6V2T

X-ray structure of a sugar N-formyltransferase from Shewanella sp FDAARGOS_354


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


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Literature

Misannotations of the Genes Encoding Sugar N-formyltransferases.

Girardi, N.M.Thoden, J.B.Holden, H.M.

(2019) Protein Sci. --: --

  • DOI: 10.1002/pro.3807
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tens of thousands of bacterial genome sequences are now known due to the development of rapid and inexpensive sequencing technologies. An important key to utilizing these vast amounts of data in a biologically meaningful way is to infer the function ...

    Tens of thousands of bacterial genome sequences are now known due to the development of rapid and inexpensive sequencing technologies. An important key to utilizing these vast amounts of data in a biologically meaningful way is to infer the function of the proteins encoded in the genomes via bioinformatics techniques. Whereas these approaches are absolutely critical to the annotation of gene function, there are still issues of misidentifications, which must be experimentally corrected. For example, many of the bacterial DNA sequences encoding sugar N-formyltransferases have been annotated as l-methionyl-tRNA transferases in the databases. These mistakes may be due in part to the fact that until recently the structures and functions of these enzymes were not well known. Herein we describe the misannotation of two genes, WP_088211966.1 and WP_096244125.1, from Shewanella spp. and Pseudomonas congelans, respectively. Although the proteins encoded by these genes were originally suggested to function as l-methionyl-tRNA transferases, we demonstrate that they actually catalyze the conversion of dTDP-4-amino-4,6-dideoxy-d-glucose to dTDP-4-formamido-4,6-dideoxy-d-glucose utilizing N 10 -formyltetrahydrofolate as the carbon source. For this analysis, the genes encoding these enzymes were cloned and the corresponding proteins purified. X-ray structures of the two proteins were determined to high resolution and kinetic analyses were conducted. Both enzymes display classical Michaelis-Menten kinetics and adopt the characteristic three-dimensional structure fold previously observed for other sugar N-formyltransferases. The results presented herein will aid in the future annotation of these fascinating enzymes. This article is protected by copyright. All rights reserved.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
dTDP-4-amino-4,6-dideoxyglucose formyltransferase
A, B
267Shewanella sp. FDAARGOS_354Mutation(s): 0 
Find proteins for A0A1Z4A6S6 (Shewanella sp. FDAARGOS_354)
Go to UniProtKB:  A0A1Z4A6S6
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0FX
Query on 0FX

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Download CCD File 
A, B
dTDP-4-amino-4,6-dideoxyglucose
C16 H27 N3 O14 P2
UIVJXHWSIFBBCY-LPGAPTBISA-N
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

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Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FOL
Query on FOL

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Download CCD File 
A, B
FOLIC ACID
C19 H19 N7 O6
OVBPIULPVIDEAO-LBPRGKRZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.184 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 78.966α = 90.00
b = 202.472β = 90.00
c = 74.439γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
PHASERphasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2020-01-08
    Type: Initial release