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(-) Description

Title :  CRYSTAL STRUCTURE OF A EUKARYOTIC POLYPHOSPHATE POLYMERASE IN COMPLEX WITH ORTHOPHOSPHATE
 
Authors :  E. D. Lenherr, M. Hothorn, K. Scheffzek
Date :  02 Feb 09  (Deposition) - 05 May 09  (Release) - 05 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Polyphosphate Polymerase, Polyphosphate Kinase, Vtc Complex, Vacuolar Transporter Chaperone, Tunnel Enzyme, Membrane, Phosphoprotein, Transmembrane, Vacuole, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Hothorn, H. Neumann, E. D. Lenherr, M. Wehner, V. Rybin, P. O. Hassa, A. Uttenweiler, M. Reinhardt, A. Schmidt, J. Seiler, A. G. Ladurner, C. Herrmann, K. Scheffzek, A. Mayer
Catalytic Core Of A Membrane-Associated Eukaryotic Polyphosphate Polymerase.
Science V. 324 513 2009
PubMed-ID: 19390046  |  Reference-DOI: 10.1126/SCIENCE.1168120
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VACUOLAR TRANSPORTER CHAPERONE 4
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETM11
    Expression System StrainBL21 (DE3) RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 189-480
    GeneJ1345, PHM3, VTC4, YJL012C
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymPHOSPHATE METABOLISM PROTEIN 3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2PO44Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:241 , ARG A:264 , LYS A:281 , SER A:457 , LYS A:458 , PHE A:459BINDING SITE FOR RESIDUE PO4 A 1000
2AC2SOFTWAREHOH A:115 , ARG A:264 , ARG A:266 , TYR A:268 , GLU A:279 , LYS A:294 , ARG A:296BINDING SITE FOR RESIDUE PO4 A 1001
3AC3SOFTWAREHOH A:104 , HIS A:283 , SER A:292 , HOH A:481BINDING SITE FOR RESIDUE PO4 A 1002
4AC4SOFTWAREHOH A:62 , GLU A:245 , ASN A:387 , PHE A:388BINDING SITE FOR RESIDUE PO4 A 1003
5AC5SOFTWAREHOH A:14 , ILE A:208 , THR A:378 , GLU A:379 , LEU A:380 , PHE A:420 , TYR A:422 , ALA A:423BINDING SITE FOR RESIDUE EDO A 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G3T)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:407 -Pro A:408
2Leu A:433 -Gly A:434

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G3T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G3T)

(-) Exons   (0, 0)

(no "Exon" information available for 3G3T)

(-) 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:274
 aligned with VTC4_YEAST | P47075 from UniProtKB/Swiss-Prot  Length:721

    Alignment length:282
                                   203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473  
           VTC4_YEAST   194 FVRQTTKYWVHPDNITELKLIILKHLPVLVFNTNKEFEREDSAITSIYFDNENLDLYYGRLRKDEGAEAHRLRWYGGMSTDTIFVERKTHREDWTGEKSVKARFALKERHVNDFLKGKYTVDQVFAKMRKEGKKPMNEIENLEALASEIQYVMLKKKLRPVVRSFYNRTAFQLPGDARVRISLDTELTMVREDNFDGVDRTHKNWRRTDIGVDWPFKQLDDKDICRFPYAVLEVKLQTQLGQEPPEWVRELVGSHLVEPVPKFSKFIHGVATLLNDKVDSIP 475
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeehhhhhhhhhhhhhh.....--------hhhh.eeeeeeee...hhhhhhhhh.....eeeeeeee......eeeeeeee..hhhhh...eeeeeeee..hhhhhhh...hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..eeeeeeeeeeeeeeee............................hhh.eee...eeeeeeeee......hhhhhhhhh....ee....hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3g3t A 194 FVRQTTKYWVHPDNITELKLIILKHLPVL--------EREDSAITSIYFDNENLDLYYGRLRKDEGAEAHRLRWYGGMSTDTIFVERKTHREDWTGEKSVKARFALKERHVNDFLKGKYTVDQVFAKMRKEGKKPMNEIENLEALASEIQYVMLKKKLRPVVRSFYNRTAFQLPGDARVRISLDTELTMVREDNFDGVDRTHKNWRRTDIGVDWPFKQLDDKDICRFPYAVLEVKLQTQLGQEPPEWVRELVGSHLVEPVPKFSKFIHGVATLLNDKVDSIP 475
                                   203       213        |-       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473  
                                                      222      231                                                                                                                                                                                                                                                    

   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 3G3T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3G3T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G3T)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VTC4_YEAST | P47075)
molecular function
    GO:0008976    polyphosphate kinase activity    Catalysis of the reaction: ATP + phosphate(n) = ADP + phosphate(n+1).
    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).
biological process
    GO:0016237    lysosomal microautophagy    The transfer of cytosolic components into the lysosomal compartment by direct invagination of the lysosomal membrane without prior sequestration into an autophagosome. The engulfing membranes fuse, resulting in the lysosomal delivery of the cargo wrapped in a single membrane derived from the invaginated lysosomal membrane. In S. cerevisiae, the vacuole is the lysosomal compartment.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006797    polyphosphate metabolic process    The chemical reactions and pathways involving a polyphosphate, the anion or salt of polyphosphoric acid.
    GO:0007034    vacuolar transport    The directed movement of substances into, out of or within a vacuole.
    GO:0042144    vacuole fusion, non-autophagic    The fusion of two vacuole membranes to form a single vacuole.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0000329    fungal-type vacuole membrane    The lipid bilayer surrounding a vacuole, the shape of which correlates with cell cycle phase. The membrane separates its contents from the cytoplasm of the cell. An example of this structure is found in Saccharomyces cerevisiae.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0031310    intrinsic component of vacuolar membrane    The component of the vacuolar membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005774    vacuolar membrane    The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.
    GO:0033254    vacuolar transporter chaperone complex    A protein complex that contains four related proteins that have been implicated in several membrane-related processes, such as sorting of H+-translocating ATPases, endocytosis, ER-Golgi trafficking, vacuole fusion, vacuolar polyphosphate homeostasis and the microautophagic scission of vesicles into the vacuolar lumen. The complex is enriched at the vacuolar membrane, but also found in other cellular compartments, including the ER and the cell periphery. In Saccharomyces, the subunits are Vtc1p, Vtc2p, Vtc3p and Vtc4p.
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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 Related Entries

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

UniProtKB/Swiss-Prot
        VTC4_YEAST | P470753g3q 3g3r 3g3u 5iig 5iiq 5iit 5lnc

(-) Related Entries Specified in the PDB File

3g3o CRYSTAL STRUCTURE OF THE CATALYTICALLY IMPAIRED SUBUNIT VTC2P THAT IS PART OF THE SAME MEMBRANE-INTEGRAL PROTEIN COMPLEX
3g3q EUKARYOTIC POLYPHOSPHATE POLYMERASE IN COMPLEX WITH A PHOSPHATE POLYMER
3g3r EUKARYOTIC POLYPHOSPHATE POLYMERASE IN COMPLEX WITH APPNHP- MN2+
3g3u STRUCTURE OF A EUKARYOTIC POLYPHOSPHATE POLYMERASE IN COMPLEX WITH PYROPHOSPHATE