PDBsum entry 3lwt

Go to PDB code: 
protein links
Hydrolase PDB id
Protein chain
457 a.a. *
Waters ×168
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of the yeast sac1: implications for its phosphoinositide phosphatase function
Structure: Phosphoinositide phosphatase sac1. Chain: x. Fragment: cytosolic portion of yeast sac1. Synonym: recessive suppressor of secretory defect. Engineered: yes
Source: Saccharomyces cerevisiae. Brewer's yeast,lager beer yeast,yeast. Organism_taxid: 4932. Gene: rsd1, sac1, ykl212w. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.96Å     R-factor:   0.201     R-free:   0.243
Authors: Y.Mao,A.Manford,T.Xia,A.K.Saxena,C.Stefan,F.Hu,S.D.Emr
Key ref: A.Manford et al. (2010). Crystal structure of the yeast Sac1: implications for its phosphoinositide phosphatase function. EMBO J, 29, 1489-1498. PubMed id: 20389282
24-Feb-10     Release date:   05-May-10    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P32368  (SAC1_YEAST) -  Phosphoinositide phosphatase SAC1
623 a.a.
457 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     phosphoric ester hydrolase activity     1 term  


EMBO J 29:1489-1498 (2010)
PubMed id: 20389282  
Crystal structure of the yeast Sac1: implications for its phosphoinositide phosphatase function.
A.Manford, T.Xia, A.K.Saxena, C.Stefan, F.Hu, S.D.Emr, Y.Mao.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21295699 C.J.Stefan, A.G.Manford, D.Baird, J.Yamada-Hanff, Y.Mao, and S.D.Emr (2011).
Osh proteins regulate phosphoinositide metabolism at ER-plasma membrane contact sites.
  Cell, 144, 389-401.  
21145456 M.R.Wenk (2010).
Lipidomics: new tools and applications.
  Cell, 143, 888-895.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.