7PKJ

Streptococcus pyogenes apo GapN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Non-phosphorylating Glyceraldehyde-3-Phosphate Dehydrogenase GapN Is a Potential New Drug Target in Streptococcus pyogenes.

Eisenberg, P.Albert, L.Teuffel, J.Zitzow, E.Michaelis, C.Jarick, J.Sehlke, C.Grosse, L.Bader, N.Nunes-Alves, A.Kreikemeyer, B.Schindelin, H.Wade, R.C.Fiedler, T.

(2022) Front Microbiol 13: 802427-802427

  • DOI: https://doi.org/10.3389/fmicb.2022.802427
  • Primary Citation of Related Structures:  
    7PKC, 7PKJ

  • PubMed Abstract: 

    The strict human pathogen Streptococcus pyogenes causes infections of varying severity, ranging from self-limiting suppurative infections to life-threatening diseases like necrotizing fasciitis or streptococcal toxic shock syndrome. Here, we show that the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase GapN is an essential enzyme for S. pyogenes . GapN converts glyceraldehyde 3-phosphate into 3-phosphoglycerate coupled to the reduction of NADP to NADPH. The knock-down of gapN by antisense peptide nucleic acids (asPNA) significantly reduces viable bacterial counts of S. pyogenes laboratory and macrolide-resistant clinical strains in vitro . As S. pyogenes lacks the oxidative part of the pentose phosphate pathway, GapN appears to be the major NADPH source for the bacterium. Accordingly, other streptococci that carry a complete pentose phosphate pathway are not prone to asPNA-based gapN knock-down. Determination of the crystal structure of the S. pyogenes GapN apo-enzyme revealed an unusual cis-peptide in proximity to the catalytic binding site. Furthermore, using a structural modeling approach, we correctly predicted competitive inhibition of S. pyogenes GapN by erythrose 4-phosphate, indicating that our structural model can be used for in silico screening of specific GapN inhibitors. In conclusion, the data provided here reveal that GapN is a potential target for antimicrobial substances that selectively kill S. pyogenes and other streptococci that lack the oxidative part of the pentose phosphate pathway.


  • Organizational Affiliation

    Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical Centre, Rostock, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
A, B, C, D, E
A, B, C, D, E, F, G, H
496Streptococcus pyogenes M49 591Mutation(s): 0 
Gene Names: gapNKUN4944_10090SPNIH35_06470
UniProt
Find proteins for Q99Z67 (Streptococcus pyogenes serotype M1)
Explore Q99Z67 
Go to UniProtKB:  Q99Z67
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99Z67
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
DB [auth H]
EB [auth H]
AA [auth D],
BA [auth D],
CA [auth D],
DB [auth H],
EB [auth H],
J [auth A],
K [auth A],
KA [auth E],
LA [auth E],
O [auth B],
P [auth B],
PA [auth F],
Q [auth B],
TA [auth G],
U [auth C],
UA [auth G],
V [auth C],
W [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AB [auth G]
BB [auth G]
DA [auth D]
EA [auth D]
FA [auth D]
AB [auth G],
BB [auth G],
DA [auth D],
EA [auth D],
FA [auth D],
FB [auth H],
GA [auth D],
GB [auth H],
HA [auth D],
IA [auth D],
L [auth A],
M [auth A],
MA [auth E],
NA [auth E],
QA [auth F],
R [auth B],
RA [auth F],
S [auth B],
VA [auth G],
WA [auth G],
X [auth C],
XA [auth G],
Y [auth C],
YA [auth G],
ZA [auth G]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME
Query on BME

Download Ideal Coordinates CCD File 
CB [auth H]
I [auth A]
JA [auth E]
N [auth B]
OA [auth F]
CB [auth H],
I [auth A],
JA [auth E],
N [auth B],
OA [auth F],
SA [auth G],
T [auth C],
Z [auth D]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.749α = 77.67
b = 99.893β = 75.19
c = 106.182γ = 67.12
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description