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 6YUO | pdb_00006yuo

Capsule O-acetyltransferase of Neisseria meningitidis serogroup A in complex with caged Gadolinium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.219 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6YUO

This is version 1.2 of the entry. See complete history. 

Literature

Structural and mechanistic basis of capsule O-acetylation in Neisseria meningitidis serogroup A.

Fiebig, T., Cramer, J.T., Bethe, A., Baruch, P., Curth, U., Fuhring, J.I., Buettner, F.F.R., Vogel, U., Schubert, M., Fedorov, R., Muhlenhoff, M.

(2020) Nat Commun 11: 4723-4723

  • DOI: https://doi.org/10.1038/s41467-020-18464-y
  • Primary Citation Related Structures: 
    6YUO, 6YUQ, 6YUS, 6YUV

  • PubMed Abstract: 

    O-Acetylation of the capsular polysaccharide (CPS) of Neisseria meningitidis serogroup A (NmA) is critical for the induction of functional immune responses, making this modification mandatory for CPS-based anti-NmA vaccines. Using comprehensive NMR studies, we demonstrate that O-acetylation stabilizes the labile anomeric phosphodiester-linkages of the NmA-CPS and occurs in position C3 and C4 of the N-acetylmannosamine units due to enzymatic transfer and non-enzymatic ester migration, respectively. To shed light on the enzymatic transfer mechanism, we solved the crystal structure of the capsule O-acetyltransferase CsaC in its apo and acceptor-bound form and of the CsaC-H228A mutant as trapped acetyl-enzyme adduct in complex with CoA. Together with the results of a comprehensive mutagenesis study, the reported structures explain the strict regioselectivity of CsaC and provide insight into the catalytic mechanism, which relies on an unexpected Gln-extension of a classical Ser-His-Asp triad, embedded in an α/β-hydrolase fold.


  • Organizational Affiliation: 
    • Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany. Fiebig.Timm@mh-hannover.de.

Macromolecule Content 

  • Total Structure Weight: 59.3 kDa 
  • Atom Count: 3,952 
  • Modeled Residue Count: 485 
  • Deposited Residue Count: 510 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SacC
A, B
255Neisseria meningitidis serogroup AMutation(s): 0 
Gene Names: sacC
UniProt
Find proteins for O68216 (Neisseria meningitidis serogroup A)
Explore O68216 
Go to UniProtKB:  O68216
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO68216
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GD3
(Subject of Investigation/LOI)

Query on GD3



Download:Ideal Coordinates CCD File
E [auth B],
H [auth B]
GADOLINIUM ION
Gd
RJOJUSXNYCILHH-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
G [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO

Query on EDO



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

Query on CL



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.219 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.93α = 90
b = 132.93β = 90
c = 69.27γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
CRANK2phasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany262794208
German Research Foundation (DFG)Germany412824531

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2020-10-14
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references