Crystal structure of the WbkC N-formyltransferase (F142A variant) from Brucella melitensis

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

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Biochemical Characterization of WbkC, an N-Formyltransferase from Brucella melitensis.

Riegert, A.S.Chantigian, D.P.Thoden, J.B.Tipton, P.A.Holden, H.M.

(2017) Biochemistry 56: 3657-3668

  • DOI: https://doi.org/10.1021/acs.biochem.7b00494
  • Primary Citation of Related Structures:  
    5VYR, 5VYS, 5VYT, 5VYU

  • PubMed Abstract: 

    It has become increasingly apparent within the last several years that unusual N-formylated sugars are often found on the O-antigens of such Gram negative pathogenic organisms as Francisella tularensis, Campylobacter jejuni, and Providencia alcalifaciens, among others. Indeed, in some species of Brucella, for example, the O-antigen contains 1,2-linked 4-formamido-4,6-dideoxy-α-d-mannosyl groups. These sugars, often referred to as N-formylperosamine, are synthesized in pathways initiating with GDP-mannose. One of the enzymes required for the production of N-formylperosamine, namely, WbkC, was first identified in 2000 and was suggested to function as an N-formyltransferase. Its biochemical activity was never experimentally verified, however. Here we describe a combined structural and functional investigation of WbkC from Brucella melitensis. Four high resolution X-ray structures of WbkC were determined in various complexes to address its active site architecture. Unexpectedly, the quaternary structure of WbkC was shown to be different from that previously observed for other sugar N-formyltransferases. Additionally, the structures revealed a second binding site for a GDP molecule distinct from that required for GDP-perosamine positioning. In keeping with this additional binding site, kinetic data with the wild type enzyme revealed complex patterns. Removal of GDP binding by mutating Phe 142 to an alanine residue resulted in an enzyme variant displaying normal Michaelis-Menten kinetics. These data suggest that this nucleotide binding pocket plays a role in enzyme regulation. Finally, by using an alternative substrate, we demonstrate that WbkC can be utilized to produce a trideoxysugar not found in nature.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gdp-mannose 4,6-dehydratase / gdp-4-amino-4,6-dideoxy-d-mannose formyltransferase
A, B, C, D
261Brucella melitensis bv. 1 str. 16MMutation(s): 2 
Gene Names: BMEI1418
EC: 2.1.2 (PDB Primary Data), (PDB Primary Data)
Find proteins for F8WJP6 (Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094))
Explore F8WJP6 
Go to UniProtKB:  F8WJP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF8WJP6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FON

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
M [auth D]
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
Query on GDP

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
N [auth D]
C10 H15 N5 O11 P2
Query on CL

Download Ideal Coordinates CCD File 
K [auth C],
L [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.315α = 90
b = 68.021β = 90
c = 236.035γ = 90
Software Package:
Software NamePurpose
SAINTdata reduction
SADABSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM115921

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2017-07-26
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description