8A0C

Capsular polysaccharide synthesis multienzyme in complex with CMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

A multi-enzyme machine polymerizes the Haemophilus influenzae type b capsule.

Cifuente, J.O.Schulze, J.Bethe, A.Di Domenico, V.Litschko, C.Budde, I.Eidenberger, L.Thiesler, H.Ramon Roth, I.Berger, M.Claus, H.D'Angelo, C.Marina, A.Gerardy-Schahn, R.Schubert, M.Guerin, M.E.Fiebig, T.

(2023) Nat Chem Biol 19: 865-877

  • DOI: https://doi.org/10.1038/s41589-023-01324-3
  • Primary Citation of Related Structures:  
    8A0C, 8A0M

  • PubMed Abstract: 

    Bacterial capsules have critical roles in host-pathogen interactions. They provide a protective envelope against host recognition, leading to immune evasion and bacterial survival. Here we define the capsule biosynthesis pathway of Haemophilus influenzae serotype b (Hib), a Gram-negative bacterium that causes severe infections in infants and children. Reconstitution of this pathway enabled the fermentation-free production of Hib vaccine antigens starting from widely available precursors and detailed characterization of the enzymatic machinery. The X-ray crystal structure of the capsule polymerase Bcs3 reveals a multi-enzyme machine adopting a basket-like shape that creates a protected environment for the synthesis of the complex Hib polymer. This architecture is commonly exploited for surface glycan synthesis by both Gram-negative and Gram-positive pathogens. Supported by biochemical studies and comprehensive 2D nuclear magnetic resonance, our data explain how the ribofuranosyltransferase CriT, the phosphatase CrpP, the ribitol-phosphate transferase CroT and a polymer-binding domain function as a unique multi-enzyme assembly.


  • Organizational Affiliation

    Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bcs3
A, B
1,173Haemophilus influenzaeMutation(s): 0 
Gene Names: bcs3'bcs3
UniProt
Find proteins for Q2ERG0 (Haemophilus influenzae)
Explore Q2ERG0 
Go to UniProtKB:  Q2ERG0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2ERG0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C5P (Subject of Investigation/LOI)
Query on C5P

Download Ideal Coordinates CCD File 
R [auth B]CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
L [auth B]
Q [auth B]
H [auth A],
I [auth A],
J [auth A],
L [auth B],
Q [auth B],
T [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
K [auth A],
S [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.97α = 90
b = 164.78β = 90
c = 302.567γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2.multiplexdata reduction
xia2.multiplexdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany412824531
Ministry of Economy and Competitiveness (MINECO)SpainPID2019-105649RB-I00
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI149297

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references
  • Version 1.2: 2023-07-05
    Changes: Structure summary
  • Version 1.3: 2023-07-12
    Changes: Database references