7SMG

Crystal structure of a (p)ppApp hydrolase from Bacteroides caccae

PDB DOI: https://doi.org/10.2210/pdb7SMG/pdb

Classification: HYDROLASE
Organism(s): Bacteroides caccae ATCC 43185
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-10-25 Released: 2022-11-09
Deposition Author(s): Ahmad, S., Alexei, A.G., Tsang, K.K., Trilesky, S., Kim, Y., Whitney, J.C.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.234
R-Value Work: 0.201
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Identification of a broadly conserved family of enzymes that hydrolyze (p)ppApp.

Ahmad, S., Gordon, I.J., Tsang, K.K., Alexei, A.G., Sychantha, D., Colautti, J., Trilesky, S.L., Kim, Y., Wang, B., Whitney, J.C.

(2023) Proc Natl Acad Sci U S A 120: e2213771120-e2213771120

PubMed: 36989297 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1073/pnas.2213771120
Primary Citation of Related Structures:
7SMG

PubMed Abstract:
Bacteria produce a variety of nucleotide second messengers to adapt to their surroundings. Although chemically similar, the nucleotides guanosine penta- and tetraphosphate [(p)ppGpp] and adenosine penta- and tetraphosphate [(p)ppApp] have distinct functions in bacteria. (p)ppGpp mediates survival under nutrient-limiting conditions and its intracellular levels are regulated by synthetases and hydrolases belonging to the RelA-SpoT homolog (RSH) family of enzymes. By contrast, (p)ppApp is not known to be involved in nutrient stress responses and is synthesized by RSH-resembling toxins that inhibit the growth of bacterial cells. However, it remains unclear whether there exists a family of hydrolases that specifically act on (p)ppApp to reverse its toxic effects. Here, we present the structure and biochemical characterization of adenosine 3'-pyrophosphohydrolase 1 (Aph1), the founding member of a monofunctional (p)ppApp hydrolase family of enzymes. Our work reveals that Aph1 adopts a histidine-aspartate (HD)-domain fold characteristic of phosphohydrolase metalloenzymes and its activity mitigates the growth inhibitory effects of (p)ppApp-synthesizing toxins. Using an informatic approach, we identify over 2,000 putative (p)ppApp hydrolases that are widely distributed across bacterial phyla and found in diverse genomic contexts, and we demonstrate that 12 representative members hydrolyze ppApp. In addition, our in silico analyses reveal a unique molecular signature that is specific to (p)ppApp hydrolases, and we show that mutation of two residues within this signature broadens the specificity of Aph1 to promiscuously hydrolyze (p)ppGpp in vitro. Overall, our findings indicate that like (p)ppGpp hydrolases, (p)ppApp hydrolases are widespread in bacteria and may play important and underappreciated role(s) in bacterial physiology.

Organizational Affiliation

Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada.

Macromolecule Content

Total Structure Weight: 70.96 kDa
Atom Count: 4,963
Modelled Residue Count: 571
Deposited Residue Count: 596
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(p)ppApp hydrolase	A, B, C, D	149	Bacteroides caccae ATCC 43185	Mutation(s): 0 Gene Names: BACCAC_01146
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D]	E [auth A] F [auth A] I [auth B] J [auth B] K [auth B] E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], O [auth C], P [auth C], S [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain R [auth C] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C]	H [auth A], M [auth B], N [auth B], R [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D]	G [auth A], L [auth B], Q [auth C], T [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain T [auth D]