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(-) Description

Title :  CRYSTAL STRUCTURE OF SUBUNIT C (VMA5P) OF THE YEAST V-ATPASE
 
Authors :  N. Nelson, F. Frolow, O. Drory
Date :  04 Aug 04  (Deposition) - 23 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. Drory, F. Frolow, N. Nelson
Crystal Structure Of Yeast V-Atpase Subunit C Reveals Its Stator Function
Embo Rep. V. 5 1148 2004
PubMed-ID: 15540116  |  Reference-DOI: 10.1038/SJ.EMBOR.7400294
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VACUOLAR ATP SYNTHASE SUBUNIT C
    ChainsA
    EC Number3.6.3.14
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A(+)
    Expression System StrainC43, BL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneVMA5
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymSUBUNIT C VMA5P OF YEAST V-ATPASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1TLA1Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:8 , ALA A:220 , LYS A:335 , ASN A:336 , LEU A:337 , SER A:338 , HOH A:1371 , HOH A:1410 , HOH A:1421 , HOH A:1488 , HOH A:1489 , HOH A:1700 , HOH A:1701BINDING SITE FOR RESIDUE TLA A 1343

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U7L)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:321 -Pro A:322

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U7L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U7L)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YKL080W1YKL080W.1XI:284674-2858521179VATC_YEAST1-3923921A:5-392 (gaps)388

(-) 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:364
 aligned with VATC_YEAST | P31412 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:388
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384        
           VATC_YEAST     5 LYTANDFILISLPQNAQPVTAPGSKTDSWFNETLIGGRAFVSDFKIPEFKIGSLDTLIVESEELSKVDNQIGASIGKIIEILQGLNETSTNAYRTLPINNMPVPEYLENFQWQTRKFKLDKSIKDLITLISNESSQLDADVRATYANYNSAKTNLAAAERKKTGDLSVRSLHDIVKPEDFVLNSEHLTTVLVAVPKSLKSDFEKSYETLSKNVVPASASVIAEDAEYVLFNVHLFKKNVQEFTTAAREKKFIPREFNYSEELIDQLKKEHDSAASLEQSLRVQLVRLAKTAYVDVFINWFHIKALRVYVESVLRYGLPPHFNIKIIAVPPKNLSKCKSELIDAFGFLGGNAFMKDKKGKINKQDTSLHQYASLVDTEYEPFVMYIINL 392
               SCOP domains d1u7la_ A: Vacuolar ATP synthase subunit C                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1u7lA01 A:5-49,A:323-392                     1u7lA02 A:50-171,A:262-322 subunit c (vma5p) of the yeast v-atpase, domain 2                                              1u7lA03 A:172-261  [code=3.30.70.100, no name defined]                                    1u7lA02 A:50-171,A:262-322                                   1u7lA01 A:5-49,A:323-392 Vacuolar a                        tp synthase CATH domains
               Pfam domains ------V-ATPase_C-1u7lA01 A:11-386                                                                                                                                                                                                                                                                                                                                                             ------ Pfam domains
         Sec.struct. author ....eeeeeeeee...........hhhhhhhhhhhhhh.eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhh......eeeeeeeee..hhhhhhhhhhhh.........eeeee...eeeeeeeee..hhhhhhhhhhhh..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee...hhhhhhhhhhhhhhhhhh....------------------------....eeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:5-392 (gaps) UniProt: 1-392 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                            Transcript 1
                 1u7l A   5 LYTANDFILISLPQNAQPVTAPGSKTDSWFNETLIGGRAFVSDFKIPEFKIGSLDTLIVESEELSKVDNQIGASIGKIIEILQGLNETSTNAYRTLPINNMPVPEYLENFQWQTRKFKLDKSIKDLITLISNESSQLDADVRATYANYNSAKTNLAAAERKKTGDLSVRSLHDIVKPEDFVLNSEHLTTVLVAVPKSLKSDFEKSYETLSKNVVPASASVIAEDAEYVLFNVHLFKKNVQEFTTAAREKKFIPREFNYSEELIDQLKKEHDSAASLEQSLRVQLVRLAKTAYVDVFINWFHIKALRVYVESVLRYGLPPHFNIKIIAVPPKNLSKCKSELIDAFGFLGGNAFM------------------------YEPFVMYIINL 392
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354  |      -         -       384        
                                                                                                                                                                                                                                                                                                                                                                                          357                      382          

   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/Biological Unit

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VATC_YEAST | P31412)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0015078    hydrogen ion transmembrane transporter activity    Enables the transfer of hydrogen ions from one side of a membrane to the other.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0046961    proton-transporting ATPase activity, rotational mechanism    Catalysis of the transfer of protons from one side of a membrane to the other according to the reaction: ATP + H2O + H+(in) = ADP + phosphate + H+(out), by a rotational mechanism.
biological process
    GO:0015991    ATP hydrolysis coupled proton transport    The transport of protons against an electrochemical gradient, using energy from ATP hydrolysis.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0015992    proton transport    The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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.
    GO:0007035    vacuolar acidification    Any process that reduces the pH of the vacuole, measured by the concentration of the hydrogen ion.
cellular component
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0033180    proton-transporting V-type ATPase, V1 domain    A protein complex that forms part of a proton-transporting V-type ATPase and catalyzes ATP hydrolysis. The V1 complex consists of: (1) a globular headpiece with three alternating copies of subunits A and B that form a ring, (2) a central rotational stalk composed of single copies of subunits D and F, and (3) a peripheral stalk made of subunits C, E, G and H. Subunits A and B mediate the hydrolysis of ATP at three reaction sites associated with subunit A.
    GO:0005774    vacuolar membrane    The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.
    GO:0000221    vacuolar proton-transporting V-type ATPase, V1 domain    The V1 domain of a proton-transporting V-type ATPase found in the vacuolar membrane.
    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
        VATC_YEAST | P314123j9t 3j9u 3j9v 4dl0 4efa 5vox 5voy 5voz

(-) Related Entries Specified in the PDB File

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