2YLL | pdb_00002yll

Inhibition of the pneumococcal virulence factor StrH and molecular insights into N-glycan recognition and hydrolysis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.200 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 
    0.163 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2YLL

This is version 1.2 of the entry. See complete history

Literature

Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis.

Pluvinage, B.Higgins, M.A.Abbott, D.W.Robb, C.Dalia, A.B.Deng, L.Weiser, J.N.Parsons, T.B.Fairbanks, A.J.Vocadlo, D.J.Boraston, A.B.

(2011) Structure 19: 1603

  • DOI: https://doi.org/10.1016/j.str.2011.08.011
  • Primary Citation Related Structures: 
    2YL5, 2YL6, 2YL8, 2YL9, 2YLA, 2YLL

  • PubMed Abstract: 

    The complete degradation of N-linked glycans by the pathogenic bacterium Streptococcus pneumoniae is facilitated by the large multimodular cell wall-attached exo-β-D-N-acetylglucosaminidase StrH. Structural dissection of this virulence factor using X-ray crystallography showed it to have two structurally related glycoside hydrolase family 20 catalytic domains, which displayed the expected specificity for complex N-glycans terminating in N-acetylglucosamine but exhibited unexpected differences in their preferences for the substructures present in these glycans. The structures of the two catalytic domains in complex with unhydrolyzed substrates, including an N-glycan possessing a bisecting N-acetylglucosamine residue, revealed the specific architectural features in the active sites that confer their differential specificities. Inhibitors of StrH are demonstrated to be effective tools in modulating the interaction of StrH with components of the host, such as the innate immune system. Overall, new structural and functional insight into a carbohydrate-mediated component of the pneumococcus-host interaction is provided.


  • Organizational Affiliation
    • Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada.

Macromolecule Content 

  • Total Structure Weight: 59.42 kDa 
  • Atom Count: 4,122 
  • Modeled Residue Count: 436 
  • Deposited Residue Count: 454 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BETA-N-ACETYLHEXOSAMINIDASE454Streptococcus pneumoniae TIGR4Mutation(s): 0 
EC: 3.2.1.52
UniProt
Find proteins for P49610 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore P49610 
Go to UniProtKB:  P49610
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49610
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE4

Query on PE4



Download:Ideal Coordinates CCD File
D [auth A]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
IOD

Query on IOD



Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth A]
BA [auth A]
BB [auth A]
CA [auth A]
AA [auth A],
AB [auth A],
BA [auth A],
BB [auth A],
CA [auth A],
CB [auth A],
DA [auth A],
DB [auth A],
EA [auth A],
EB [auth A],
FA [auth A],
FB [auth A],
G [auth A],
GA [auth A],
GB [auth A],
H [auth A],
HA [auth A],
HB [auth A],
I [auth A],
IA [auth A],
IB [auth A],
J [auth A],
JA [auth A],
JB [auth A],
K [auth A],
KA [auth A],
KB [auth A],
L [auth A],
LA [auth A],
LB [auth A],
M [auth A],
MA [auth A],
MB [auth A],
N [auth A],
NA [auth A],
NB [auth A],
O [auth A],
OA [auth A],
OB [auth A],
P [auth A],
PA [auth A],
PB [auth A],
Q [auth A],
QA [auth A],
QB [auth A],
R [auth A],
RA [auth A],
RB [auth A],
S [auth A],
SA [auth A],
SB [auth A],
T [auth A],
TA [auth A],
TB [auth A],
U [auth A],
UA [auth A],
UB [auth A],
V [auth A],
VA [auth A],
W [auth A],
WA [auth A],
X [auth A],
XA [auth A],
Y [auth A],
YA [auth A],
Z [auth A],
ZA [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.200 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 0.163 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.52α = 90
b = 109.42β = 90
c = 112.36γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2011-11-23
    Changes: Database references, Structure summary
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other