6YUQ | pdb_00006yuq

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.221 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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: 60.26 kDa 
  • Atom Count: 4,037 
  • Modeled Residue Count: 490 
  • 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 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BMX
(Subject of Investigation/LOI)

Query on BMX



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A]
2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannopyranose
C8 H16 N O9 P
BRGMHAYQAZFZDJ-UOLFYFMNSA-N
BM3
(Subject of Investigation/LOI)

Query on BM3



Download:Ideal Coordinates CCD File
I [auth A]2-acetamido-2-deoxy-alpha-D-mannopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-UOLFYFMNSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
J [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



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

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
(Subject of Investigation/LOI)

Query on CL



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.221 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.483α = 90
b = 137.483β = 90
c = 70.253γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHENIXmodel building
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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: 2024-01-24
    Changes: Data collection, Database references, Refinement description