4WPG | pdb_00004wpg

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

• PDB DOI: https://doi.org/10.2210/pdb4WPG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptococcus pyogenes
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-18 Released: 2015-09-09 
• Deposition Author(s): van der Beek, S.L., Le Breton, Y., Ferenbach, A.T., van Aalten, D.M.F., Navratilova, I., McIver, K., van Sorge, N.M., Dorfmueller, H.C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.155 (Depositor), 0.153 (DCC) 
• R-Value Work: 
  0.129 (Depositor), 0.127 (DCC) 
• R-Value Observed: 
  0.130 (Depositor) 

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

• PubMed: 26278404 
• DOI: https://doi.org/10.1111/mmi.13169
• Primary Citation Related Structures: 
  4WPG


• 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 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.
Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, 3124 Biosciences Research Building, College Park, MD 20742, USA.
Division of Molecular Microbiology, University of Dundee, School of Life Sciences, Dow Street, DD1 5EH, Dundee, UK.
Complex Carbohydrate Research Center, Department of Chemistry, The University of Georgia, 315 Riverbend Road, Athens, USA.
Division of Biological Chemistry and Drug Discovery, University of Dundee, School of Life Sciences, Dow Street, DD1 5EH, Dundee, UK.
Rutherford Appleton Laboratory, Research Complex at Harwell, OX11 0FA, Didcot, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.87 kDa 
• Atom Count: 2,803 
• Modeled Residue Count: 287 
• Deposited Residue Count: 289 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dTDP-4-dehydrorhamnose reductase	A	289	Streptococcus pyogenes	Mutation(s): 0  Gene Names: GacA EC: 1.1.1.133
UniProt
Find proteins for Q9A0G6 (Streptococcus pyogenes serotype M1) Explore Q9A0G6  Go to UniProtKB:  Q9A0G6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	C [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
MPD	B [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.155 (Depositor), 0.153 (DCC) 
• R-Value Work:  0.129 (Depositor), 0.127 (DCC) 
• R-Value Observed: 0.130 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.482	α = 66.3
b = 45.977	β = 81.21
c = 48.867	γ = 95.27

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Coot	model building
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-09 
Deposition Author(s): van der Beek, S.L., Le Breton, Y., Ferenbach, A.T., van Aalten, D.M.F., Navratilova, I., McIver, K., van Sorge, N.M., Dorfmueller, H.C.

Revision History  

• Version 1.0: 2015-09-09
  Type: Initial release
  
• Version 1.1: 2016-01-27
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references