Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE YEAST SAC1: IMPLICATIONS FOR ITS PHOSPHOINOSITIDE PHOSPHATASE FUNCTION
 
Authors :  Y. Mao, A. Manford, T. Xia, A. K. Saxena, C. Stefan, F. Hu, S. D. Emr
Date :  24 Feb 10  (Deposition) - 05 May 10  (Release) - 07 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  X
Biol. Unit 1:  X  (1x)
Biol. Unit 2:  X  (2x)
Keywords :  Sac1, Sac3/Fig4, Phosphoinositide Phosphatase, Lipid Metabolism, Endoplasmic Reticulum, Hydrolase, Membrane, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Manford, T. Xia, A. K. Saxena, C. Stefan, F. Hu, S. D. Emr, Y. Mao
Crystal Structure Of The Yeast Sac1: Implications For Its Phosphoinositide Phosphatase Function.
Embo J. V. 29 1489 2010
PubMed-ID: 20389282  |  Reference-DOI: 10.1038/EMBOJ.2010.57

(-) Compounds

Molecule 1 - PHOSPHOINOSITIDE PHOSPHATASE SAC1
    ChainsX
    EC Number3.1.3.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETSUMO
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCYTOSOLIC PORTION OF YEAST SAC1
    GeneRSD1, SAC1, YKL212W
    Organism CommonBREWER'S YEAST,LAGER BEER YEAST,YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymRECESSIVE SUPPRESSOR OF SECRETORY DEFECT

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit X
Biological Unit 1 (1x)X
Biological Unit 2 (2x)X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3LWT)

(-) Sites  (0, 0)

(no "Site" information available for 3LWT)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LWT)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Ala X:146 -Ser X:147
2Phe X:210 -Arg X:211
3Lys X:270 -Tyr X:271
4His X:339 -Glu X:340
5Gly X:454 -Thr X:455

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LWT)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SACPS50275 Sac phosphatase domain profile.SAC1_YEAST115-454  1X:115-454
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SACPS50275 Sac phosphatase domain profile.SAC1_YEAST115-454  1X:115-454
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SACPS50275 Sac phosphatase domain profile.SAC1_YEAST115-454  2X:115-454

(-) Exons   (0, 0)

(no "Exon" information available for 3LWT)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain X from PDB  Type:PROTEIN  Length:457
 aligned with SAC1_YEAST | P32368 from UniProtKB/Swiss-Prot  Length:623

    Alignment length:457
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       
           SAC1_YEAST     - -MTGPIVYVQNADGIFFKLAEGKGTNDAVIHLANQDQGVRVLGAEEFPVQGEVVKIASLMGFIKLKLNRYAIIANTVEETGRFNGHVFYRVLQHSIVSTKFNSRIDSEEAEYIKLLELHLKNSTFYFSYTYDLTNSLQRNEKVGPAASWKTADERFFWNHYLTEDLRNFAHQDPRIDSFIQPVIYGYAKTVDAVLNATPIVLGLITRRSIFRAGTRYFRRGVDKDGNVGNFNETEQILLAENPESEKIHVFSFLQTRGSVPIYWAEINNLKYKPNLVLGENSLDATKKHFDQQKELYGDNYLVNLVNQKGHELPVKEGYESVVHALNDPKIHYVYFDFHHECRKMQWHRVKLLIDHLEKLGLSNEDFFHKVIDSNGNTVEIVNEQHSVVRTNCMDCLDRTNVVQSVLAQWVLQKEFESADVVATGSTWEDNAPLLTSYQNLWADNADAVSVAYSGTG 456
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------Syja_N-3lwtX01 X:55-348                                                                                                                                                                                                                                                                               ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee..eeeeee.........eeeee.....eeeehhhhh......eee.eeeeeeee..eeeeeeeeeeeeeeee..eeeeeeeeeeeee.......hhhhhhhhhhhhhhhhhh..ee........hhhhhhhhh...hhhhh.......hhhhhhhhhhhh.hhhhhhhh......eeeeeeeee..eeeeeeeeeee......................eeeeeeeeeee......eeeeeeeeeee....................hhhhhhhhhhhhhhhhhhhheeeeeee.......hhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhh......eeeee.....eeeeee...eeeeee...hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------SAC  PDB: X:115-454 UniProt: 115-454                                                                                                                                                                                                                                                                                                                -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lwt X   0 SMTGPIVYVQNADGIFFKLAEGKGTNDAVIHLANQDQGVRVLGAEEFPVQGEVVKIASLMGFIKLKLNRYAIIANTVEETGRFNGHVFYRVLQHSIVSTKFNSRIDSEEAEYIKLLELHLKNSTFYFSYTYDLTNSLQRNEKVGPAASWKTADERFFWNHYLTEDLRNFAHQDPRIDSFIQPVIYGYAKTVDAVLNATPIVLGLITRRSIFRAGTRYFRRGVDKDGNVGNFNETEQILLAENPESEKIHVFSFLQTRGSVPIYWAEINNLKYKPNLVLGENSLDATKKHFDQQKELYGDNYLVNLVNQKGHELPVKEGYESVVHALNDPKIHYVYFDFHHECRKMQWHRVKLLIDHLEKLGLSNEDFFHKVIDSNGNTVEIVNEQHSVVRTNCMDCLDRTNVVQSVLAQWVLQKEFESADVVATGSTWEDNAPLLTSYQNLWADNADAVSVAYSGTG 456
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3LWT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LWT)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain X   (SAC1_YEAST | P32368)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0043813    phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity    Catalysis of the reaction: phosphatidylinositol-3,5-bisphosphate + H2O = phosphatidylinositol-3-phosphate + orthophosphate.
    GO:0004438    phosphatidylinositol-3-phosphatase activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 3-phosphate + H2O = 1-phosphatidyl-1D-myo-inositol + phosphate.
    GO:0043812    phosphatidylinositol-4-phosphate phosphatase activity    Catalysis of the reaction: phosphatidylinositol-4-phosphate + H2O = phosphatidylinositol + orthophosphate.
    GO:0042578    phosphoric ester hydrolase activity    Catalysis of the reaction: RPO-R' + H2O = RPOOH + R'H. This reaction is the hydrolysis of any phosphoric ester bond, any ester formed from orthophosphoric acid, O=P(OH)3.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0046856    phosphatidylinositol dephosphorylation    The process of removing one or more phosphate groups from a phosphatidylinositol.
    GO:0036092    phosphatidylinositol-3-phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphatidylinositol-3-phosphate, a phosphatidylinositol monophosphate carrying the phosphate group at the 3-position.
cellular component
    GO:0005797    Golgi medial cisterna    The middle Golgi cisterna (or cisternae).
    GO:0035339    SPOTS complex    A multiprotein complex at least composed of serine palmitoyltransferases and ORM proteins (known as ORMDL proteins in mammals and other higher vertebrates) that plays a key role in sphingolipid homeostasis.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0030173    integral component of Golgi membrane    The component of the Golgi membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0030176    integral component of endoplasmic reticulum membrane    The component of the endoplasmic reticulum membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3lwt)
 
  Sites
(no "Sites" information available for 3lwt)
 
  Cis Peptide Bonds
    Ala X:146 - Ser X:147   [ RasMol ]  
    Gly X:454 - Thr X:455   [ RasMol ]  
    His X:339 - Glu X:340   [ RasMol ]  
    Lys X:270 - Tyr X:271   [ RasMol ]  
    Phe X:210 - Arg X:211   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3lwt
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SAC1_YEAST | P32368
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.3.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  SAC1_YEAST | P32368
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SAC1_YEAST | P323684tu3

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3LWT)