PDBsum entry 5lcd

Transferase

PDB id: 5lcd

Contents

Protein chains

256 a.a.

Ligands

AMP ×4

PO4 ×4

SO4 ×10

Metals

_MG

Waters ×76

PDB id:

5lcd

Name:

Transferase

Title:

Structure of polyphosphate kinase from meiothermus ruber bound to amp

Structure:

Polyphosphate:amp phosphotransferase. Chain: a, b, c, d. Engineered: yes. Other_details: the residues met -19 to his 0 have been introduced by the expression tag of pet28a met 1 in chains a,b,c and d is the initiating methionine

Source:

Meiothermus ruber h328. Organism_taxid: 1297799. Gene: mrh_2468. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.66Å R-factor: 0.210 R-free: 0.253

Authors:

S.Gerhardt,O.Einsle,F.Kemper,N.Schwarzer

Key ref:

A.E.Parnell et al. (2018). Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures. Proc Natl Acad Sci U S A, 115, 3350-3355. PubMed id: 29531036

Date:

21-Jun-16 Release date: 21-Jun-17

Protein chains

A0A0S7ASE9  () -

Proc Natl Acad Sci U S A 115:3350-3355 (2018)

PubMed id: 29531036

Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures.

A.E.Parnell, S.Mordhorst, F.Kemper, M.Giurrandino, J.P.Prince, N.J.Schwarzer, A.Hofer, D.Wohlwend, H.J.Jessen, S.Gerhardt, O.Einsle, P.C.F.Oyston, J.N.Andexer, P.L.Roach.

ABSTRACT

Inorganic polyphosphate is a ubiquitous, linear biopolymer built of up to thousands of phosphate residues that are linked by energy-rich phosphoanhydride bonds. Polyphosphate kinases of the family 2 (PPK2) use polyphosphate to catalyze the reversible phosphorylation of nucleotide phosphates and are highly relevant as targets for new pharmaceutical compounds and as biocatalysts for cofactor regeneration. PPK2s can be classified based on their preference for nucleoside mono- or diphosphates or both. The detailed mechanism of PPK2s and the molecular basis for their substrate preference is unclear, which is mainly due to the lack of high-resolution structures with substrates or substrate analogs. Here, we report the structural analysis and comparison of a class I PPK2 (ADP-phosphorylating) and a class III PPK2 (AMP- and ADP-phosphorylating), both complexed with polyphosphate and/or nucleotide substrates. Together with complementary biochemical analyses, these define the molecular basis of nucleotide specificity and are consistent with a Mg²⁺catalyzed in-line phosphoryl transfer mechanism. This mechanistic insight will guide the development of PPK2 inhibitors as potential antibacterials or genetically modified PPK2s that phosphorylate alternative substrates.