7P0H

Crystal structure of Helicobacter pylori ComF fused to an artificial alphaREP crystallization helper(named B2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

ComFC mediates transport and handling of single-stranded DNA during natural transformation.

Damke, P.P.Celma, L.Kondekar, S.M.Di Guilmi, A.M.Marsin, S.Depagne, J.Veaute, X.Legrand, P.Walbott, H.Vercruyssen, J.Guerois, R.Quevillon-Cheruel, S.Radicella, J.P.

(2022) Nat Commun 13: 1961-1961

  • DOI: 10.1038/s41467-022-29494-z
  • Primary Citation of Related Structures:  
    7P0H

  • PubMed Abstract: 
  • The ComFC protein is essential for natural transformation, a process that plays a major role in the spread of antibiotic resistance genes and virulence factors across bacteria. However, its role remains largely unknown. Here, we show that Helicobacter pylori ComFC is involved in DNA transport through the cell membrane, and is required for the handling of the single-stranded DNA once it is delivered into the cytoplasm ...

    The ComFC protein is essential for natural transformation, a process that plays a major role in the spread of antibiotic resistance genes and virulence factors across bacteria. However, its role remains largely unknown. Here, we show that Helicobacter pylori ComFC is involved in DNA transport through the cell membrane, and is required for the handling of the single-stranded DNA once it is delivered into the cytoplasm. The crystal structure of ComFC includes a zinc-finger motif and a putative phosphoribosyl transferase domain, both necessary for the protein's in vivo activity. Furthermore, we show that ComFC is a membrane-associated protein with affinity for single-stranded DNA. Our results suggest that ComFC provides the link between the transport of the transforming DNA into the cytoplasm and its handling by the recombination machinery.


    Organizational Affiliation

    Université de Paris-Cité, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, F-92260, Fontenay aux Roses, France. pablo.radicella@cea.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Helicobacter pylori ComF fused to an artificial alphaREP crystallization helper (named B2)A, B, C, D427synthetic constructHelicobacter pylori 26695
This entity is chimeric
Mutation(s): 0 
UniProt
Find proteins for O26008 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O26008 
Go to UniProtKB:  O26008
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO26008
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PRP (Subject of Investigation/LOI)
Query on PRP

Download Ideal Coordinates CCD File 
DA [auth D],
F [auth A],
P [auth B],
V [auth C]
1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose
C5 H13 O14 P3
PQGCEDQWHSBAJP-TXICZTDVSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth C],
FA [auth D],
GA [auth D],
H [auth A],
I [auth A],
AA [auth C],
FA [auth D],
GA [auth D],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
R [auth B],
S [auth B],
X [auth C],
Y [auth C],
Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
CA [auth D],
E [auth A],
O [auth B],
U [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BA [auth C],
EA [auth D],
G [auth A],
HA [auth D],
N [auth A],
BA [auth C],
EA [auth D],
G [auth A],
HA [auth D],
N [auth A],
Q [auth B],
T [auth B],
W [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.88α = 80.23
b = 87.98β = 76.44
c = 122.79γ = 76.39
Software Package:
Software NamePurpose
STARANISOdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French Infrastructure for Integrated Structural Biology (FRISBI)FranceANR-10-INSB-05-01

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2022-04-27
    Changes: Database references