6RN5

PptA from Streptomyces chartreusis

• PDB DOI: https://doi.org/10.2210/pdb6RN5/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Streptomyces chartreusis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-05-08 Released: 2019-06-19 
• Deposition Author(s): Werten, S., Rustmeier, N.H., Hinrichs, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.237 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Literature

Structural and biochemical analysis of a phosin from Streptomyces chartreusis reveals a combined polyphosphate- and metal-binding fold.

Werten, S., Rustmeier, N.H., Gemmer, M., Virolle, M.J., Hinrichs, W.

(2019) FEBS Lett 593: 2019-2029

• PubMed: 31183865 
• DOI: https://doi.org/10.1002/1873-3468.13476
• Primary Citation of Related Structures:  
  6RN5


• PubMed Abstract: 
  

  X-ray crystallographic analysis of a phosin (PptA) from Steptomyces chartreusis reveals a metal-associated, lozenge-shaped fold featuring a 5-10 Å wide, positively charged tunnel that traverses the protein core. Two distinct metal-binding sites were identified in which the predominant metal ion was Cu ²⁺ . In solution, PptA forms stable homodimers that bind with nanomolar affinity to polyphosphate, a stress-related biopolymer acting as a phosphate and energy reserve in conditions of nutrient depletion. A single protein dimer interacts with 14-15 consecutive phosphate moieties within the polymer. Our observations suggest that PptA plays a role in polyphosphate metabolism, mobilisation or sensing, possibly by acting in concert with polyphosphate kinase (Ppk). Like Ppk, phosins may influence antibiotic synthesis by streptomycetes.

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Organizational Affiliation: 

Division of Biological Chemistry, Biocenter, Medical University of Innsbruck, Austria.

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: SAXS, gel filtration

Macromolecule Content

• Total Structure Weight: 40.29 kDa 
• Atom Count: 2,317 
• Modelled Residue Count: 283 
• Deposited Residue Count: 376 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHAD domain protein	A	376	Streptomyces chartreusis	Mutation(s): 0  Gene Names: SCNRRL3882_4295
UniProt
Find proteins for A0A2N9BBV4 (Streptomyces chartreusis NRRL 3882) Explore A0A2N9BBV4  Go to UniProtKB:  A0A2N9BBV4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CU (Subject of Investigation/LOI)	B [auth A], C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
CO3	J [auth A]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.237 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.303	α = 90
b = 132.233	β = 90
c = 116.398	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-19 
Deposition Author(s): Werten, S., Rustmeier, N.H., Hinrichs, W.

Revision History  

• Version 1.0: 2019-06-19
  Type: Initial release
  
• Version 1.1: 2019-08-21
  Changes: Data collection, Database references
• Version 1.2: 2020-08-12
  Changes: Derived calculations, Structure summary
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references, Derived calculations