4BRH

Legionella pneumophila NTPDase1 crystal form II (closed) in complex with MG AND THIAMINE PHOSPHOVANADATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Crystallographic snapshots along the reaction pathway of nucleoside triphosphate diphosphohydrolases.

Zebisch, M.Krauss, M.Schafer, P.Lauble, P.Strater, N.

(2013) Structure 21: 1460-1475

  • DOI: https://doi.org/10.1016/j.str.2013.05.016
  • Primary Citation of Related Structures:  
    4BQZ, 4BR0, 4BR2, 4BR4, 4BR5, 4BR7, 4BR9, 4BRA, 4BRC, 4BRD, 4BRE, 4BRF, 4BRG, 4BRH, 4BRI, 4BRK, 4BRL, 4BRM, 4BRN, 4BRO, 4BRP, 4BRQ

  • PubMed Abstract: 

    In vertebrates, membrane-bound ecto-nucleoside triphosphate diphosphohydrolases (NTPDases) on the cell surface are responsible for signal conversion and termination in purinergic signaling by extracellular nucleotides. Here we present apo and complex structures of the rat NTPDase2 extracellular domain and Legionella pneumophila NTPDase1, including a high-resolution structure with a transition-state analog. Comparison of ATP and ADP binding modes shows how NTPDases engage the same catalytic site for hydrolysis of nucleoside triphosphates and diphosphates. We find that this dual specificity is achieved at the expense of base specificity. Structural and mutational studies indicate that a conserved active-site water is replaced by the phosphate product immediately after phosphoryl transfer. Partial base specificity for purines in LpNTPDase1 is based on a different intersubunit base binding site for pyrimidine bases. A comparison of the bacterial enzyme in six independent crystal forms shows that NTPDases can undergo a domain closure motion of at least 17°.


  • Organizational Affiliation

    Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Faculty of Chemistry and Mineralogy, University of Leipzig, 04103 Leipzig, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I
A, B
368Legionella pneumophilaMutation(s): 0 
EC: 3.6.1.5
UniProt
Find proteins for Q5ZUA2 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZUA2 
Go to UniProtKB:  Q5ZUA2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZUA2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DVT
Query on DVT

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
DECAVANADATE
O28 V10
WOYKCMUEHQAMTC-UHFFFAOYSA-N
TMV
Query on TMV

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C [auth A],
H [auth B]
THIAMINE-PHOSPHOVANADATE
C12 H21 N4 O8 P S V
FXAJDHPXAUOYGO-UHFFFAOYSA-J
MES
Query on MES

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL
Query on GOL

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

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G [auth A],
M [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.435α = 90
b = 85.759β = 106.44
c = 72.306γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references
  • Version 1.2: 2013-12-25
    Changes: Structure summary
  • Version 2.0: 2019-01-30
    Changes: Atomic model, Data collection, Database references