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(-) Description

Title :  CRYSTAL STRUCTURE OF SEMET VPS75
 
Authors :  J. L. Keck, C. E. Berndsen, T. Tsubota, S. E. Lindner, S. Lee, J. M. Holton P. D. Kaufman, J. M. Denu
Date :  15 Feb 08  (Deposition) - 12 Aug 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.42
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Chromatin, Hat, Histone Chaperone, Nucleus, Phosphoprotein, Protein Transport, Transport, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. E. Berndsen, T. Tsubota, S. E. Lindner, S. Lee, J. M. Holton, P. D. Kaufman, J. L. Keck, J. M. Denu
Molecular Functions Of The Histone Acetyltransferase Chaperone Complex Rtt109-Vps75
Nat. Struct. Mol. Biol. V. 15 948 2008
PubMed-ID: 19172748  |  Reference-DOI: 10.1038/NSMB.1459

(-) Compounds

Molecule 1 - VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21 ROSETTA
    Expression System Vector Type: PLASMID
    Gene: VPS75
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3C9B)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C9B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3C9B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C9B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3C9B)

(-) Exons   (0, 0)

(no "Exon" information available for 3C9B)

(-) 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:198
 aligned with VPS75_YEAST | P53853 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:211
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 
          VPS75_YEAST    11 HAKAFLGLAKCEEEVDAIEREVELYRLNKMKPVYEKRDAYIDEIAEFWKIVLSQHVSFANYIRASDFKYIDTIDKIKVEWLALESEMYDTRDFSITFHFHGIEGDFKEQQVTKVFQIKKGKDDQEDGILTSEPVPIEWPQSYDSINPDLIKDKRSPEGKKKYRQGMKTIFGWFRWTGLKPGKEFPHGDSLASLFSEEIYPFCVKYYAEAQR 221
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh.eeeeeeee.hhh........eeeeeee.........eeeeeeeeee.------..eeee.......hhhhhhhh....-------hhhhhhhhh.hhhhhh............hhhhhhhhhhhh...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c9b A  11 HAKAFLGLAKCEEEVDAIEREVELYRLNKmKPVYEKRDAYIDEIAEFWKIVLSQHVSFANYIRASDFKYIDTIDKIKVEWLALESEmYDTRDFSITFHFHGIEGDFKEQQVTKVFQIKK------DGILTSEPVPIEWPQSYDSINPDLI-------GKKKYRQGmKTIFGWFRWTGLKPGKEFPHGDSLASLFSEEIYPFCVKYYAEAQR 221
                                    20        30        40        50        60        70        80        90      |100       110       120        |-     | 140       150       160       170     | 180       190       200       210       220 
                                                        40-MSE                                                   97-MSE                         129    136                     160     168     176-MSE                                         


Chain B from PDB  Type:PROTEIN  Length:199
 aligned with VPS75_YEAST | P53853 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:205
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216     
          VPS75_YEAST    17 GLAKCEEEVDAIEREVELYRLNKMKPVYEKRDAYIDEIAEFWKIVLSQHVSFANYIRASDFKYIDTIDKIKVEWLALESEMYDTRDFSITFHFHGIEGDFKEQQVTKVFQIKKGKDDQEDGILTSEPVPIEWPQSYDSINPDLIKDKRSPEGKKKYRQGMKTIFGWFRWTGLKPGKEFPHGDSLASLFSEEIYPFCVKYYAEAQR 221
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh.eeeeeeee.hhh........eeeeeee.........eeeeeeeeee.------..eeee.......hhhhhhhh........hhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c9b B  17 GLAKCEEEVDAIEREVELYRLNKmKPVYEKRDAYIDEIAEFWKIVLSQHVSFANYIRASDFKYIDTIDKIKVEWLALESEmYDTRDFSITFHFHGIEGDFKEQQVTKVFQIKK------DGILTSEPVPIEWPQSYDSINPDLIKDKRSPEGKKKYRQGmKTIFGWFRWTGLKPGKEFPHGDSLASLFSEEIYPFCVKYYAEAQR 221
                                    26        36   |    46        56        66        76        86        96|      106       116       126  |    136       146       156       166       176       186       196       206       216     
                                                  40-MSE                                                   97-MSE                         129    136                                     176-MSE
   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 3C9B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3C9B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C9B)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (VPS75_YEAST | P53853)
molecular function
    GO:0010698    acetyltransferase activator activity    Binds to and increases the activity of an acetyltransferase, an enzyme which catalyzes the transfer of an acetyl group to an acceptor molecule.
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
biological process
    GO:0006303    double-strand break repair via nonhomologous end joining    The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
    GO:0006334    nucleosome assembly    The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:2000617    positive regulation of histone H3-K9 acetylation    Any process that activates or increases the frequency, rate or extent of histone H3-K9 acetylation.
    GO:0035066    positive regulation of histone acetylation    Any process that activates or increases the frequency, rate or extent of the addition of an acetyl group to a histone protein.
    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: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:0000785    chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
    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:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        VPS75_YEAST | P53853: 2zd7 3c9d 3dm7 3q33 3q35 3q66 3q68 5agc

(-) Related Entries Specified in the PDB File

3c9d VPS75