7P0H | pdb_00007p0h

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

PDB DOI: https://doi.org/10.2210/pdb7P0H/pdb

Classification: RECOMBINATION
Organism(s): synthetic construct, Helicobacter pylori 26695
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2021-06-29 Released: 2022-04-06
Deposition Author(s): Celma, L., Walbott, H., Legrand, P., Quevillon-Cheruel, S.
Funding Organization(s): French Infrastructure for Integrated Structural Biology (FRISBI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.245 (Depositor), 0.257 (DCC)
R-Value Work:
0.221 (Depositor), 0.229 (DCC)
R-Value Observed:
0.222 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 35414142 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-022-29494-z
Primary Citation 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 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 Paris-Saclay, CEA, Stabilité Génétique Cellules Souches et Radiations, Institut de Biologie François Jacob, F-92260, Fontenay aux Roses, France.

Macromolecule Content

Total Structure Weight: 191.79 kDa
Atom Count: 13,138
Modeled Residue Count: 1,644
Deposited Residue Count: 1,708
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Helicobacter pylori ComF fused to an artificial alphaREP crystallization helper (named B2)	A, B, C, D	427	synthetic construct, Helicobacter 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O26008
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PRP (Subject of Investigation/LOI) Query on PRP Download:Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain P [auth B] SDF format, chain F [auth A] SDF format, chain DA [auth D] MOL2 format, chain V [auth C] MOL2 format, chain P [auth B] MOL2 format, chain F [auth A] MOL2 format, chain DA [auth D] mmCIF format, chain V [auth C] mmCIF format, chain P [auth B] mmCIF format, chain F [auth A] mmCIF format, chain DA [auth D]	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		Interactions Focus chain DA [auth D] Focus chain F [auth A] Focus chain P [auth B] Focus chain V [auth C] Interactions & Density Focus chain DA [auth D] Focus chain F [auth A] Focus chain P [auth B] Focus chain V [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain GA [auth D] SDF format, chain FA [auth D] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain AA [auth C]	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		Interactions Focus chain AA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain O [auth B] SDF format, chain E [auth A] SDF format, chain CA [auth D] MOL2 format, chain U [auth C] MOL2 format, chain O [auth B] MOL2 format, chain E [auth A] MOL2 format, chain CA [auth D] mmCIF format, chain U [auth C] mmCIF format, chain O [auth B] mmCIF format, chain E [auth A] mmCIF format, chain CA [auth D]	CA [auth D], E [auth A], O [auth B], U [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain E [auth A] Focus chain O [auth B] Focus chain U [auth C] Interactions & Density Focus chain CA [auth D] Focus chain E [auth A] Focus chain O [auth B] Focus chain U [auth C]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain T [auth B] SDF format, chain Q [auth B] SDF format, chain N [auth A] SDF format, chain HA [auth D] SDF format, chain G [auth A] SDF format, chain EA [auth D] SDF format, chain BA [auth C] MOL2 format, chain W [auth C] MOL2 format, chain T [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain BA [auth C] mmCIF format, chain W [auth C] mmCIF format, chain T [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain BA [auth C]	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		Interactions Focus chain BA [auth C] Focus chain EA [auth D] Focus chain G [auth A] Focus chain HA [auth D] Focus chain N [auth A] Focus chain Q [auth B] Focus chain T [auth B] Focus chain W [auth C] Interactions & Density Focus chain BA [auth C] Focus chain EA [auth D] Focus chain G [auth A] Focus chain HA [auth D] Focus chain N [auth A] Focus chain Q [auth B] Focus chain T [auth B] Focus chain W [auth C]