24IO | pdb_000024io

Crystal structure of the RelSeq N-terminal domain from Streptococcus equisimilis in complex with pppGpp

PDB DOI: https://doi.org/10.2210/pdb24IO/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus dysgalactiae subsp. equisimilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2026-03-04 Released: 2026-03-18
Deposition Author(s): Korban, S.A., Kasatsky, P.S., Spiridonova, Z.A., Gurzhiy, V.V., Paleskava, A.V., Konevega, A.L., Vinogradova, D.S.
Funding Organization(s): Russian Science Foundation, St. Petersburg State University

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.299 (Depositor), 0.294 (DCC)
R-Value Work:
0.242 (Depositor), 0.239 (DCC)
R-Value Observed:
0.245 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Structural Basis of pppGpp Binding to the N-Terminal Domain of the Bifunctional RelA/SpoT Homolog Rel Seq : Crystal Structure and MD Analysis.

Korban, S.A., Spiridonova, Z.A., Kasatsky, P.S., Shvetsov, A.V., Gurzhiy, V.V., Paleskava, A., Kulminskaya, A.A., Konevega, A.L., Vinogradova, D.S.

(2026) Int J Mol Sci 27

PubMed: 42353222 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3390/ijms27125509
Primary Citation Related Structures:
24IO

PubMed Abstract:
RelA/SpoT homologue family enzymes participate in controlling the cellular levels of the alarmone (p)ppGpp, thereby activating the stringent response and promoting survival under stress conditions. These proteins contain an N-terminal catalytic domain and a C-terminal regulatory domain. They catalyze both the synthesis of ppGpp/pppGpp from ATP and GDP/GTP and their hydrolysis to GDP/GTP and pyrophosphate. Here, we report the crystal structure of the N-terminal domain of Rel from Streptococcus equisimilis in complex with pppGpp at 3.2 Å resolution. The asymmetric unit contains a dimer with asymmetric ligation: pppGpp occupies only the synthetase site in one monomer, whereas in the other monomer, it is bound in both the hydrolase and synthetase sites. The two monomers exhibit distinct conformational states, with pronounced rearrangements of the flexible loops surrounding the binding pockets, including the α2/α3 and α8/α9 loops that act as steric gates. Molecular dynamics simulations support the dual binding arrangement and reveal additional probable transient binding sites, including a region in the linker between hydrolase and synthetase subdomains. These findings provide a structural framework for understanding how pppGpp binding modulates the opposing catalytic activities of bifunctional Rel enzymes and suggest possible mechanisms for (p)ppGpp-mediated autoregulation.

Organizational Affiliation

Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", Gatchina 188300, Russia.

Macromolecule Content

Total Structure Weight: 94.79 kDa
Atom Count: 5,519
Modeled Residue Count: 657
Deposited Residue Count: 786
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional (p)ppGpp synthase/hydrolase RelA	A, B	393	Streptococcus dysgalactiae subsp. equisimilis	Mutation(s): 0 Gene Names: relA, rel EC: 2.7.6.5 (PDB Primary Data), 3.1.7.2 (PDB Primary Data)
UniProt
Find proteins for Q54089 (Streptococcus dysgalactiae subsp. equisimilis) Explore Q54089 Go to UniProtKB: Q54089
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q54089
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0O2 (Subject of Investigation/LOI) Query on 0O2 Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain P [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain P [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	P [auth A], T [auth B], U [auth B]	guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate) C₁₀ H₁₈ N₅ O₂₀ P₅ KCPMACXZAITQAX-UUOKFMHZSA-N		Interactions Focus chain P [auth A] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain P [auth A] Focus chain T [auth B] Focus chain U [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain V [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain V [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain V [auth B]	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], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], O [auth A], Q [auth A], R [auth A], V [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] 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 O [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain V [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] 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 O [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain V [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain S [auth B] MOL2 format, chain N [auth A] MOL2 format, chain S [auth B] mmCIF format, chain N [auth A] mmCIF format, chain S [auth B]	N [auth A], S [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain S [auth B] Interactions & Density Focus chain N [auth A] Focus chain S [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain W [auth B] MOL2 format, chain W [auth B] mmCIF format, chain W [auth B]	W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain W [auth B] Interactions & Density Focus chain W [auth B]