5HUH

Crystal Structure of NadE from Streptococcus pyogenes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Streptococcus pyogenes quinolinate-salvage pathway-structural and functional studies of quinolinate phosphoribosyl transferase and NH3 -dependent NAD(+) synthetase.

Booth, W.T.Morris, T.L.Mysona, D.P.Shah, M.J.Taylor, L.K.Karlin, T.W.Clary, K.Majorek, K.A.Offermann, L.R.Chruszcz, M.

(2017) FEBS J. 284: 2425-2441

  • DOI: 10.1111/febs.14136
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Streptococcus pyogenes, also known as Group A Strep (GAS), is an obligate human pathogen that is responsible for millions of infections and numerous deaths per year. Infection manifestations can range from simple, acute pharyngitis to more complex, n ...

    Streptococcus pyogenes, also known as Group A Strep (GAS), is an obligate human pathogen that is responsible for millions of infections and numerous deaths per year. Infection manifestations can range from simple, acute pharyngitis to more complex, necrotizing fasciitis. To date, most treatments for GAS infections involve the use of common antibiotics including tetracycline and clindamycin. Unfortunately, new strains have been identified that are resistant to these drugs, therefore, new targets must be identified to treat drug-resistant strains. This work is focused on the structural and functional characterization of three proteins: spNadC, spNadD, and spNadE. These enzymes are involved in the biosynthesis of nicotinamide adenine dinucleotide (NAD + ). The structures of spNadC and spNadE were determined. SpNadC is suggested to play a role in GAS virulence, while spNadE, functions as an NAD synthetase and is considered to be a new drug target. Determination of the spNadE structure uncovered a putative, NH 3 channel, which may provide insight into the mechanistic details of NH 3 -dependent NAD + synthetases in prokaryotes.


    Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA.,Department of Chemistry, Davidson College, NC, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NH(3)-dependent NAD(+) synthetase
A, B
307Streptococcus pyogenes serotype M49 (strain NZ131)Mutation(s): 0 
Gene Names: nadE
EC: 6.3.1.5
Find proteins for A0A0H3BZ89 (Streptococcus pyogenes serotype M49 (strain NZ131))
Go to UniProtKB:  A0A0H3BZ89
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.521α = 90.00
b = 93.104β = 90.00
c = 128.569γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-07-12
    Type: Database references
  • Version 1.2: 2017-08-23
    Type: Database references