7PV7 | pdb_00007pv7

Crystal structure of dimeric Porphyromonas gingivalis PorX, a type 9 secretion system response regulator.

PDB DOI: https://doi.org/10.2210/pdb7PV7/pdb

Classification: SIGNALING PROTEIN
Organism(s): Porphyromonas gingivalis W83
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-10-01 Released: 2022-12-14
Deposition Author(s): Schmitz, C.A., Madej, M., Potempa, J., Sola, M.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.215 (Depositor)
R-Value Work:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Response regulator PorX coordinates oligonucleotide signalling and gene expression to control the secretion of virulence factors.

Schmitz, C., Madej, M., Nowakowska, Z., Cuppari, A., Jacula, A., Ksiazek, M., Mikruta, K., Wisniewski, J., Pudelko-Malik, N., Saran, A., Zeytuni, N., Mlynarz, P., Lamont, R.J., Uson, I., Siksnys, V., Potempa, J., Sola, M.

(2022) Nucleic Acids Res 50: 12558-12577

PubMed: 36464236 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/nar/gkac1103
Primary Citation Related Structures:
7PV7, 7PVA

PubMed Abstract:
The PglZ family of proteins belongs to the alkaline phosphatase superfamily, which consists of metallohydrolases with limited sequence identity but similar metal-coordination architectures in otherwise divergent active sites. Proteins with a well-defined PglZ domain are ubiquitous among prokaryotes as essential components of BREX phage defence systems and two-component systems (TCSs). Whereas other members of the alkaline phosphatase superfamily are well characterized, the activity, structure and biological function of PglZ family proteins remain unclear. We therefore investigated the structure and function of PorX, an orphan response regulator of the Porphyromonas gingivalis TCS containing a putative PglZ effector domain. The crystal structure of PorX revealed a canonical receiver domain, a helical bundle, and an unprecedented PglZ domain, similar to the general organization of the phylogenetically related BREX-PglZ proteins. The PglZ domain of PorX features an active site cleft suitable for large substrates. An extensive search for substrates revealed that PorX is a phosphodiesterase that acts on cyclic and linear oligonucleotides, including signalling molecules such as cyclic oligoadenylates. These results, combined with mutagenesis, biophysical and enzymatic analysis, suggest that PorX coordinates oligonucleotide signalling pathways and indirectly regulates gene expression to control the secretion of virulence factors.

Organizational Affiliation

Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Barcelona E-08028, Spain.

Macromolecule Content

Total Structure Weight: 251.16 kDa
Atom Count: 18,453
Modeled Residue Count: 2,054
Deposited Residue Count: 2,092
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Response regulator	A [auth D], B [auth C], C [auth B], D [auth A]	523	Porphyromonas gingivalis W83	Mutation(s): 0 Gene Names: PG_0928
UniProt
Find proteins for Q7MVV4 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MVV4 Go to UniProtKB: Q7MVV4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7MVV4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain QA [auth A] SDF format, chain Q [auth C] SDF format, chain PA [auth A] SDF format, chain P [auth C] SDF format, chain OA [auth A] SDF format, chain NA [auth A] SDF format, chain MA [auth A] SDF format, chain H [auth D] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain R [auth C] MOL2 format, chain QA [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain PA [auth A] MOL2 format, chain P [auth C] MOL2 format, chain OA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain H [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain R [auth C] mmCIF format, chain QA [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain PA [auth A] mmCIF format, chain P [auth C] mmCIF format, chain OA [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain H [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] H [auth D] AA [auth B], BA [auth B], CA [auth B], DA [auth B], H [auth D], MA [auth A], NA [auth A], OA [auth A], P [auth C], PA [auth A], Q [auth C], QA [auth A], R [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain H [auth D] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain P [auth C] Focus chain PA [auth A] Focus chain Q [auth C] Focus chain QA [auth A] Focus chain R [auth C] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain H [auth D] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain P [auth C] Focus chain PA [auth A] Focus chain Q [auth C] Focus chain QA [auth A] Focus chain R [auth C]
BEF (Subject of Investigation/LOI) Query on BEF Download:Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain W [auth C] SDF format, chain TA [auth A] SDF format, chain L [auth C] SDF format, chain K [auth D] SDF format, chain IA [auth A] SDF format, chain HA [auth B] SDF format, chain E [auth D] MOL2 format, chain X [auth B] MOL2 format, chain W [auth C] MOL2 format, chain TA [auth A] MOL2 format, chain L [auth C] MOL2 format, chain K [auth D] MOL2 format, chain IA [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain E [auth D] mmCIF format, chain X [auth B] mmCIF format, chain W [auth C] mmCIF format, chain TA [auth A] mmCIF format, chain L [auth C] mmCIF format, chain K [auth D] mmCIF format, chain IA [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain E [auth D]	E [auth D] HA [auth B] IA [auth A] K [auth D] L [auth C] E [auth D], HA [auth B], IA [auth A], K [auth D], L [auth C], TA [auth A], W [auth C], X [auth B]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain E [auth D] Focus chain HA [auth B] Focus chain IA [auth A] Focus chain K [auth D] Focus chain L [auth C] Focus chain TA [auth A] Focus chain W [auth C] Focus chain X [auth B] Interactions & Density Focus chain E [auth D] Focus chain HA [auth B] Focus chain IA [auth A] Focus chain K [auth D] Focus chain L [auth C] Focus chain TA [auth A] Focus chain W [auth C] Focus chain X [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain LA [auth A] SDF format, chain KA [auth A] SDF format, chain G [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain LA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain G [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain LA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain G [auth D]	G [auth D] KA [auth A] LA [auth A] N [auth C] O [auth C] G [auth D], KA [auth A], LA [auth A], N [auth C], O [auth C], Z [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth D] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain Z [auth B] Interactions & Density Focus chain G [auth D] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain Z [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain RA [auth A] SDF format, chain I [auth D] SDF format, chain EA [auth B] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain RA [auth A] MOL2 format, chain I [auth D] MOL2 format, chain EA [auth B] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain RA [auth A] mmCIF format, chain I [auth D] mmCIF format, chain EA [auth B]	EA [auth B] I [auth D] RA [auth A] S [auth C] T [auth C] EA [auth B], I [auth D], RA [auth A], S [auth C], T [auth C], U [auth C]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain I [auth D] Focus chain RA [auth A] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain EA [auth B] Focus chain I [auth D] Focus chain RA [auth A] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain V [auth C] SDF format, chain SA [auth A] SDF format, chain M [auth C] SDF format, chain JA [auth A] SDF format, chain J [auth D] SDF format, chain GA [auth B] SDF format, chain FA [auth B] SDF format, chain F [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain V [auth C] MOL2 format, chain SA [auth A] MOL2 format, chain M [auth C] MOL2 format, chain JA [auth A] MOL2 format, chain J [auth D] MOL2 format, chain GA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain F [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain V [auth C] mmCIF format, chain SA [auth A] mmCIF format, chain M [auth C] mmCIF format, chain JA [auth A] mmCIF format, chain J [auth D] mmCIF format, chain GA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain F [auth D]	F [auth D] FA [auth B] GA [auth B] J [auth D] JA [auth A] F [auth D], FA [auth B], GA [auth B], J [auth D], JA [auth A], M [auth C], SA [auth A], V [auth C], Y [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth D] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain J [auth D] Focus chain JA [auth A] Focus chain M [auth C] Focus chain SA [auth A] Focus chain V [auth C] Focus chain Y [auth B] Interactions & Density Focus chain F [auth D] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain J [auth D] Focus chain JA [auth A] Focus chain M [auth C] Focus chain SA [auth A] Focus chain V [auth C] Focus chain Y [auth B]