of a C-glycoside synthase/PRPP complex.

Gao, S., Radadiya, A., Li, W., Liu, H., Zhu, W., de Crecy-Lagard, V., Richards, N.G.J., Naismith, J.H.

(2020) Chem Commun (Camb) 56: 7617-7620

  • DOI: https://doi.org/10.1039/d0cc02834g
  • Primary Citation of Related Structures:  
    6YQQ

  • PubMed Abstract: 

    The enzyme ForT catalyzes C-C bond formation between 5'-phosphoribosyl-1'-pyrophosphate (PRPP) and 4-amino-1H-pyrazole-3,5-dicarboxylate to make a key intermediate in the biosynthesis of formycin A 5'-phosphate by Streptomyces kaniharaensis. We report the 2.5 Å resolution structure of the ForT/PRPP complex and locate active site residues critical for PRPP recognition and catalysis.

    • Organizational Affiliation: 

    Research Complex at Harwell, Didcot, OX11 0FA, UK and BSRC, University of St Andrews, St Andrews, KY16 9ST, UK.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ForT-PRPP complex341Streptomyces kaniharaensisMutation(s): 0 
Gene Names: cof6, F7Q99_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
Binding Affinity Annotations 
IDSourceBinding Affinity
PRP Binding MOAD:  6YQQ Kd: 4000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.084α = 90
b = 81.084β = 90
c = 110.975γ = 90
Software Package:
Software NamePurpose
xia2data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data processing
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-20
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2020-12-02
    Changes: Database references, Structure summary
  • Version 1.3: 2021-06-30
    Changes: Database references, Refinement description, Source and taxonomy, Structure summary
  • Version 1.4: 2024-05-01
    Changes: Data collection, Database references, Refinement description