5LDB

Crystal Structure of Polyphosphate Kinase from Meiothermus ruber bound to ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

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

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

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

  • DOI: https://doi.org/10.1073/pnas.1710741115
  • Primary Citation of Related Structures:  
    5LC9, 5LCD, 5LD1, 5LDB, 5LL0, 5LLB, 5LLF, 5MAQ, 5O6K, 5O6M

  • PubMed 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 Mg 2+ 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.


  • Organizational Affiliation

    Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyphosphate:AMP phosphotransferase
A, B, C, D
287Meiothermus ruber H328Mutation(s): 0 
Gene Names: MrH_2468
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
M [auth C],
O [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
N [auth C],
P [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
L [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
Q [auth D],
R [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 165.619α = 90
b = 165.619β = 90
c = 95.15γ = 90
Software Package:
Software NamePurpose
autoPROCdata collection
Aimlessdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2018-03-21
    Changes: Database references
  • Version 1.2: 2018-04-11
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description