6CI4 | pdb_00006ci4

Crystal structure of the formyltransferase PseJ from Anoxybacillus kamchatkensis soaked with UDP-4-amino-4,6-dideoxy-L-AltNAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 
    0.211 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.186 (Depositor) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6CI4

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structural Insight into a Novel Formyltransferase and Evolution to a Nonribosomal Peptide Synthetase Tailoring Domain.

Reimer, J.M.Harb, I.Ovchinnikova, O.G.Jiang, J.Whitfield, C.Schmeing, T.M.

(2018) ACS Chem Biol 13: 3161-3172

  • DOI: https://doi.org/10.1021/acschembio.8b00739
  • Primary Citation Related Structures: 
    6CI2, 6CI4, 6CI5, 6EDK

  • PubMed Abstract: 

    Nonribosomal peptide synthetases (NRPSs) increase the chemical diversity of their products by acquiring tailoring domains. Linear gramicidin synthetase starts with a tailoring formylation (F) domain, which likely originated from a sugar formyltransferase (FT) gene. Here, we present studies on an Anoxybacillus kamchatkensis sugar FT representative of the prehorizontal gene transfer FT. Gene cluster analysis reveals that this FT acts on a UDP-sugar in a novel pathway for synthesis of a 7-formamido derivative of CMP-pseudaminic acid. We recapitulate the pathway up to and including the formylation step in vitro, experimentally demonstrating the role of the FT. We also present X-ray crystal structures of the FT alone and with ligands, which unveil contrasts with other structurally characterized sugar FTs and show close structural similarity with the F domain. The structures reveal insights into the adaptations that were needed to co-opt and evolve a sugar FT into a functional and useful NRPS domain.


  • Organizational Affiliation
    • Department of Biochemistry , McGill University , Montréal , Québec H3G 0B1 , Canada.

Macromolecule Content 

  • Total Structure Weight: 26.2 kDa 
  • Atom Count: 1,719 
  • Modeled Residue Count: 190 
  • Deposited Residue Count: 217 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
formyltransferase PseJ217Anoxybacillus ayderensis G10Mutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F5P

Query on F5P



Download:Ideal Coordinates CCD File
B [auth A](2R,3R,4S,5R,6S)-3-(acetylamino)-5-amino-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate
C17 H28 N4 O15 P2
FUUMLYWEEZBCQR-NAGKVERXSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free:  0.211 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.186 (Depositor) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.425α = 90
b = 73.78β = 103.474
c = 41.805γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaFDN-148472

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2018-11-07
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-28
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description