9H8J | pdb_00009h8j

Crystal Structure of Polyphosphate kinase 2-II (PPK2-II) from Lysinibacillus fusiformis in apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.253 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Insights into Broad-Range Polyphosphate Kinase 2-II Enzymes Applicable for Pyrimidine Nucleoside Diphosphate Synthesis.

Kuge, M.Keppler, M.Friedrich, F.Saleem-Batcha, R.Winter, J.Prucker, I.Germer, P.Gerhardt, S.Einsle, O.Jung, M.Jessen, H.J.Andexer, J.N.

(2025) Chembiochem 26: e202400970-e202400970

  • DOI: https://doi.org/10.1002/cbic.202400970
  • Primary Citation of Related Structures:  
    9GP9, 9H8J, 9H8K, 9H8L

  • PubMed Abstract: 

    Polyphosphate kinases (PPK) play crucial roles in various biological processes, including energy storage and stress responses, through their interaction with inorganic polyphosphate (polyP) and the intracellular nucleotide pool. Members of the PPK family 2 (PPK2s) catalyse polyP‑consuming phosphorylation of nucleotides. In this study, we characterised two PPK2 enzymes from Bacillus cereus (BcPPK2) and Lysinibacillus fusiformis (LfPPK2) to investigate their substrate specificity and potential for selective nucleotide synthesis. Both enzymes exhibited a broad substrate scope, selectively converting over 85% of pyrimidine nucleoside monophosphates (NMPs) to nucleoside diphosphates (NDPs), while nucleoside triphosphate (NTP) formation was observed only with purine NMPs. Preparative enzymatic synthesis of cytidine diphosphate (CDP) was applied to achieve an yield of 49%. Finally, structural analysis of five crystal structures of BcPPK2 and LfPPK2 provided insights into their active sites and substrate interactions. This study highlights PPK2-II enzymes as promising biocatalysts for the efficient and selective synthesis of pyrimidine NDPs.


  • Organizational Affiliation
    • University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, GERMANY.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyphosphate kinaseA [auth B],
B [auth A],
C,
D
269Lysinibacillus fusiformisMutation(s): 0 
Gene Names: BG258_19905
UniProt
Find proteins for A0A1E4R1F9 (Lysinibacillus fusiformis)
Explore A0A1E4R1F9 
Go to UniProtKB:  A0A1E4R1F9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1E4R1F9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SIN
Query on SIN

Download Ideal Coordinates CCD File 
I [auth A]SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth B]
F [auth B]
G [auth A]
H [auth A]
J [auth C]
E [auth B],
F [auth B],
G [auth A],
H [auth A],
J [auth C],
K [auth C],
L [auth D],
M [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.253 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.112α = 90
b = 71.931β = 92.59
c = 97.69γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany527572100

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-02-12
    Changes: Database references
  • Version 1.2: 2025-03-12
    Changes: Database references