Cubic crystal form of PIR1 dual specificity phosphatase core

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 

Starting Model: experimental
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Structure of Human PIR1, an Atypical Dual-Specificity Phosphatase.

Sankhala, R.S.Lokareddy, R.K.Cingolani, G.

(2014) Biochemistry 53: 862-871

  • DOI: https://doi.org/10.1021/bi401240x
  • Primary Citation of Related Structures:  
    4MBB, 4NYH

  • PubMed Abstract: 

    PIR1 is an atypical dual-specificity phosphatase (DSP) that dephosphorylates RNA with a higher specificity than phosphoproteins. Here we report the atomic structure of a catalytically inactive mutant (C152S) of the human PIR1 phosphatase core (PIR1-core, residues 29-205), refined at 1.20 Å resolution. PIR1-core shares structural similarities with DSPs related to Vaccinia virus VH1 and with RNA 5'-phosphatases such as the baculovirus RNA triphosphatase and the human mRNA capping enzyme. The PIR1 active site cleft is wider and deeper than that of VH1 and contains two bound ions: a phosphate trapped above the catalytic cysteine C152 exemplifies the binding mode expected for the γ-phosphate of RNA, and ∼6 Å away, a chloride ion coordinates the general base R158. Two residues in the PIR1 phosphate-binding loop (P-loop), a histidine (H154) downstream of C152 and an asparagine (N157) preceding R158, make close contacts with the active site phosphate, and their nonaliphatic side chains are essential for phosphatase activity in vitro. These residues are conserved in all RNA 5'-phosphatases that, analogous to PIR1, lack a "general acid" residue. Thus, a deep active site crevice, two active site ions, and conserved P-loop residues stabilizing the γ-phosphate of RNA are defining features of atypical DSPs that specialize in dephosphorylating 5'-RNA.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Thomas Jefferson University , 233 South 10th Street, Philadelphia, Pennsylvania 19107, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA/RNP complex-1-interacting phosphatase184Homo sapiensMutation(s): 1 
Gene Names: DUSP11PIR1
EC: 3.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for O75319 (Homo sapiens)
Explore O75319 
Go to UniProtKB:  O75319
GTEx:  ENSG00000144048 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75319
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.74α = 90
b = 92.74β = 90
c = 92.74γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2014-02-26
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description