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(-) Description

Title :  CRYSTAL STRUCTURE OF THE REGULATORY SUBUNIT H OF THE V-TYPE ATPASE OF SACCHAROMYCES CEREVISIAE
 
Authors :  M. Sagermann, T. H. Stevens, B. W. Matthews
Date :  10 Dec 00  (Deposition) - 20 Jun 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Heat Repeat, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sagermann, T. H. Stevens, B. W. Matthews
Crystal Structure Of The Regulatory Subunit H Of The V-Type Atpase Of Saccharomyces Cerevisiae.
Proc. Natl. Acad. Sci. Usa V. 98 7134 2001
PubMed-ID: 11416198  |  Reference-DOI: 10.1073/PNAS.131192798
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VACUOLAR ATP SYNTHASE SUBUNIT H
    Chains: A
    EC Number: 3.6.1.34
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX4T3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: VMA13, V-ATPASE H SUBUNIT, VACUOLAR PROTON PUMP H SUBUNIT, V-ATPASE 54 KDA SUBUNIT

 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
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:9 , SER A:10 , THR A:11 , HIS A:12 , TYR A:184 , ARG A:188 , GLN A:241BINDING SITE FOR RESIDUE SO4 A 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HO8)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ile A:282 -Lys A:283

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HO8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1HO8)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPR036W1YPR036W.1XVI:643833-6452691437VATH_YEAST1-4784781A:2-478 (gaps)477

(-) 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:447
 aligned with VATH_YEAST | P41807 from UniProtKB/Swiss-Prot  Length:478

    Alignment length:477
                                    11        21        31        41        51        61        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       351       361       371       381       391       401       411       421       431       441       451       461       471       
           VATH_YEAST     2 GATKILMDSTHFNEIRSIIRSRSVAWDALARSEELSEIDASTAKALESILVKKNIGDGLSSSNNAHSGFKVNGKTLIPLIHLLSTSDNEDCKKSVQNLIAELLSSDKYGDDTVKFFQEDPKQLEQLFDVSLKGDFQTVLISGFNVVSLLVQNGLHNVKLVEKLLKNNNLINILQNIEQMDTCYVCIRLLQELAVIPEYRDVIWLHEKKFMPTLFKILQRATDSQLATRIVATNSNHLGIQLQYHSLLLIWLLTFNPVFANELVQKYLSDFLDLLKLVKITIKEKVSRLCISIILQCCSTRVKQHKKVIKQLLLLGNALPTVQSLSERKYSDEELRQDISNLKEILENEYQELTSFDEYVAELDSKLLCWSPPHVDNGFWSDNIDEFKKDNYKIFRQLIELLQAKVRNGDVNAKQEKIIIQVALNDITHVVELLPESIDVLDKTGGKADIMELLNHSDSRVKYEALKATQAIIGYTFK 478
               SCOP domains d1ho8a_ A: Regulatory subunit H of the V-type ATPase                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1ho8A01 A:2-354 Leucine-rich Repeat Variant                                                                                                                                                                                                                                                                                                                      -----------1ho8A02 A:366-477  [code=1.25.40.150, no name defined]                                                          - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhh..hhhhhhhh...hhhhhhhhhhhhhhhhh-----------------.....hhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-------------.hhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:2-478 (gaps) UniProt: 1-478 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                     Transcript 1
                 1ho8 A   2 GATKILMDSTHFNEIRSIIRSRSVAWDALARSEELSEIDASTAKALESILVK-----------------KVNGKTLIPLIHLLSTSDNEDCKKSVQNLIAELLSSDKYGDDTVKFFQEDPKQLEQLFDVSLKGDFQTVLISGFNVVSLLVQNGLHNVKLVEKLLKNNNLINILQNIEQMDTCYVCIRLLQELAVIPEYRDVIWLHEKKFMPTLFKILQRATD-------------HLGIQLQYHSLLLIWLLTFNPVFANELVQKYLSDFLDLLKLVKITIKEKVSRLCISIILQCCSTRVKQHKKVIKQLLLLGNALPTVQSLSERKYSDEELRQDISNLKEILENEYQELTSFDEYVAELDSKLLCWSPPHVDNGFWSDNIDEFKKDNYKIFRQLIELLQAKVRNGDVNAKQEKIIIQVALNDITHVVELLPESIDVLDKTGGKADIMELLNHSDSRVKYEALKATQAIIGYTFK 478
                                    11        21        31        41        51 |       -        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 |       -     | 241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       
                                                                              53                71                                                                                                                                                     223           237
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HO8)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VATH_YEAST | P41807)
molecular function
    GO:0016820    hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances    Catalysis of the hydrolysis of an acid anhydride to directly drive the transport of a substance across a membrane.
    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: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: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
        VATH_YEAST | P41807: 3j9t 3j9u 3j9v 5bw9 5d80 5vox 5voy 5voz

(-) Related Entries Specified in the PDB File

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