3RL4

Rat metallophosphodiesterase MPPED2 G252H Mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Unique utilization of a phosphoprotein phosphatase fold by a mammalian phosphodiesterase associated with WAGR syndrome.

Dermol, U.Janardan, V.Tyagi, R.Visweswariah, S.S.Podobnik, M.

(2011) J Mol Biol 412: 481-494

  • DOI: 10.1016/j.jmb.2011.07.060
  • Primary Citation of Related Structures:  
    3RL5, 3RL3, 3RL4

  • PubMed Abstract: 
  • Metallophosphoesterase-domain-containing protein 2 (MPPED2) is a highly evolutionarily conserved protein with orthologs found from worms to humans. The human MPPED2 gene is found in a region of chromosome 11 that is deleted in patients with WAGR (Wilms tumor, aniridia, genitourinary anomalies, and mental retardation) syndrome, and MPPED2 may function as a tumor suppressor ...

    Metallophosphoesterase-domain-containing protein 2 (MPPED2) is a highly evolutionarily conserved protein with orthologs found from worms to humans. The human MPPED2 gene is found in a region of chromosome 11 that is deleted in patients with WAGR (Wilms tumor, aniridia, genitourinary anomalies, and mental retardation) syndrome, and MPPED2 may function as a tumor suppressor. However, the precise cellular roles of MPPED2 are unknown, and its low phosphodiesterase activity suggests that substrate hydrolysis may not be its prime function. We present here the structures of MPPED2 and two mutants, which show that the poor activity of MPPED2 is not only a consequence of the substitution of an active-site histidine residue by glycine but also due to binding of AMP or GMP to the active site. This feature, enhanced by structural elements of the protein, allows MPPED2 to utilize the conserved phosphoprotein-phosphatase-like fold in a unique manner, ensuring that its enzymatic activity can be combined with a possible role as a scaffolding or adaptor protein.


    Related Citations: 
    • Characterization of an evolutionatily conserved metallophosphoesterase that is expressed in the fetal brain and associated with the WAGR syndrome
      Tyagi, R., Shenoy, A.R., Visweswariah, S.S.
      (2009) J Biol Chem 284: 5217
    • A mycobacterial cyclic AMP phosphodiesterase that moonlights as a modifier of cell wall permeability
      Podobnik, M., Tyagi, R., Matange, N., Dermol, U., Gupta, A.K., Mattoo, R., Seshardi, K., Visweswariah, S.S.
      (2009) J Biol Chem 284: 32846
    • Structural and biochemical analysis of the Rv0805 cyclic nucleotide phosphodiesterase from Mycobacterium tuberculosis
      Shenoy, A.R., Capuder, M., Draskovic, P., Lamba, D., Visweswariah, S.S., Podobnik, M.
      (2007) J Mol Biol 365: 211
    • The Rv0805 Gene from Mycobacterium tuberculosis Encodes a 3',5'-Cyclic Nucleotide Phosphodiesterase: Biochemical and Mutational Analysis
      Shenoy, A.R., Sreenath, N., Podobnik, M., Kovacevic, M., Visweswariah, S.S.
      (2005) Biochemistry 44: 15695

    Organizational Affiliation

    Laboratory for Biosynthesis and Biotransformation, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Metallophosphoesterase MPPED2A296Rattus norvegicusMutation(s): 1 
Gene Names: Mpped2
EC: 3.1
UniProt
Find proteins for B1WBP0 (Rattus norvegicus)
Explore B1WBP0 
Go to UniProtKB:  B1WBP0
Protein Feature View
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  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5GPIC50:  3800   nM  Binding MOAD
5GPIC50 :  3800   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.06α = 90
b = 69.385β = 102.96
c = 47.234γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-10
    Type: Initial release
  • Version 1.1: 2012-01-04
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description