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(-) Description

Title :  CRYSTAL STRUCTURE OF SLM1-PH DOMAIN IN COMPLEX WITH D-MYO-INOSITOL-4-PHOSPHATE
 
Authors :  K. Anand, K. Maeda, A. C. Gavin
Date :  04 Nov 11  (Deposition) - 13 Jun 12  (Release) - 13 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Anand, K. Maeda, A. C. Gavin
Structural Analyses Of Slm1-Ph Domain Demonstrate Ligand Binding In The Non-Canonical Site
Plos One V. 7 36526 2012
PubMed-ID: 22574179  |  Reference-DOI: 10.1371/JOURNAL.PONE.0036526

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE-BINDING PROTEIN SLM1
    Chains: A, B, C, D
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Common: BAKER'S YEAST
    Expression System Taxid: 4932
    Fragment: PH DOMAIN, RESIDUES 469-583
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: SYNTHETIC LETHAL WITH MSS4 PROTEIN 1, TORC2 EFFECTOR PROTEIN SLM1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1I4D3Ligand/IonD-MYO-INOSITOL-4-PHOSPHATE
2PO47Ligand/IonPHOSPHATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:493 , ASN A:495 , PHE A:496 , HIS A:498 , THR C:493 , ASN C:495 , PHE C:496 , HIS C:498BINDING SITE FOR RESIDUE PO4 A1583
02AC2SOFTWARETHR B:493 , ASN B:495 , PHE B:496 , HIS B:498 , HOH B:2002 , THR D:493 , ASN D:495 , PHE D:496 , HIS D:498BINDING SITE FOR RESIDUE PO4 B1584
03AC3SOFTWARELYS B:480 , HIS B:557 , ASN B:558BINDING SITE FOR RESIDUE PO4 B1585
04AC4SOFTWARELYS D:480 , HIS D:557 , ASN D:558BINDING SITE FOR RESIDUE PO4 D1583
05AC5SOFTWARELYS A:480 , HIS A:557 , ASN A:558BINDING SITE FOR RESIDUE PO4 A1584
06AC6SOFTWAREHIS C:525 , ARG C:527 , LYS C:528 , TYR C:566 , HOH C:2070BINDING SITE FOR RESIDUE PO4 C1582
07AC7SOFTWAREARG D:478 , TYR D:485 , LYS D:542BINDING SITE FOR RESIDUE PO4 D1584
08AC8SOFTWARETYR A:485 , SER A:539 , LYS A:542 , LYS A:562 , HOH A:2075BINDING SITE FOR RESIDUE I4D A1585
09AC9SOFTWARETYR B:485 , SER B:539 , LYS B:542 , LYS B:562BINDING SITE FOR RESIDUE I4D B1586
10BC1SOFTWARELYS C:480 , HIS C:557 , ASN C:558BINDING SITE FOR RESIDUE I4D C1583

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A6K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4A6K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A6K)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.SLM1_YEAST468-581
 
 
 		  4A:469-581
B:469-581
C:469-581
D:469-581

(-) Exons   (0, 0)

(no "Exon" information available for 4A6K)

(-) Sequences/Alignments

Asymmetric/Biological 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:110
 aligned with SLM1_YEAST | P40485 from UniProtKB/Swiss-Prot  Length:686

    Alignment length:142
                                   450       460       470       480       490       500       510       520       530       540       550       560       570       580  
           SLM1_YEAST   441 DPNFLLPNLPMRTFKEIVYKYQFDPLTYEIKSGFLERRSKFLKSYSKGYYVLTPNFLHEFKTADRKKDLVPVMSLALSECTVTEHSRKNSTSSPNSTGSDAKFVLHAKQNGIIRRGHNWVFKADSYESMMSWFDNLKILTST 582
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .----------------------....-..eeeeeeeee....eeeeeeeee...eeeee............eeee...eeeeee....---------...eeeeee..........eeeee..hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------PH_DOMAIN  PDB: A:469-581 UniProt: 468-581                                                                        - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a6k A 464 D----------------------HPFT-EIKSGFLERRSKFLKSYSKGYYVLTPNFLHEFKTADRKKDLVPVMSLALSECTVTEHSRKN---------SDAKFVLHAKQNGIIRRGHNWVFKADSYESMMSWFDNLKILTST 582
                            |        -         -   |  |470       480       490       500       510       520        |-       540       550       560       570       580  
                            |                    465  | |                                                         529       539                                           
                          464                       468 |                                                                                                                 
                                                      469                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:110
 aligned with SLM1_YEAST | P40485 from UniProtKB/Swiss-Prot  Length:686

    Alignment length:120
                                   473       483       493       503       513       523       533       543       553       563       573       583
           SLM1_YEAST   464 DPLTYEIKSGFLERRSKFLKSYSKGYYVLTPNFLHEFKTADRKKDLVPVMSLALSECTVTEHSRKNSTSSPNSTGSDAKFVLHAKQNGIIRRGHNWVFKADSYESMMSWFDNLKILTSTS 583
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....-..eeeeeeeee....eeeeeeeee...eeeee............eeee...eeeeee....---------...eeeeee..........eeeee..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----PH_DOMAIN  PDB: B:469-581 UniProt: 468-581                                                                        -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4a6k B 465 HPFT-EIKSGFLERRSKFLKSYSKGYYVLTPNFLHEFKTADRKKDLVPVMSLALSECTVTEHSRKN---------SDAKFVLHAKQNGIIRRGHNWVFKADSYESMMSWFDNLKILTSTS 583
                               | | 473       483       493       503       513       523     |   -     | 543       553       563       573       583
                             468 |                                                         529       539                                            
                               469                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:109
 aligned with SLM1_YEAST | P40485 from UniProtKB/Swiss-Prot  Length:686

    Alignment length:119
                                   472       482       492       502       512       522       532       542       552       562       572         
           SLM1_YEAST   463 FDPLTYEIKSGFLERRSKFLKSYSKGYYVLTPNFLHEFKTADRKKDLVPVMSLALSECTVTEHSRKNSTSSPNSTGSDAKFVLHAKQNGIIRRGHNWVFKADSYESMMSWFDNLKILTS 581
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..----..eeeeeeeee....eeeeeeeee...eeeee............eeee...eeeeee......------....eeeeee..........eeeee..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PH_DOMAIN  PDB: C:469-581 UniProt: 468-581                                                                         PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 4a6k C 467 FT----EIKSGFLERRSKFLKSYSKGYYVLTPNFLHEFKTADRKKDLVPVMSLALSECTVTEHSRKNST------GSDAKFVLHAKQNGIIRRGHNWVFKADSYESMMSWFDNLKILTS 581
                             |    |472       482       492       502       512       522        |-     | 542       552       562       572         
                           468  469                                                           531    538                                           


Chain D from PDB  Type:PROTEIN  Length:107
 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 ...-..eeeeeeeee....eeeeeeeee...eeeee............eeee...eeeeee....----------..eeeeee..........eeeee..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---PH_DOMAIN  PDB: D:469-581 UniProt: 468-581                                                                        - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 4a6k D 466 PFT-EIKSGFLERRSKFLKSYSKGYYVLTPNFLHEFKTADRKKDLVPVMSLALSECTVTEHSRKN----------DAKFVLHAKQNGIIRRGHNWVFKADSYESMMSWFDNLKILTST 582
                              | |  474       484       494       504       514       524    |    -     | 544       554       564       574        
                            468 |                                                         529        540                                          
                              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 4A6K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4A6K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A6K)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (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 | P40485: 3nsu 4a5k 4a6f 4a6h

(-) Related Entries Specified in the PDB File

4a5k STRUCTURAL ANALYSES OF SLM1-PH DOMAIN DEMONSTRATE LIGAND BINDING IN THE NON-CANONICAL SITE
4a6f CRYSTAL STRUCTURE OF SLM1-PH DOMAIN IN COMPLEX WITH PHOSPHOSERINE
4a6h CRYSTAL STRUCTURE OF SLM1-PH DOMAIN IN COMPLEX WITH INOSITOL-4-PHOSPHATE