5O58

Structure of the inactive T.maritima PDE (TM1595) D80N D154N mutant with substrate 5'-pApG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and Biophysical Analysis of the Soluble DHH/DHHA1-Type Phosphodiesterase TM1595 from Thermotoga maritima.

Drexler, D.J.Muller, M.Rojas-Cordova, C.A.Bandera, A.M.Witte, G.

(2017) Structure 25: 1887-1897.e4

  • DOI: 10.1016/j.str.2017.10.001
  • Primary Citation of Related Structures:  5O1U, 5O25, 5O4Z, 5O70, 5O7F

  • PubMed Abstract: 
  • The concentration of messenger molecules in bacterial cells needs to be tightly regulated. This can be achieved by either controlling the synthesis rate, degradation, or export by specific transporters, respectively. The regulation of the essential s ...

    The concentration of messenger molecules in bacterial cells needs to be tightly regulated. This can be achieved by either controlling the synthesis rate, degradation, or export by specific transporters, respectively. The regulation of the essential second messenger c-di-AMP is achieved by modulation of the diadenylate cyclase activity as well as by specific phosphodiesterases that hydrolyze c-di-AMP in the cell. We provide here structural and biochemical data on the DHH-type phosphodiesterase TmPDE (TM1595) from Thermotoga maritima. Our analysis shows that TmPDE is preferentially degrading linear dinucleotides, such as 5'-pApA, 5'-pGpG, and 5'-pApG, compared with cyclic dinucleotide substrates. The high-resolution structural data provided here describe all steps of the PDE reaction: the ligand-free enzyme, two substrate-bound states, and three post-reaction states. We can furthermore show that Pde2 from Streptococcus pneumoniae shares both structural features and substrate specificity based on small-angle X-ray scattering data and biochemical assays.


    Organizational Affiliation

    Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
phosphodiesterase TM1595
A
338N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*AP*G)-3')B2synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

Download SDF File 
Download CCD File 
A
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.158 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 70.370α = 90.00
b = 88.340β = 90.00
c = 124.270γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
German Research FoundationGermany3717/3-1
German Research FoundationGermanyGRK1721

Revision History 

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Database references
  • Version 1.2: 2017-12-06
    Type: Database references
  • Version 1.3: 2017-12-13
    Type: Database references