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(-) Description

Title :  CRYSTAL STRUCTURE OF YEAST VPS74-N-TERM TRUNCATION VARIANT
 
Authors :  K. R. Schmitz, S. Li, T. G. Setty, K. M. Ferguson
Date :  18 Feb 08  (Deposition) - 22 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.05
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Beta Hairpin, Vps, Golgi Localization, Vps74, Tetramer, Golgi Apparatus, Phosphoprotein, Protein Transport, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. R. Schmitz, J. Liu, S. Li, T. G. Setty, C. S. Wood, C. G. Burd, K. M. Ferguson
Golgi Localization Of Glycosyltransferases Requires A Vps74P Oligomer.
Dev. Cell V. 14 523 2008
PubMed-ID: 18410729  |  Reference-DOI: 10.1016/J.DEVCEL.2008.02.016
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 74
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: VPS74
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2ZII)

(-) Sites  (0, 0)

(no "Site" information available for 2ZII)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZII)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:294 -Pro A:295
2Tyr B:294 -Pro B:295
3Tyr C:294 -Pro C:295
4Tyr D:294 -Pro D:295

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZII)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZII)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZII)

(-) 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:281
 aligned with VPS74_YEAST | Q06385 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:281
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342 
          VPS74_YEAST    63 NIPTLTLMEEVLLMGLRDREGYLSFWNDSISYALRGCIIIELALRGKIRILDDSARKRFDLSERLIEVIDSSKTGEVLLDETLQLMKNDEPLSISNWIDLLSGETWNLLKINYQLKQVRERLAKGLVDKGVLRTEMKNFFLFDMATHPIADASCKEAIKRRVLSVLVSRNMELSYNEYFPETTSFKIIRTLALICGSYGANVLENVLTTLEYEKRDKAISRAEEIMAQFSQYPFDLEKETELGVSVNLNKEVKEEIENNPGHDLQLEVIAGVFEVFSRMDM 343
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ziiA00 A:63-343 yeast vps74-n-term truncation variant domain like                                                                                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhh.eeee.......hhhhhhhhhhhhh...eehhhhhhhhh....hhhhhhhh..hhhhhhhhhhhhh.....eeee....eeee.....hhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zii A  63 NIPTLTLMEEVLLMGLRDREGYLSFWNDSISYALRGCIIIELALRGKIRILDDSARKRFDLSERLIEVIDSSKTGEVLLDETLQLMKNDEPLSISNWIDLLSGETWNLLKINYQLKQVRERLAKGLVDKGVLRTEMKNFFLFDMATHPIADASCKEAIKRRVLSVLVSRNMELSYNEYFPETTSFKIIRTLALICGSYGANVLENVLTTLEYEKRDKAISRAEEIMAQFSQYPFDLEKETELGVSVNLNKEVKEEIENNPGHDLQLEVIAGVFEVFSRMDM 343
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342 


Chain B from PDB  Type:PROTEIN  Length:281
 aligned with VPS74_YEAST | Q06385 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:281
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341 
          VPS74_YEAST    62 INIPTLTLMEEVLLMGLRDREGYLSFWNDSISYALRGCIIIELALRGKIRILDDSARKRFDLSERLIEVIDSSKTGEVLLDETLQLMKNDEPLSISNWIDLLSGETWNLLKINYQLKQVRERLAKGLVDKGVLRTEMKNFFLFDMATHPIADASCKEAIKRRVLSVLVSRNMELSYNEYFPETTSFKIIRTLALICGSYGANVLENVLTTLEYEKRDKAISRAEEIMAQFSQYPFDLEKETELGVSVNLNKEVKEEIENNPGHDLQLEVIAGVFEVFSRMD 342
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ziiB00 B:62-342 yeast vps74-n-term truncation variant domain like                                                                                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh............hhhhhhhhhhhhhhhhhhh...ee...hhhhhhhhhh.eee........hhhhhhhhhhhhh...eehhhhhhhhh..............hhhhhhhhhhhhh.....eeee....eeee....hhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhh....hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zii B  62 INIPTLTLMEEVLLMGLRDREGYLSFWNDSISYALRGCIIIELALRGKIRILDDSARKRFDLSERLIEVIDSSKTGEVLLDETLQLMKNDEPLSISNWIDLLSGETWNLLKINYQLKQVRERLAKGLVDKGVLRTEMKNFFLFDMATHPIADASCKEAIKRRVLSVLVSRNMELSYNEYFPETTSFKIIRTLALICGSYGANVLENVLTTLEYEKRDKAISRAEEIMAQFSQYPFDLEKETELGVSVNLNKEVKEEIENNPGHDLQLEVIAGVFEVFSRMD 342
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341 


Chain C from PDB  Type:PROTEIN  Length:279
 aligned with VPS74_YEAST | Q06385 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:279
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332         
          VPS74_YEAST    63 NIPTLTLMEEVLLMGLRDREGYLSFWNDSISYALRGCIIIELALRGKIRILDDSARKRFDLSERLIEVIDSSKTGEVLLDETLQLMKNDEPLSISNWIDLLSGETWNLLKINYQLKQVRERLAKGLVDKGVLRTEMKNFFLFDMATHPIADASCKEAIKRRVLSVLVSRNMELSYNEYFPETTSFKIIRTLALICGSYGANVLENVLTTLEYEKRDKAISRAEEIMAQFSQYPFDLEKETELGVSVNLNKEVKEEIENNPGHDLQLEVIAGVFEVFSRM 341
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ziiC00 C:63-341 yeast vps74-n-term truncation variant domain like                                                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhhh.eeee.......hhhhhhhhhhhhh...eehhhhhhhhhh.............hhhhhhhhhhhhh.....eeee....eeee....hhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zii C  63 NIPTLTLMEEVLLMGLRDREGYLSFWNDSISYALRGCIIIELALRGKIRILDDSARKRFDLSERLIEVIDSSKTGEVLLDETLQLMKNDEPLSISNWIDLLSGETWNLLKINYQLKQVRERLAKGLVDKGVLRTEMKNFFLFDMATHPIADASCKEAIKRRVLSVLVSRNMELSYNEYFPETTSFKIIRTLALICGSYGANVLENVLTTLEYEKRDKAISRAEEIMAQFSQYPFDLEKETELGVSVNLNKEVKEEIENNPGHDLQLEVIAGVFEVFSRM 341
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332         


Chain D from PDB  Type:PROTEIN  Length:283
 aligned with VPS74_YEAST | Q06385 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:283
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341   
          VPS74_YEAST    62 INIPTLTLMEEVLLMGLRDREGYLSFWNDSISYALRGCIIIELALRGKIRILDDSARKRFDLSERLIEVIDSSKTGEVLLDETLQLMKNDEPLSISNWIDLLSGETWNLLKINYQLKQVRERLAKGLVDKGVLRTEMKNFFLFDMATHPIADASCKEAIKRRVLSVLVSRNMELSYNEYFPETTSFKIIRTLALICGSYGANVLENVLTTLEYEKRDKAISRAEEIMAQFSQYPFDLEKETELGVSVNLNKEVKEEIENNPGHDLQLEVIAGVFEVFSRMDML 344
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ziiD00 D:62-344 yeast vps74-n-term truncation variant domain like                                                                                                                                                                                                                          CATH domains
           Pfam domains (1) -------GPP34-2ziiD01 D:69-321                                                                                                                                                                                                                                       ----------------------- Pfam domains (1)
           Pfam domains (2) -------GPP34-2ziiD02 D:69-321                                                                                                                                                                                                                                       ----------------------- Pfam domains (2)
           Pfam domains (3) -------GPP34-2ziiD03 D:69-321                                                                                                                                                                                                                                       ----------------------- Pfam domains (3)
           Pfam domains (4) -------GPP34-2ziiD04 D:69-321                                                                                                                                                                                                                                       ----------------------- Pfam domains (4)
         Sec.struct. author ......hhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhh.eee.......hhhhhhhhhhhhh....hhhhhhhhhh....hhhhhhhh..hhhhhhhhhhhhh.....eeee....eeee.....hhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zii D  62 INIPTLTLMEEVLLMGLRDREGYLSFWNDSISYALRGCIIIELALRGKIRILDDSARKRFDLSERLIEVIDSSKTGEVLLDETLQLMKNDEPLSISNWIDLLSGETWNLLKINYQLKQVRERLAKGLVDKGVLRTEMKNFFLFDMATHPIADASCKEAIKRRVLSVLVSRNMELSYNEYFPETTSFKIIRTLALICGSYGANVLENVLTTLEYEKRDKAISRAEEIMAQFSQYPFDLEKETELGVSVNLNKEVKEEIENNPGHDLQLEVIAGVFEVFSRMDML 344
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341
   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 2ZII)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: GPP34] (3)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (VPS74_YEAST | Q06385)
molecular function
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0070273    phosphatidylinositol-4-phosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' position.
biological process
    GO:0048193    Golgi vesicle transport    The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles.
    GO:0030968    endoplasmic reticulum unfolded protein response    The series of molecular signals generated as a consequence of the presence of unfolded proteins in the endoplasmic reticulum (ER) or other ER-related stress; results in changes in the regulation of transcription and translation.
    GO:0006487    protein N-linked glycosylation    A protein glycosylation process in which a carbohydrate or carbohydrate derivative unit is added to a protein via the N4 atom of peptidyl-asparagine, the omega-N of arginine, or the N1' atom peptidyl-tryptophan.
    GO:0035269    protein O-linked mannosylation    The transfer of mannose from dolichyl activated mannose to the hydroxyl group of a seryl or threonyl residue of a protein acceptor molecule, to form an O-linked protein-sugar linkage.
    GO:0034067    protein localization to Golgi apparatus    A process in which a protein is transported to, or maintained in, a location within the Golgi apparatus.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0060304    regulation of phosphatidylinositol dephosphorylation    Any process that modulates the frequency, rate or extent of the chemical reaction involving the removal of one or more phosphate groups from a phosphatidylinositol.
    GO:0006890    retrograde vesicle-mediated transport, Golgi to ER    The directed movement of substances from the Golgi back to the endoplasmic reticulum, mediated by vesicles bearing specific protein coats such as COPI or COG.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0032580    Golgi cisterna membrane    The lipid bilayer surrounding any of the thin, flattened compartments that form the central portion of the Golgi complex.
    GO:0005797    Golgi medial cisterna    The middle Golgi cisterna (or cisternae).
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0019898    extrinsic component of membrane    The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

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 Related Entries

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

UniProtKB/Swiss-Prot
        VPS74_YEAST | Q06385: 2zih 4tu3

(-) Related Entries Specified in the PDB File

2zih CRYSTAL STRUCTURE OF FULL-LENGTH VPS74