7RTY | pdb_00007rty

Crystal Structure of PsfC from Pseudomonas syringae PB-5123

• PDB DOI: https://doi.org/10.2210/pdb7RTY/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Pseudomonas syringae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-08-16 Released: 2021-09-15 
• Deposition Author(s): Ongpipattanakul, C., Nair, S.K.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.257 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Literature

Biosynthesis of fosfomycin in pseudomonads reveals an unexpected enzymatic activity in the metallohydrolase superfamily.

Simon, M.A., Ongpipattanakul, C., Nair, S.K., van der Donk, W.A.

(2021) Proc Natl Acad Sci U S A 118

• PubMed: 34074759 
• DOI: https://doi.org/10.1073/pnas.2019863118
• Primary Citation Related Structures: 
  7RTY


• PubMed Abstract: 
  

  The epoxide-containing phosphonate natural product fosfomycin is a broad-spectrum antibiotic used in the treatment of cystitis. Fosfomycin is produced by both the plant pathogen Pseudomonas syringae and soil-dwelling streptomycetes. While the streptomycete pathway has recently been fully elucidated, the pseudomonad pathway is still mostly elusive. Through a systematic evaluation of heterologous expression of putative biosynthetic enzymes, we identified the central enzyme responsible for completing the biosynthetic pathway in pseudomonads. The missing transformation involves the oxidative decarboxylation of the intermediate 2-phosphonomethylmalate to a new intermediate, 3-oxo-4-phosphonobutanoate, by PsfC. Crystallographic studies reveal that PsfC unexpectedly belongs to a new class of diiron metalloenzymes that are part of the polymerase and histidinol phosphatase superfamily.

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Organizational Affiliation: 
• Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801.
Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801.
Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801.
Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801; [e-mail] [e-mail].
Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801; [e-mail] [e-mail].
HHMI, University of Illinois at Urbana-Champaign, Urbana, IL 61801.
Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 54.34 kDa 
• Atom Count: 3,911 
• Modeled Residue Count: 488 
• Deposited Residue Count: 490 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PsfC	A, B	245	Pseudomonas syringae	Mutation(s): 0
UniProt
Find proteins for I6QY72 (Pseudomonas syringae) Explore I6QY72  Go to UniProtKB:  I6QY72

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE2 (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth B], F [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.257 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.831	α = 90
b = 106.831	β = 90
c = 83.01	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-09-15 
Deposition Author(s): Ongpipattanakul, C., Nair, S.K.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2021-09-15
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection