7EPQ

Crystal structure of exopolyphosphatase (PPX) from Porphyromonas gingivalis in complex with sulfate and magnesium ions

Summary for 7EPQ

• Entry DOI: 10.2210/pdb7epq/pdb
• Descriptor: Putative exopolyphosphatase, SULFATE ION, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: polyphosphate, exopolyphosphatase, complex, ppx/gppa, metal binding protein
• Biological source: Porphyromonas gingivalis ATCC 33277
• Total number of polymer chains: 2
• Total formula weight: 69346.88

Authors

Zhang, A. (deposition date: 2021-04-27, release date: 2022-05-11, Last modification date: 2023-11-29)

Primary citation

Zhang, A.,Lu, Z.,Xu, Y.,Qi, T.,Li, W.,Zhang, L.,Cui, Z.
The structure of exopolyphosphatase (PPX) from Porphyromonas gingivalis in complex with substrate analogs and magnesium ions reveals the basis for polyphosphate processivity.
J.Struct.Biol., 213:107767-107767, 2021

PubMed Abstract: The enzymes exopolyphosphatase/guanosine pentaphosphate phosphohydrolase (PPX/GppA) play important roles in the bacterial stringent response. PPX degrades inorganic polyphosphate (polyP), a polymer composed of a few to hundreds of phosphate residues supporting cell survival in the stationary phase. The crystal structure of PPX from Porphyromonas gingivalis (PgPPX) in complex with catalytic magnesium ions and several sulfate ions was solved. PgPPX contained two domains and represented a "closed" configuration. Four sulfate ions forming a linear dispersed chain were observed in the aqueduct of the PPX dimer, which the long polyP chain most likely occupied. The side chain of R255 stretched into the cavity where polyP could be located, obstructing the entrance of larger substrates such as NTP and NDP. This study provided the first view into the structure of the PPX/GppA homolog in complex with magnesium ions and substrate analogs and explained how PgPPX implemented its functionality.

PubMed: 34214602
DOI: 10.1016/j.jsb.2021.107767

Experimental method

X-RAY DIFFRACTION (2.2 Å)