3LWT

Crystal structure of the Yeast Sac1: Implications for its phosphoinositide phosphatase function


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the yeast Sac1: implications for its phosphoinositide phosphatase function.

Manford, A.Xia, T.Saxena, A.K.Stefan, C.Hu, F.Emr, S.D.Mao, Y.

(2010) EMBO J 29: 1489-1498

  • DOI: https://doi.org/10.1038/emboj.2010.57
  • Primary Citation of Related Structures:  
    3LWT

  • PubMed Abstract: 

    Sac family phosphoinositide (PI) phosphatases are an essential family of CX(5)R(T/S)-based enzymes, involved in numerous aspects of cellular function such as PI homeostasis, cellular signalling, and membrane trafficking. Genetic deletions of several Sac family members result in lethality in animal models and mutations of the Sac3 gene have been found in human hereditary diseases. In this study, we report the crystal structure of a founding member of this family, the Sac phosphatase domain of yeast Sac1. The 2.0 A resolution structure shows that the Sac domain comprises of two closely packed sub-domains, a novel N-terminal sub-domain and the PI phosphatase catalytic sub-domain. The structure further shows a striking conformation of the catalytic P-loop and a large positively charged groove at the catalytic site. These findings suggest an unusual mechanism for its dephosphorylation function. Homology structural modeling of human Fig4/Sac3 allows the mapping of several disease-related mutations and provides a framework for the understanding of the molecular mechanisms of human diseases.


  • Organizational Affiliation

    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoinositide phosphatase SAC1A [auth X]505Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RSD1SAC1YKL212W
EC: 3.1.3 (PDB Primary Data), 3.1.3.64 (UniProt)
UniProt
Find proteins for P32368 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32368 
Go to UniProtKB:  P32368
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32368
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.158α = 90
b = 94.732β = 90
c = 155.439γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL2Mapmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL2Mapphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references