9GRN | pdb_00009grn

Crystal structure of the engineered C-terminal phosphatase domain from Saccharomyces cerevisiae Vip1 (apo, loop deletion residues 848-918)

PDB DOI: https://doi.org/10.2210/pdb9GRN/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2024-09-11 Released: 2025-02-26
Deposition Author(s): Raia, P., Lee, K., Hothorn, M.
Funding Organization(s): Swiss National Science Foundation, Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.294 (Depositor), 0.296 (DCC)
R-Value Work:
0.244 (Depositor), 0.245 (DCC)
R-Value Observed:
0.247 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

A small signaling domain controls PPIP5K phosphatase activity in phosphate homeostasis.

Raia, P., Lee, K., Bartsch, S.M., Rico-Resendiz, F., Portugal-Calisto, D., Vadas, O., Panse, V.G., Fiedler, D., Hothorn, M.

(2025) Nat Commun 16: 1753-1753

PubMed: 39966396 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-025-56937-0
Primary Citation Related Structures:
9GR8, 9GRH, 9GRN, 9GRO

PubMed Abstract:
Inositol pyrophosphates (PP-InsPs) are eukaryotic nutrient messengers. The N-terminal kinase domain of diphosphoinositol pentakisphosphate kinase (PPIP5K) generates the messenger 1,5-InsP ₈, the C-terminal phosphatase domain catalyzes PP-InsP breakdown. The balance between kinase and phosphatase activities regulates 1,5-InsP ₈ levels. Here, we present crystal structures of the apo and substrate-bound PPIP5K phosphatase domain from S. cerevisiae (ScVip1 ^PD). ScVip1 ^PD is a phytase-like inositol 1-pyrophosphate histidine phosphatase with two conserved catalytic motifs. The enzyme has a strong preference for 1,5-InsP ₈ and is inhibited by inorganic phosphate. It contains an α-helical insertion domain stabilized by a structural Zn ²⁺ binding site, and a unique GAF domain that channels the substrate to the active site. Mutations that alter the active site, restrict the movement of the GAF domain, or change the substrate channel's charge inhibit the enzyme activity in vitro, and Arabidopsis VIH2 in planta. Our work reveals the structure, enzymatic mechanism and regulation of eukaryotic PPIP5K phosphatases.

Organizational Affiliation

Structural Plant Biology Laboratory, Department of Plant Sciences, University of Geneva, Geneva, Switzerland.

Macromolecule Content

Total Structure Weight: 237.76 kDa
Atom Count: 15,726
Modeled Residue Count: 1,895
Deposited Residue Count: 2,028
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase	A, B, C, D	507	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: VIP1, YLR410W EC: 2.7.4.24
UniProt
Find proteins for Q06685 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06685 Go to UniProtKB: Q06685
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q06685
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LPC Query on LPC Download:Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B] mmCIF format, chain T [auth B]	T [auth B]	[1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE C₂₂ H₄₇ N O₇ P VXUOFDJKYGDUJI-OAQYLSRUSA-O		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain F [auth A] SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain Q [auth B] SDF format, chain S [auth B] SDF format, chain U [auth B] SDF format, chain Y [auth C] SDF format, chain V [auth B] SDF format, chain R [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain GA [auth C] SDF format, chain EA [auth C] SDF format, chain E [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain V [auth B] MOL2 format, chain R [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain E [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth B] mmCIF format, chain U [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain V [auth B] mmCIF format, chain R [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain E [auth A]	AA [auth C] E [auth A] EA [auth C] F [auth A] FA [auth C] AA [auth C], E [auth A], EA [auth C], F [auth A], FA [auth C], G [auth A], GA [auth C], H [auth A], I [auth A], J [auth A], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], N [auth A], Q [auth B], R [auth B], S [auth B], U [auth B], V [auth B], Y [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain Y [auth C] Interactions & Density Focus chain AA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain Y [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain JA [auth C] SDF format, chain O [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain PA [auth D] SDF format, chain P [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain P [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain P [auth A]	JA [auth C] O [auth A] P [auth A] PA [auth D] W [auth B] JA [auth C], O [auth A], P [auth A], PA [auth D], W [auth B], X [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain JA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth D] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain JA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth D] Focus chain W [auth B] Focus chain X [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain IA [auth C] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain Z [auth C] SDF format, chain HA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain HA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain HA [auth C]	BA [auth C] CA [auth C] DA [auth C] HA [auth C] IA [auth C] BA [auth C], CA [auth C], DA [auth C], HA [auth C], IA [auth C], MA [auth D], NA [auth D], OA [auth D], Z [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain Z [auth C] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain Z [auth C]