6YQQ | pdb_00006yqq

ForT-PRPP complex

• PDB DOI: https://doi.org/10.2210/pdb6YQQ/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Streptomyces kaniharaensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-04-18 Released: 2020-05-20 
• Deposition Author(s): Naismith, J.H., Gao, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.265 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.257 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: other

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

• PubMed: 32515440 
• DOI: https://doi.org/10.1039/d0cc02834g
• Primary Citation 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.

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Organizational Affiliation: 
• Research Complex at Harwell, Didcot, OX11 0FA, UK and BSRC, University of St Andrews, St Andrews, KY16 9ST, UK.
School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK.
Division of Structural Biology, University of Oxford, Oxford, OX3 7BN, UK. [e-mail].
BSRC, University of St Andrews, St Andrews, KY16 9ST, UK.
Department of Chemistry and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA.
Department of Microbiology, University of Florida, Gainesville, FL 32611, USA.
School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK and Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA.
Division of Structural Biology, University of Oxford, Oxford, OX3 7BN, UK. [e-mail] and The Rosalind Franklin Institute, Didcot, OX11 0FA, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 37.08 kDa 
• Atom Count: 2,430 
• Modeled Residue Count: 320 
• Deposited Residue Count: 341 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ForT-PRPP complex	A	341	Streptomyces kaniharaensis	Mutation(s): 0  Gene Names: cof6, F7Q99_03185
UniProt
Find proteins for A0A5S9CYM0 (Streptomyces kaniharaensis) Explore A0A5S9CYM0  Go to UniProtKB:  A0A5S9CYM0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PRP (Subject of Investigation/LOI)	D [auth A]	1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose C5 H13 O14 P3 PQGCEDQWHSBAJP-TXICZTDVSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.265 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.257 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.084	α = 90
b = 81.084	β = 90
c = 110.975	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data processing
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-20 
Deposition Author(s): Naismith, J.H., Gao, S.

Revision History  

• 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