7PKC

Streptococcus pyogenes Apo-GapN C284S variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

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, I, J, K, L, M, N, O, P
496Streptococcus pyogenes M49 591Mutation(s): 1 
Gene Names: gapNKUN4944_10090SPNIH35_06470
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
AB [auth K]
CA [auth E]
CB [auth L]
DA [auth E]
AA [auth D],
AB [auth K],
CA [auth E],
CB [auth L],
DA [auth E],
DB [auth L],
EB [auth L],
FA [auth F],
GA [auth F],
HB [auth M],
IB [auth M],
JA [auth G],
KA [auth G],
KB [auth N],
MA [auth H],
MB [auth O],
NA [auth H],
NB [auth O],
PB [auth P],
Q [auth A],
QB [auth P],
R [auth A],
SA [auth I],
T [auth B],
U [auth B],
UA [auth J],
VA [auth J],
W [auth C],
X [auth C],
Z [auth D],
ZA [auth K]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth D]
BB [auth K]
EA [auth E]
FB [auth L]
GB [auth L]
BA [auth D],
BB [auth K],
EA [auth E],
FB [auth L],
GB [auth L],
HA [auth F],
IA [auth F],
JB [auth M],
LA [auth G],
LB [auth N],
OA [auth H],
OB [auth O],
PA [auth H],
QA [auth H],
RA [auth H],
RB [auth P],
S [auth A],
SB [auth P],
TA [auth I],
TB [auth P],
V [auth B],
WA [auth J],
XA [auth J],
Y [auth C],
YA [auth J]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.665α = 96.36
b = 126.036β = 104.81
c = 148.393γ = 84.23
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 fundedGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Refinement description