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(-) Description

Title :  CRYSTAL STRUCTURE OF THE VPS27P UBIQUITIN INTERACTING MOTIF (UIM)
 
Authors :  R. D. Fisher, B. Wang, S. L. Alam, D. S. Higginson, R. Rich, D. Myszka, W. I. Sundquist, C. P. Hill
Date :  20 Feb 03  (Deposition) - 22 Jul 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  A  (2x)
Keywords :  Alpha-Helix, Coiled-Coil, Tetramer, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. D. Fisher, B. Wang, S. L. Alam, D. S. Higginson, H. Robinson, W. I. Sundquist, C. P. Hill
Structure And Ubiquitin Binding Of The Ubiquitin-Interactin Motif.
J. Biol. Chem. V. 278 28976 2003
PubMed-ID: 12750381  |  Reference-DOI: 10.1074/JBC.M302596200

(-) Compounds

Molecule 1 - VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VPS27
    Chains: A
    Engineered: YES
    Fragment: RESIDUES 301-320
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN SACCHAROMYCES CEREVISIAE VPS27P AND WAS SYNTHESIZED BY STANDARD PEPTIDE SYNTHESIS METHODS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A
Biological Unit 3 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1ZN3Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:3 , ASP A:5 , GLU A:16 , GLU A:19 , ZN A:102BINDING SITE FOR RESIDUE ZN A 101
2AC2SOFTWAREASP A:5 , GLU A:16 , ZN A:101 , HOH A:205BINDING SITE FOR RESIDUE ZN A 102
3AC3SOFTWAREGLU A:1 , GLU A:18 , ALA A:20BINDING SITE FOR RESIDUE ZN A 103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O06)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1O06)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O06)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UIMPS50330 Ubiquitin-interacting motif (UIM) domain profile.VPS27_YEAST258-277
301-320		  1-
A:1-20
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UIMPS50330 Ubiquitin-interacting motif (UIM) domain profile.VPS27_YEAST258-277
301-320		  1-
A:1-20
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UIMPS50330 Ubiquitin-interacting motif (UIM) domain profile.VPS27_YEAST258-277
301-320		  2-
A:1-20
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UIMPS50330 Ubiquitin-interacting motif (UIM) domain profile.VPS27_YEAST258-277
301-320		  2-
A:1-20

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YNR006W1YNR006W.1XIV:636989-6388571869VPS27_YEAST1-6226221A:1-2020

(-) 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:20
 aligned with VPS27_YEAST | P40343 from UniProtKB/Swiss-Prot  Length:622

    Alignment length:20
                                   310       320
          VPS27_YEAST   301 EEDPDLKAAIQESLREAEEA 320
               SCOP domains d1o06a_ A:           SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE UIM  PDB: A:1-20     PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-2 Transcript 1
                 1o06 A   1 EEDPDLKAAIQESLREAEEA  20
                                    10        20
   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  (1, 1)

Asymmetric Unit
(-)
Class: Peptides (792)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1O06)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1O06)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (VPS27_YEAST | P40343)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0032266    phosphatidylinositol-3-phosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' position.
    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).
    GO:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
biological process
    GO:0006886    intracellular protein transport    The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
    GO:0045324    late endosome to vacuole transport    The directed movement of substances from late endosomes to the vacuole. In yeast, after transport to the prevacuolar compartment, endocytic content is delivered to the late endosome and on to the vacuole. This pathway is analogous to endosome to lysosome transport.
    GO:0045053    protein retention in Golgi apparatus    The retention of proteins within the Golgi apparatus. Golgi-localized carbohydrate-modifying enzymes have a short N-terminal domain that faces the cytosol, a single transmembrane alpha helix, and a large C-terminal domain that faces the Golgi lumen and that contains the catalytic site. How the membrane-spanning alpha helix in a Golgi enzyme causes its localization and prevents its movement to the plasma membrane is not known.
    GO:0006623    protein targeting to vacuole    The process of directing proteins towards the vacuole, usually using signals contained within the protein.
cellular component
    GO:0033565    ESCRT-0 complex    A protein complex required for the recycling of Golgi proteins, formation of lumenal membranes and sorting of ubiquitinated proteins into those membranes. This complex includes Vps1p and Hse1p in yeast and the Hrs and STAM proteins in mammals.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  1o06
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  VPS27_YEAST | P40343
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 Related Entries

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

UniProtKB/Swiss-Prot
        VPS27_YEAST | P40343: 1q0v 1q0w 1vfy 2kdi 2pjw 3r42 5ucl

(-) Related Entries Specified in the PDB File

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