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(-) Description

Title :  STRUCTURE OF THE RTT109-ACCOA/VPS75 COMPLEX AND IMPLICATIONS FOR CHAPERONE-MEDIATED HISTONE ACETYLATION
 
Authors :  Y. Tang, H. Yuan, K. Meeth, R. Marmorstein
Date :  21 Dec 10  (Deposition) - 02 Feb 11  (Release) - 23 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Rtt109:Vps75=2:2 Stoichiometry Complex, Acetyl Coenzyme A (Acoa) Bound, Autoacetylation At Rtt109 Lys290, Nuclear, Transferase- Chaperone Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Tang, M. A. Holbert, N. Delgoshaie, H. Wurtele, B. Guillemette, K. Meeth, H. Yuan, P. Drogaris, E. H. Lee, C. Durette, P. Thibault, A. Verreault, P. A. Cole, R. Marmorstein
Structure Of The Rtt109-Accoa/Vps75 Complex And Implication For Chaperone-Mediated Histone Acetylation.
Structure V. 19 221 2011
PubMed-ID: 21256037  |  Reference-DOI: 10.1016/J.STR.2010.12.012
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HISTONE ACETYLTRANSFERASE
    ChainsA
    EC Number2.3.1.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Plasmid6HIS-TEV-PCDF-DUET
    Expression System StrainBL21(DE3) GOLD
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneKIM2, L1377, REM50, RTT109, YLL002W
    Organism CommonBREWER'S YEAST,LAGER BEER YEAST,YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymREGULATOR OF TY1 TRANSPOSITION PROTEIN 109
 
Molecule 2 - VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidGST-TEV-PRSF-DUET
    Expression System StrainBL21(DE3) GOLD
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1-232
    GeneN0890, VPS75, YNL246W
    Organism CommonBREWER'S YEAST,LAGER BEER YEAST,YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1ACO1Ligand/IonACETYL COENZYME *A
2ALY1Mod. Amino AcidN(6)-ACETYLLYSINE
3EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1ACO2Ligand/IonACETYL COENZYME *A
2ALY2Mod. Amino AcidN(6)-ACETYLLYSINE
3EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:85 , SER A:86 , ALA A:88 , ASP A:89 , THR A:90 , VAL A:98 , VAL A:100 , ARG A:101 , PHE A:192 , ARG A:194 , PRO A:195 , ALA A:196 , TYR A:199 , LYS A:210 , HIS A:211 , LEU A:213 , TRP A:221 , TRP A:222 , EDO A:437BINDING SITE FOR RESIDUE ACO A 999
2AC2SOFTWARESER A:86 , PHE A:192 , ARG A:194 , TYR A:199 , ACO A:999BINDING SITE FOR RESIDUE EDO A 437

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q35)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q35)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q35)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RTT109_HATPS51728 Rtt109-type histone acetyltransferase (HAT) domain profile.RT109_YEAST2-404  1A:2-404
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RTT109_HATPS51728 Rtt109-type histone acetyltransferase (HAT) domain profile.RT109_YEAST2-404  2A:2-404

(-) Exons   (0, 0)

(no "Exon" information available for 3Q35)

(-) Sequences/Alignments

Asymmetric 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:394
 aligned with RT109_YEAST | Q07794 from UniProtKB/Swiss-Prot  Length:436

    Alignment length:404
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400    
          RT109_YEAST     1 MSLNDFLSSVLPVSEQFEYLSLQSIPLETHAVVTPNKDDKRVPKSTIKTQHFFSLFHQGKVFFSLEVYVYVTLWDEADAERLIFVSKADTNGYCNTRVSVRDITKIILEFILSIDPNYYLQKVKPAIRSYKKISPELISAASTPARTLRILARRLKQSGSTVLKEIESPRFQQDLYLSFTCPREILTKICLFTRPASQYLFPDSSKNSKKHILNGEELMKWWGFILDRLLIECFQNDTQAKLRIPGEDPARVRSYLRGMKYPLWQVGDIFTSKENSLAVYNIPLFPDDPKARFIHQLAEEDRLLKVSLSSFWIELQERQEFKLSVTSSVMGISGYSLATPSLFPSSADVIVPKSRKQFRAIKKYITGEEYDTEEGAIEAFTNIRDFLLLRMATNLQSLTGKREH 404
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --KAT11-3q35A01 A:3-404                                                                                                                                                                                                                                                                                                                                                                                              Pfam domains
         Sec.struct. author .hhhhhhhh......eeeeeeee...eee...............eeeeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeeeee........hhhhhhhhhhhhhhhh..hhhhh........----.........hhhhhhhhhhhhhhhh.......------..............eeeeeeee.........hhhhh......hhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhh.......ee..........hhhhh......hhhhhhhhhhhhh......hhhhhhhhhhh..........eeeeeee...................hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...eeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -RTT109_HAT  PDB: A:2-404 UniProt: 2-404                                                                                                                                                                                                                                                                                                                                                                             PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q35 A   1 MSLNDFLSSVLPVSEQFEYLSLQSIPLETHAVVTPNKDDKRVPKSTIKTQHFFSLFHQGKVFFSLEVYVYVTLWDEADAERLIFVSKADTNGYCNTRVSVRDITKIILEFILSIDPNYYLQKVKPAIRS----SPELISAASTPARTLRILARRLKQSGSTVLKE------QQDLYLSFTCPREILTKICLFTRPASQYLFPDSSKNSKKHILNGEELMKWWGFILDRLLIECFQNDTQAKLRIPGEDPARVRSYLRGMKYPLWQVGDIFTSKENSLAVYNIPLFPDDPkARFIHQLAEEDRLLKVSLSSFWIELQERQEFKLSVTSSVMGISGYSLATPSLFPSSADVIVPKSRKQFRAIKKYITGEEYDTEEGAIEAFTNIRDFLLLRMATNLQSLTGKREH 404
                                    10        20        30        40        50        60        70        80        90       100       110       120        |-   |   140       150       160    |    - |     180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400    
                                                                                                                                                          129  134                            165    172                                                                                                                   290-ALY                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:213
 aligned with VPS75_YEAST | P53853 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:218
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218        
          VPS75_YEAST     9 NEHAKAFLGLAKCEEEVDAIEREVELYRLNKMKPVYEKRDAYIDEIAEFWKIVLSQHVSFANYIRASDFKYIDTIDKIKVEWLALESEMYDTRDFSITFHFHGIEGDFKEQQVTKVFQIKKGKDDQEDGILTSEPVPIEWPQSYDSINPDLIKDKRSPEGKKKYRQGMKTIFGWFRWTGLKPGKEFPHGDSLASLFSEEIYPFCVKYYAEAQRDLEDE 226
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains NAP-3q35B01 B:9-220                                                                                                                                                                                                 ------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhh.eeeeeeee.hhh........eeeeeee.........eeeeeeeeee..-----..eeee........hhhhh.hhhhh....hhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q35 B   9 NEHAKAFLGLAKCEEEVDAIEREVELYRLNKMKPVYEKRDAYIDEIAEFWKIVLSQHVSFANYIRASDFKYIDTIDKIKVEWLALESEMYDTRDFSITFHFHGIEGDFKEQQVTKVFQIKKG-----DGILTSEPVPIEWPQSYDSINPDLIKDKRSPEGKKKYRQGMKTIFGWFRWTGLKPGKEFPHGDSLASLFSEEIYPFCVKYYAEAQRDLEDE 226
                                    18        28        38        48        58        68        78        88        98       108       118       128 |     138       148       158       168       178       188       198       208       218        
                                                                                                                                                   130   136                                                                                          

   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 3Q35)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q35)

(-) Pfam Domains  (2, 2)

Asymmetric Unit

(-) Gene Ontology  (24, 26)

Asymmetric Unit(hide GO term definitions)
Chain A   (RT109_YEAST | Q07794)
molecular function
    GO:0010484    H3 histone acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + histone H3 = CoA + acetyl-histone H3.
    GO:0004402    histone acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    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:0043966    histone H3 acetylation    The modification of histone H3 by the addition of an acetyl group.
    GO:0016573    histone acetylation    The modification of a histone by the addition of an acetyl group.
    GO:0043007    maintenance of rDNA    Any process involved in sustaining the fidelity and copy number of rDNA repeats.
    GO:0010526    negative regulation of transposition, RNA-mediated    Any process that decreases the frequency, rate or extent of RNA-mediated transposition. RNA-mediated transposition is a type of transpositional recombination which occurs via an RNA intermediate.
    GO:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0043618    regulation of transcription from RNA polymerase II promoter in response to stress    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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.

Chain 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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  VPS75_YEAST | P53853
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 Related Entries

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

UniProtKB/Swiss-Prot
        RT109_YEAST | Q077942rim 2zfn 3cz7 3q33 3q66 3q68 3qm0
        VPS75_YEAST | P538532zd7 3c9b 3c9d 3dm7 3q33 3q66 3q68 5agc

(-) Related Entries Specified in the PDB File

3d35 RTT109 D(130-179) BOUND WITH ACO
3dm7 VPS75 (1-232) HOMODIMER STRUCTURE
3q33 RTT109-VPS75 COMPLEX BOUND WITH ACO AND SOAKED WITH H3K9 PEPTIDE