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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CYTOPLASMIC TUNNEL DOMAIN IN YEAST VTC2P
 
Authors :  M. Hothorn, K. Scheffzek
Date :  02 Feb 09  (Deposition) - 05 May 09  (Release) - 05 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
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 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETM11
    Expression System StrainBL21 (DE3) RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 183-553
    GenePHM1, VTC2, YFL004W
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymPHOSPHATE METABOLISM PROTEIN 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:151 , ARG A:305 , ARG A:406 , GLU A:475BINDING SITE FOR RESIDUE SO4 A 1000
2AC2SOFTWAREHOH A:141 , LYS A:294 , THR A:303 , LYS A:323 , SER A:521 , ILE A:522 , PHE A:523 , HOH A:575 , HOH A:588BINDING SITE FOR RESIDUE SO4 A 1001
3AC3SOFTWAREHOH A:131 , THR A:372 , ARG A:437 , ARG A:552 , HOH A:569BINDING SITE FOR RESIDUE SO4 A 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G3O)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:202 -Phe A:203

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G3O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G3O)

(-) Exons   (0, 0)

(no "Exon" information available for 3G3O)

(-) 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 VTC2_YEAST | P43585 from UniProtKB/Swiss-Prot  Length:828

    Alignment length:352
                                   211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551  
           VTC2_YEAST   202 NFRSFKFWVHNDNLMEVKTRILRHLPVLVYANVPSENDDLVNRFESDISNNDEIVGSSSSTSSVEHGLGARSFDPLINTLYFDNEHFELYNDKLLKLNSAPTLRLRWTGQLSDKPDIFLEKKTLIEDEATGKSEFDLTKLQLKQKFINGFIFEGDKKFKEQTLKKLKESGTAGRDLERLEEDFSEIQNFIIKNELQPVFRTVYTRTAFQIPGDDKIRVTIDSNIVFIKEDSFDRERPIRDPNTWHRTDIDANVANPLKFLRGGEYAKFPYSVMEIKVKSSLDSSMSASSMISNVKLPKKHGQWLNDLTNSHLVKEIPKFSIFVQGVASLYGDDEKLDILPFWLPDLETDIRQ 553
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeehhhhhhhhhhhhhh......--------------------------------------------...eeeeeee...hhhhhhhhhh.....eeeeeee.hhhhh..eeeeeeee.-------..eeeeeeeehhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeee.......eeeeeeeeeeeee................................hhh.eee...eeeeeee.----------...--------.hhhhhhhhh....ee....hhhhhhhhhhhhhhh.........--....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g3o A 202 NFRSFKFWVHNDNLmEVKTRILRHLPVLV--------------------------------------------DPLINTLYFDNEHFELYNDKLLKLNSAPTLRLRWTGQLSDKPDIFLEKKTLI-------SEFDLTKLQLKQKFINGFIFEGDKKFKEQTLKKLKESGTAGRDLERLEEDFSEIQNFIIKNELQPVFRTVYTRTAFQIPGDDKIRVTIDSNIVFIKEDSFDRERPIRDPNTWHRTDIDANVANPLKFLRGGEYAKFPYSVmEIKVK----------SmI--------HGQWLNDLTNSHLVKEIPKFSIFVQGVASLYGDDEKLDILPFWL--LETDIRQ 553
                                   211    |  221        |-         -         -         -         -   |   281       291       301       311       321    |    -  |    341       351       361       371       381       391       401       411       421       431       441       451       461       471  |    | -       491|      501       511       521       531       541  |  | 551  
                                        216-MSE       230                                          275                                                326     334                                                                                                                                         474-MSE9        490||      501                                        544  |      
                                                                                                                                                                                                                                                                                                                           491-MSE                                                 547      
                                                                                                                                                                                                                                                                                                                            492                                                             

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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  (0, 0)

(no "SCOP Domain" information available for 3G3O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3G3O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G3O)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VTC2_YEAST | P43585)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
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:0006797    polyphosphate metabolic process    The chemical reactions and pathways involving a polyphosphate, the anion or salt of polyphosphoric acid.
    GO:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
    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: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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