6BYF

Crystal structure of the core catalytic domain of PP-IP phosphatase SIW14 from S. cerevisiae in complex with citrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and biochemical characterization of Siw14: A protein-tyrosine phosphatase fold that metabolizes inositol pyrophosphates.

Wang, H.Gu, C.Rolfes, R.J.Jessen, H.J.Shears, S.B.

(2018) J Biol Chem 293: 6905-6914

  • DOI: 10.1074/jbc.RA117.001670
  • Primary Citation of Related Structures:  
    6BYF

  • PubMed Abstract: 
  • Inositol pyrophosphates (PP-InsPs) are "energetic" intracellular signals that are ubiquitous in animals, plants, and fungi; structural and biochemical characterization of PP-InsP metabolic enzymes provides insight into their evolution, reaction mechanisms, and regulation ...

    Inositol pyrophosphates (PP-InsPs) are "energetic" intracellular signals that are ubiquitous in animals, plants, and fungi; structural and biochemical characterization of PP-InsP metabolic enzymes provides insight into their evolution, reaction mechanisms, and regulation. Here, we describe the 2.35-Å-resolution structure of the catalytic core of Siw14, a 5-PP-InsP phosphatase from Saccharomyces cerevisiae and a member of the protein tyrosine-phosphatase (PTP) superfamily. Conclusions that we derive from structural data are supported by extensive site-directed mutagenesis and kinetic analyses, thereby attributing new functional significance to several key residues. We demonstrate the high activity and exquisite specificity of Siw14 for the 5-diphosphate group of PP-InsPs. The three structural elements that demarcate a 9.2-Å-deep substrate-binding pocket each have spatial equivalents in PTPs, but we identify how these are specialized for Siw14 to bind and hydrolyze the intensely negatively charged PP-InsPs. ( a ) The catalytic P-loop with the C X 5 R(S/T) PTP motif contains additional, positively charged residues. ( b ) A loop between the α5 and α6 helices, corresponding to the Q-loop in PTPs, contains a lysine and an arginine that extend into the catalytic pocket due to displacement of the α5 helix orientation through intramolecular crowding caused by three bulky, hydrophobic residues. ( c ) The general-acid loop in PTPs is replaced in Siw14 with a flexible loop that does not use an aspartate or glutamate as a general acid. We propose that an acidic residue is not required for phosphoanhydride hydrolysis.


    Organizational Affiliation

    From the Inositol Signaling Group, Signal Transduction Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase SIW14
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I
170Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SIW14YNL032WN2746OCA3
EC: 3.1.3.48 (PDB Primary Data), 3.6.1.52 (UniProt)
UniProt
Find proteins for P53965 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53965 
Go to UniProtKB:  P53965
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
J [auth A] , L [auth B] , M [auth C] , O [auth D] , R [auth E] , S [auth F] , T [auth G] , V [auth H] , 
J [auth A],  L [auth B],  M [auth C],  O [auth D],  R [auth E],  S [auth F],  T [auth G],  V [auth H],  W [auth I]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
K [auth A], N [auth C], P [auth D]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
Q [auth D], U [auth G]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A , B , C , D , E , F , G , H , 
A,  B,  C,  D,  E,  F,  G,  H,  I
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.968α = 90
b = 92.968β = 90
c = 814.716γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-12-20 
  • Released Date: 2018-03-21 
  • Deposition Author(s): Wang, H., Shears, S.B.

Funding OrganizationLocationGrant Number
NIH/NIEHSUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-03-28
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-16
    Changes: Data collection, Database references