4WPG

Group A Streptococcus GacA is an essential dTDP-4-dehydrorhamnose reductase (RmlD)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.129 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

GacA is essential for Group A Streptococcus and defines a new class of monomeric dTDP-4-dehydrorhamnose reductases (RmlD).

van der Beek, S.L.Le Breton, Y.Ferenbach, A.T.Chapman, R.N.van Aalten, D.M.Navratilova, I.Boons, G.J.McIver, K.S.van Sorge, N.M.Dorfmueller, H.C.

(2015) Mol.Microbiol. 98: 946-962

  • DOI: 10.1111/mmi.13169

  • PubMed Abstract: 
  • The sugar nucleotide dTDP-L-rhamnose is critical for the biosynthesis of the Group A Carbohydrate, the molecular signature and virulence determinant of the human pathogen Group A Streptococcus (GAS). The final step of the four-step dTDP-L-rhamnose bi ...

    The sugar nucleotide dTDP-L-rhamnose is critical for the biosynthesis of the Group A Carbohydrate, the molecular signature and virulence determinant of the human pathogen Group A Streptococcus (GAS). The final step of the four-step dTDP-L-rhamnose biosynthesis pathway is catalyzed by dTDP-4-dehydrorhamnose reductases (RmlD). RmlD from the Gram-negative bacterium Salmonella is the only structurally characterized family member and requires metal-dependent homo-dimerization for enzymatic activity. Using a biochemical and structural biology approach, we demonstrate that the only RmlD homologue from GAS, previously renamed GacA, functions in a novel monomeric manner. Sequence analysis of 213 Gram-negative and Gram-positive RmlD homologues predicts that enzymes from all Gram-positive species lack a dimerization motif and function as monomers. The enzymatic function of GacA was confirmed through heterologous expression of gacA in a S. mutans rmlD knockout, which restored attenuated growth and aberrant cell division. Finally, analysis of a saturated mutant GAS library using Tn-sequencing and generation of a conditional-expression mutant identified gacA as an essential gene for GAS. In conclusion, GacA is an essential monomeric enzyme in GAS and representative of monomeric RmlD enzymes in Gram-positive bacteria and a subset of Gram-negative bacteria. These results will help future screens for novel inhibitors of dTDP-L-rhamnose biosynthesis.


    Organizational Affiliation

    University Medical Center Utrecht, Medical Microbiology, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
dTDP-4-dehydrorhamnose reductase
A
289Streptococcus pyogenes serotype M1Mutation(s): 0 
Gene Names: rmlD
EC: 1.1.1.133
Find proteins for Q9A0G6 (Streptococcus pyogenes serotype M1)
Go to UniProtKB:  Q9A0G6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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

Download SDF File 
Download CCD File 
A
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.129 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 36.482α = 66.30
b = 45.977β = 81.21
c = 48.867γ = 95.27
Software Package:
Software NamePurpose
Cootmodel building
PHENIXphasing
REFMACrefinement
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2016-01-27
    Type: Database references