6N1C

Crystal structure of Inorganic pyrophosphatase from Legionella pneumophila Philadelphia 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Characterization of a family I inorganic pyrophosphatase from Legionella pneumophila Philadelphia 1.

Moorefield, J.Konuk, Y.Norman, J.O.Abendroth, J.Edwards, T.E.Lorimer, D.D.Mayclin, S.J.Staker, B.L.Craig, J.K.Barett, K.F.Barrett, L.K.Van Voorhis, W.C.Myler, P.J.McLaughlin, K.J.

(2023) Acta Crystallogr F Struct Biol Commun 79: 257-266

  • DOI: https://doi.org/10.1107/S2053230X23008002
  • Primary Citation of Related Structures:  
    6N1C

  • PubMed Abstract: 

    Inorganic pyrophosphate (PP i ) is generated as an intermediate or byproduct of many fundamental metabolic pathways, including DNA/RNA synthesis. The intracellular concentration of PP i must be regulated as buildup can inhibit many critical cellular processes. Inorganic pyrophosphatases (PPases) hydrolyze PP i into two orthophosphates (P i ), preventing the toxic accumulation of the PP i byproduct in cells and making P i available for use in biosynthetic pathways. Here, the crystal structure of a family I inorganic pyrophosphatase from Legionella pneumophila is reported at 2.0 Å resolution. L. pneumophila PPase (LpPPase) adopts a homohexameric assembly and shares the oligonucleotide/oligosaccharide-binding (OB) β-barrel core fold common to many other bacterial family I PPases. LpPPase demonstrated hydrolytic activity against a general substrate, with Mg 2+ being the preferred metal cofactor for catalysis. Legionnaires' disease is a severe respiratory infection caused primarily by L. pneumophila, and thus increased characterization of the L. pneumophila proteome is of interest.


  • Organizational Affiliation

    Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inorganic pyrophosphatase
A, B, C, D, E
A, B, C, D, E, F
186Legionella pneumophila subsp. pneumophila str. Philadelphia 1Mutation(s): 0 
Gene Names: ppalpg2764
EC: 3.6.1.1
UniProt
Find proteins for Q5ZRW2 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZRW2 
Go to UniProtKB:  Q5ZRW2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZRW2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MRD
Query on MRD

Download Ideal Coordinates CCD File 
K [auth B](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
I [auth A]
L [auth B]
M [auth C]
O [auth D]
Q [auth E]
I [auth A],
L [auth B],
M [auth C],
O [auth D],
Q [auth E],
R [auth E],
S [auth F]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
ALA
Query on ALA

Download Ideal Coordinates CCD File 
J [auth A],
P [auth E]
ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
N [auth D],
T [auth F]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.08α = 90
b = 119.94β = 109.59
c = 74.9γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MoRDaphasing
ARP/wARPmodel building
BUCCANEERmodel building
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-07-17
    Changes: Database references