4LXQ

Crystal structure WlaRD, a sugar 3N-formyl transferase in the presence of dTdp and 5-N-Formyl-THF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure of a sugar N-formyltransferase from Campylobacter jejuni.

Thoden, J.B.Goneau, M.F.Gilbert, M.Holden, H.M.

(2013) Biochemistry 52: 6114-6126

  • DOI: 10.1021/bi4009006
  • Primary Citation of Related Structures:  
    4LXQ, 4LXT, 4LXU, 4LXX, 4LXY, 4LY0, 4LY3

  • PubMed Abstract: 
  • The O-antigens, which are components of the outer membranes of Gram-negative bacteria, are responsible for the wide species variations seen in nature and are thought to play a role in bacterial virulence. They often contain unusual dideoxysugars such as 3,6-dideoxy-3-formamido-d-glucose (Qui3NFo) ...

    The O-antigens, which are components of the outer membranes of Gram-negative bacteria, are responsible for the wide species variations seen in nature and are thought to play a role in bacterial virulence. They often contain unusual dideoxysugars such as 3,6-dideoxy-3-formamido-d-glucose (Qui3NFo). Here, we describe a structural and functional investigation of the protein C8J_1081 from Campylobacter jejuni 81116, which is involved in the biosynthesis of Qui3NFo. Specifically, the enzyme, hereafter referred to as WlaRD, catalyzes the N-formylation of dTDP-3,6-dideoxy-3-amino-d-glucose (dTDP-Qui3N) using N(10)-formyltetrahydrofolate as the carbon source. For this investigation, seven X-ray structures of WlaRD, in complexes with various dTDP-linked sugars and cofactors, were determined to resolutions of 1.9 Å or better. One of the models, with bound N(10)-formyltetrahydrofolate and dTDP, represents the first glimpse of an N-formyltransferase with its natural cofactor. Another model contains the reaction products, tetrahydrofolate and dTDP-Qui3NFo. In combination, the structures provide snapshots of the WlaRD active site before and after catalysis. On the basis of these structures, three amino acid residues were targeted for study: Asn 94, His 96, and Asp 132. Mutations of any of these residues resulted in a complete loss of enzymatic activity. Given the position of His 96 in the active site, it can be postulated that it functions as the active site base to remove a proton from the sugar amino group as it attacks the carbonyl carbon of the N-10 formyl group of the cofactor. Enzyme assays demonstrate that WlaRD is also capable of utilizing dTDP-3,6-dideoxy-3-amino-d-galactose (dTDP-Fuc3N) as a substrate, albeit at a much reduced catalytic efficiency.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
WlaRD, a sugar 3N-formyl transferaseA, B274Campylobacter jejuni subsp. jejuni 81116Mutation(s): 0 
Gene Names: C8J_1081
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FON (Subject of Investigation/LOI)
Query on FON

Download Ideal Coordinates CCD File 
C [auth A], N [auth B]N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid
C20 H23 N7 O7
VVIAGPKUTFNRDU-OLZOCXBDSA-N
 Ligand Interaction
TYD (Subject of Investigation/LOI)
Query on TYD

Download Ideal Coordinates CCD File 
D [auth A], O [auth B]THYMIDINE-5'-DIPHOSPHATE
C10 H16 N2 O11 P2
UJLXYODCHAELLY-XLPZGREQSA-N
 Ligand Interaction
MPO (Subject of Investigation/LOI)
Query on MPO

Download Ideal Coordinates CCD File 
E [auth A], H [auth A], P [auth B], Q [auth B]3[N-MORPHOLINO]PROPANE SULFONIC ACID
C7 H15 N O4 S
DVLFYONBTKHTER-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B] , BA [auth B] , F [auth A] , G [auth A] , I [auth A] , R [auth B] , S [auth B] , T [auth B] , 
AA [auth B], BA [auth B], F [auth A], G [auth A], I [auth A], R [auth B], S [auth B], T [auth B], U [auth B], Y [auth B], Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth A], K [auth A], L [auth A], M [auth A], V [auth B], W [auth B], X [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.861α = 90
b = 63.259β = 110.04
c = 136.212γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-14
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references