6PD1

PntC-AEPT: fusion protein of phosphonate-specific cytidylyltransferase and 2-aminoethylphosphonate (AEP) transaminase from Treponema denticola


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis.

Rice, K.Batul, K.Whiteside, J.Kelso, J.Papinski, M.Schmidt, E.Pratasouskaya, A.Wang, D.Sullivan, R.Bartlett, C.Weadge, J.T.Van der Kamp, M.W.Moreno-Hagelsieb, G.Suits, M.D.Horsman, G.P.

(2019) Nat Commun 10: 3698-3698

  • DOI: 10.1038/s41467-019-11627-6
  • Primary Citation of Related Structures:  
    6PD1, 6PD2

  • PubMed Abstract: 
  • Phosphonates are rare and unusually bioactive natural products. However, most bacterial phosphonate biosynthetic capacity is dedicated to tailoring cell surfaces with molecules like 2-aminoethylphosphonate (AEP). Although phosphoenolpyruvate mutase (Ppm)-catalyzed installation of C-P bonds is known, subsequent phosphonyl tailoring (Pnt) pathway steps remain enigmatic ...

    Phosphonates are rare and unusually bioactive natural products. However, most bacterial phosphonate biosynthetic capacity is dedicated to tailoring cell surfaces with molecules like 2-aminoethylphosphonate (AEP). Although phosphoenolpyruvate mutase (Ppm)-catalyzed installation of C-P bonds is known, subsequent phosphonyl tailoring (Pnt) pathway steps remain enigmatic. Here we identify nucleotidyltransferases in over two-thirds of phosphonate biosynthetic gene clusters, including direct fusions to ~60% of Ppm enzymes. We characterize two putative phosphonyl tailoring cytidylyltransferases (PntCs) that prefer AEP over phosphocholine (P-Cho) - a similar substrate used by the related enzyme LicC, which is a virulence factor in Streptococcus pneumoniae. PntC structural analyses reveal steric discrimination against phosphocholine. These findings highlight nucleotidyl activation as a predominant chemical logic in phosphonate biosynthesis and set the stage for probing diverse phosphonyl tailoring pathways.


    Organizational Affiliation

    Department of Chemistry & Biochemistry, Wilfrid Laurier University, Waterloo, ON, N2L 3C5, Canada. ghorsman@wlu.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleotidyl transferase/aminotransferase, class VA, B, C, D624Treponema denticola ATCC 35405Mutation(s): 0 
Gene Names: TDE_1415
UniProt
Find proteins for Q73MU2 (Treponema denticola (strain ATCC 35405 / DSM 14222 / CIP 103919 / JCM 8153 / KCTC 15104))
Explore Q73MU2 
Go to UniProtKB:  Q73MU2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D] , F [auth A] , G [auth A] , J [auth A] , L [auth B] , N [auth B] , O [auth B] , P [auth B] , 
AA [auth D], F [auth A], G [auth A], J [auth A], L [auth B], N [auth B], O [auth B], P [auth B], S [auth C], W [auth C], Z [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
U [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A], I [auth A], M [auth B], Q [auth C], T [auth C], Y [auth D]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
V [auth C]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A], K [auth B], R [auth C], X [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.053α = 90
b = 129.012β = 92.99
c = 135.797γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
AutoPROCdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2014-05018

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-09-04
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Advisory, Derived calculations
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence