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(-) Description

Title :  A SYSTEMATIC SCREEN FOR PROTEIN-LIPID INTERACTIONS IN SACCHAROMYCES CEREVISIAE
 
Authors :  O. Gallego, C. Fernandez-Tornero, C. Aguilar-Gurrieri, C. Muller, A.
Date :  02 Jul 10  (Deposition) - 15 Dec 10  (Release) - 15 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pleckstrin Homology Domain, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. Gallego, M. J. Betts, J. Gvozdenovic-Jeremic, K. Maeda, C. Matetzki, C. Aguilar-Gurrieri, P. Beltran-Alvarez, S. Bonn, C. Fernandez-Tornero, L. J. Jensen, M. Kuhn, J. Trott, V. Rybin, C. W. Muller, P. Bork, M. Kaksonen, R. B. Russell, A. C. Gavin
A Systematic Screen For Protein-Lipid Interactions In Saccharomyces Cerevisiae.
Mol. Syst. Biol. V. 6 430 2010
PubMed-ID: 21119626  |  Reference-DOI: 10.1038/MSB.2010.87

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE-BINDING PROTEIN SLM1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET100-D/TOPO
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentPLECKSTRIN HOMOLOGY DOMAIN (UNP RESIDUES 469-583)
    GeneLIT2, SLM1, YIL105C
    Organism CommonBREWER'S YEAST,LAGER BEER YEAST,YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymTORC2 EFFECTOR PROTEIN SLM1, SYNTHETIC LETHAL WITH MSS4 PROTEIN 1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:1 , TYR A:485 , SER A:539 , LYS A:542 , LYS A:562BINDING SITE FOR RESIDUE SO4 A 901
2AC2SOFTWAREARG A:478 , LYS A:483 , LYS B:483BINDING SITE FOR RESIDUE SO4 A 1001
3AC3SOFTWARETHR A:493 , ASN A:495 , PHE A:496 , HIS A:498 , THR B:493 , ASN B:495 , PHE B:496 , HIS B:498BINDING SITE FOR RESIDUE SO4 A 2001
4AC4SOFTWARETHR A:537 , ARG B:478 , TYR B:485 , LYS B:542BINDING SITE FOR RESIDUE SO4 B 3001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NSU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.SLM1_YEAST468-581
 
  2A:469-581
B:469-581
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.SLM1_YEAST468-581
 
  1A:469-581
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.SLM1_YEAST468-581
 
  1-
B:469-581

(-) Exons   (0, 0)

(no "Exon" information available for 3NSU)

(-) 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 A from PDB  Type:PROTEIN  Length:109
 aligned with SLM1_YEAST | P40485 from UniProtKB/Swiss-Prot  Length:686

    Alignment length:118
                                   474       484       494       504       514       524       534       544       554       564       574        
           SLM1_YEAST   465 PLTYEIKSGFLERRSKFLKSYSKGYYVLTPNFLHEFKTADRKKDLVPVMSLALSECTVTEHSRKNSTSSPNSTGSDAKFVLHAKQNGIIRRGHNWVFKADSYESMMSWFDNLKILTST 582
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...-..eeeeeeee......eeeeeeee...eeeee............eeee...eeeeee................eeeeee.--------.eeeee..hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---PH_DOMAIN  PDB: A:469-581 UniProt: 468-581                                                                        - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3nsu A 466 PFT-EIKSGFLERRSKFLKSYSKGYYVLTPNFLHEFKTADRKKDLVPVMSLALSECTVTEHSRKNSTSSPNSTGSDAKFVLHAK--------HNWVFKADSYESMMSWFDNLKILTST 582
                              | |  474       484       494       504       514       524       534       544   |     -  |    564       574        
                              | |                                                                            548      557                         
                            468 |                                                                                                                 
                              469                                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:103
 aligned with SLM1_YEAST | P40485 from UniProtKB/Swiss-Prot  Length:686

    Alignment length:118
                                   474       484       494       504       514       524       534       544       554       564       574        
           SLM1_YEAST   465 PLTYEIKSGFLERRSKFLKSYSKGYYVLTPNFLHEFKTADRKKDLVPVMSLALSECTVTEHSRKNSTSSPNSTGSDAKFVLHAKQNGIIRRGHNWVFKADSYESMMSWFDNLKILTST 582
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --- PH-3nsuB01 B:469-581                                                                                             - Pfam domains (1)
           Pfam domains (2) --- PH-3nsuB02 B:469-581                                                                                             - Pfam domains (2)
         Sec.struct. author ...-..eeeeeeeee....eeeeeeeee...eeeee............eeee...eeeeee......------....eeeeee.--------.eeeee..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---PH_DOMAIN  PDB: B:469-581 UniProt: 468-581                                                                        - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3nsu B 466 PFT-EIKSGFLERRSKFLKSYSKGYYVLTPNFLHEFKTADRKKDLVPVMSLALSECTVTEHSRKNST------GSDAKFVLHAK--------HNWVFKADSYESMMSWFDNLKILTST 582
                              | |  474       484       494       504       514       524      |  -   |   544   |     -  |    564       574        
                            468 |                                                           531    538       548      557                         
                              469                                                                                                                 

   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 3NSU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PH (111)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SLM1_YEAST | P40485)
molecular function
    GO:0005546    phosphatidylinositol-4,5-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions.
    GO:0046625    sphingolipid binding    Interacting selectively and non-covalently with sphingolipids, a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid).
biological process
    GO:0031929    TOR signaling    A series of molecular signals mediated by TOR (Target of rapamycin) proteins, members of the phosphoinositide (PI) 3-kinase related kinase (PIKK) family that act as serine/threonine kinases in response to nutrient availability or growth factors.
    GO:0038203    TORC2 signaling    A series of intracellular molecular signals mediated by TORC2; TOR (rapamycin-insensitive companion of TOR) in complex with at least Rictor (regulatory-associated protein of TOR), or orthologs of, and other signaling components.
    GO:0030036    actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0051017    actin filament bundle assembly    The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness.
    GO:0070941    eisosome assembly    The aggregation, arrangement and bonding together of a set of components to form an eisosome, a cell part that is composed of the eisosome membrane or MCC domain, a furrow-like plasma membrane sub-domain and associated integral transmembrane proteins, and the proteins (eisosome filaments) that form a scaffolding lattice on the cytoplasmic face.
    GO:0016197    endosomal transport    The directed movement of substances into, out of, or mediated by an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation.
    GO:0090002    establishment of protein localization to plasma membrane    The directed movement of a protein to a specific location in the plasma membrane.
    GO:0030950    establishment or maintenance of actin cytoskeleton polarity    Any cellular process that results in the specification, formation or maintenance of polarized actin-based cytoskeletal structures.
    GO:0001558    regulation of cell growth    Any process that modulates the frequency, rate, extent or direction of cell growth.
cellular component
    GO:0031932    TORC2 complex    A protein complex that contains at least TOR (target of rapamycin) and Rictor (rapamycin-insensitive companion of TOR), or orthologs of, in complex with other signaling components. Mediates the phosphorylation and activation of PKB (also called AKT). In Saccharomyces, the complex contains Avo1p, Avo2p, Tsc11p, Lst8p, Bit61p, Slm1p, Slm2p, and Tor2p.
    GO:0032126    eisosome    A cell part that is composed of the eisosome membrane or MCC domain, a furrow-like plasma membrane sub-domain and associated integral transmembrane proteins, and the proteins (eisosome filaments) that form a scaffolding lattice on the cytoplasmic face. Eisosomes broadly affect overall plasma membrane organization.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SLM1_YEAST | P404854a5k 4a6f 4a6h 4a6k

(-) Related Entries Specified in the PDB File

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