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(-) Description

Title :  RESURRECTION OF A FUNCTIONAL PHOSPHATIDYLINOSITOL TRANSFER PROTEIN FROM A PSEUDO-SEC14 SCAFFOLD BY DIRECTED EVOLUTION
 
Authors :  E. A. Ortlund, G. Schaaf, V. A. Bankaitis
Date :  06 Jan 11  (Deposition) - 23 Feb 11  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Cral-Trio, String Motif, Signaling Protein, Directed Evolution, Pipt, Sec14, Phospholipid Transporter, Lipid, Phosphatidylinositol, Phosphatidylcholine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Schaaf, M. Dynowski, C. J. Mousley, S. D. Shah, P. Yuan, E. M. Winklbauer, M. K. De Campos, K. Trettin, M. C. Quinones, T. I. Smirnova, L. L. Yanagisawa, E. A. Ortlund, V. A. Bankaitis
Resurrection Of A Functional Phosphatidylinositol Transfer Protein From A Pseudo-Sec14 Scaffold By Directed Evolution.
Mol. Biol. Cell V. 22 892 2011
PubMed-ID: 21248202  |  Reference-DOI: 10.1091/MBC.E10-11-0903

(-) Compounds

Molecule 1 - CRAL-TRIO DOMAIN-CONTAINING PROTEIN YKL091C
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YKL091C
    Mutation: YES
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PEE1Ligand/Ion1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:113 , TYR A:124 , TYR A:137 , MET A:145 , LEU A:149 , SER A:175 , THR A:177 , ILE A:196 , SER A:203 , MET A:211 , PHE A:214 , HOH A:362 , HOH A:396 , HOH A:412 , HOH A:442 , HOH A:502BINDING SITE FOR RESIDUE PEE A 311
2AC2SOFTWAREARG A:56 , ARG A:79 , GLU A:154 , ALA A:157 , TYR A:207 , ARG A:210 , HOH A:325 , HOH A:531BINDING SITE FOR RESIDUE GOL A 3968

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q8G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q8G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q8G)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CRAL_TRIOPS50191 CRAL-TRIO lipid binding domain profile.YKJ1_YEAST101-274  1A:101-274

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YKL091C1YKL091C.1XI:270294-269362933YKJ1_YEAST1-3103101A:4-309306

(-) 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:306
 aligned with YKJ1_YEAST | P33324 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:306
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303      
           YKJ1_YEAST     4 SILDTYPQICSPNALPGTPGNLTKEQEEALLQFRSILLEKNYKERLDDSTLLRFLRARKFDINASVEMFVETERWREEYGANTIIEDYENNKEAEDKERIKLAKMYPQYYHHVDKDGRPLYFEELGGINLKKMYKITTEKQMLRNLVKEYELFATYRVPACSRRAGYLIETSCTVLDLKGISLSNAYHVLSYIKDVADISQNYYPERMGKFYIIHSPFGFSTMFKMVKPFLDPVTVSKIFILGSSYKKELLKQIPIENLPVKYGGTSVLHNPNDKFYYSDIGPWRDPRYIGPEGEIPNIFGKFTVT 309
               SCOP domains d3q8ga1 A:4-94 automated matches                                                           d3q8ga2 A:95-309 automated matches                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --------------------------CRAL_TRIO_N-3q8gA02 A:30-75                   ---------------------------CRAL_TRIO-3q8gA01 A:103-269                                                                                                                                            ---------------------------------------- Pfam domains
         Sec.struct. author hhhhhh................hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeeeee.....eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhhhhhhheee...hhhhhhhhhhhhhhhhhhhh..........hhhhh..hhhhh.............hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------CRAL_TRIO  PDB: A:101-274 UniProt: 101-274                                                                                                                                    ----------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:4-309 UniProt: 1-310 [INCOMPLETE]                                                                                                                                                                                                                                                                 Transcript 1
                 3q8g A   4 SILDTYPQICSPNALPGTPGNLTKEQEEALLQFRSILLEKNYKERLDDSTLLRFLRARKFDINASVEMFVETERWREEYGANTIIEDYENNKEAEDKERIKLAKMYPQYYHHVDKDGRPLYFAELGGINLKKMYKITTEKQMLRNLVKEYELFATYRVPACSRRAGYLIETSCTVLDLKGISLSNAYHVLSYIKDVADISQNYYPERMGKFYIIHSPFGFSTMFKMVKPFLDPVTVSKIFILGSSYKKELLKQIPIENLPVKYGGTSVLHNPNDKFYYSDIGPWRDPRYIGPEGEIPNIFGKFTVT 309
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303
   Legend:   → Mismatch (orange background)
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  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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q8G)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: CRAL_TRIO (6)
(-)
Clan: no clan defined [family: CRAL_TRIO_N] (3)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YKJ1_YEAST | P33324)
molecular function
    GO:0031210    phosphatidylcholine binding    Interacting selectively and non-covalently with phosphatidylcholine, a class of glycophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of choline.
    GO:0008525    phosphatidylcholine transporter activity    Enables the directed movement of phosphatidylcholine into, out of or within a cell, or between cells. Phosphatidylcholine refers to a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of choline.
    GO:0035091    phosphatidylinositol binding    Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    GO:0008526    phosphatidylinositol transporter activity    Enables the directed movement of phosphatidylinositol into, out of or within a cell, or between cells. Phosphatidylinositol refers to any glycophospholipids with its sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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  3q8g
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 Related Entries

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

UniProtKB/Swiss-Prot
        YKJ1_YEAST | P33324: 3b74 3b7n 3b7q 3b7z

(-) Related Entries Specified in the PDB File

3b74 CRYSTAL STRUCTURE OF YEAST SEC14 HOMOLOG SFH1 IN COMPLEX WITH PHOSPHATIDYLETHANOLAMINE
3b7n CRYSTAL STRUCTURE OF YEAST SEC14 HOMOLOG SFH1 IN COMPLEX WITH PHOSPHATIDYLINOSITOL
3b7q CRYSTAL STRUCTURE OF YEAST SEC14 HOMOLOG SFH1 IN COMPLEX WITH PHOSPHATIDYLCHOLINE
3b7z CRYSTAL STRUCTURE OF YEAST SEC14 HOMOLOG SFH1 IN COMPLEX WITH PHOSPHATIDYLCHOLINE OR PHOSPHATIDYLINOSITOL