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(-) Description

Title :  SELF-ACETYLATION MEDIATED HISTONE H3 LYSINE 56 ACETYLATION BY RTT109
 
Authors :  Y. A. Yuan
Date :  08 Jan 08  (Deposition) - 23 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Histone H3 Lysine 56 Acetylation, Dna Damage, Dna Repair, Nucleus, Transcription, Transcription Regulation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Lin, Y. A. Yuan
Structural Insights Into Histone H3 Lysine 56 Acetylation B Rtt109
Structure V. 16 1503 2008
PubMed-ID: 18707894  |  Reference-DOI: 10.1016/J.STR.2008.07.006

(-) Compounds

Molecule 1 - REGULATOR OF TY1 TRANSPOSITION PROTEIN 109
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneRTT109, KIM2, REM50
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymRTT109

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1ACO1Ligand/IonACETYL COENZYME *A
2ALY1Mod. Amino AcidN(6)-ACETYLLYSINE
3GOL1Ligand/IonGLYCEROL
4MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:86 , LYS A:87 , ALA A:88 , ASP A:89 , THR A:90 , ARG A:101 , PHE A:192 , ARG A:194 , PRO A:195 , ALA A:196 , TYR A:199 , LYS A:210 , HIS A:211 , ILE A:212 , LEU A:213 , LEU A:218 , TRP A:221 , TRP A:222 , THR A:271 , SER A:272 , HOH A:803 , HOH A:851 , HOH A:867 , HOH A:901BINDING SITE FOR RESIDUE ACO A 500
2AC2SOFTWARESER A:86 , LYS A:87 , PHE A:192 , TYR A:199 , ASP A:287 , PRO A:289BINDING SITE FOR RESIDUE GOL A 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZFN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZFN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZFN)

(-) PROSITE Motifs  (1, 1)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZFN)

(-) 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:376
 aligned with RT109_YEAST | Q07794 from UniProtKB/Swiss-Prot  Length:436

    Alignment length:408
                                1                                                                                                                                                                                                                                                                                                                                                                                                                   
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396        
          RT109_YEAST     - ----MSLNDFLSSVLPVSEQFEYLSLQSIPLETHAVVTPNKDDKRVPKSTIKTQHFFSLFHQGKVFFSLEVYVYVTLWDEADAERLIFVSKADTNGYCNTRVSVRDITKIILEFILSIDPNYYLQKVKPAIRSYKKISPELISAASTPARTLRILARRLKQSGSTVLKEIESPRFQQDLYLSFTCPREILTKICLFTRPASQYLFPDSSKNSKKHILNGEELMKWWGFILDRLLIECFQNDTQAKLRIPGEDPARVRSYLRGMKYPLWQVGDIFTSKENSLAVYNIPLFPDDPKARFIHQLAEEDRLLKVSLSSFWIELQERQEFKLSVTSSVMGISGYSLATPSLFPSSADVIVPKSRKQFRAIKKYITGEEYDTEEGAIEAFTNIRDFLLLRMATNLQSLTGKREH 404
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------KAT11-2zfnA01 A:3-404                                                                                                                                                                                                                                                                                                                                                                                              Pfam domains
         Sec.struct. author .....hhhhhhhhhh....eeeeeeee...eee...............eeeeeeeeeeeee..eeeeeeeeeeeeee.....eeeeeeeeeeee........hhhhhhhhhhhhhhh..hhhhhh............hhhhh....--------------------------------...........eeeeeeee.........hhhhh......hhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhh......eee..........hhhhh......hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...eeeeeee...................hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----RTT109_HAT  PDB: A:2-404 UniProt: 2-404                                                                                                                                                                                                                                                                                                                                                                             PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zfn A  1D MAAmmSLNDFLSSVLPVSEQFEYLSLQSIPLETHAVVTPNKDDKRVPKSTIKTQHFFSLFHQGKVFFSLEVYVYVTLWDEADAERLIFVSKADTNGYCNTRVSVRDITKIILEFILSIDPNYYLQKVKPAIRSYKKISPELISAAS--------------------------------LYLSFTCPREILTKICLFTRPASQYLFPDSSKNSKKHILNGEELmKWWGFILDRLLIECFQNDTQAKLRIPGEDPARVRSYLRGmKYPLWQVGDIFTSKENSLAVYNIPLFPDDPkARFIHQLAEEDRLLKVSLSSFWIELQERQEFKLSVTSSVmGISGYSLATPSLFPSSADVIVPKSRKQFRAIKKYITGEEYDTEEGAIEAFTNIRDFLLLRmATNLQSLTGKREH 404
                            |||||    6        16        26        36        46        56        66        76        86        96       106       116       126       136     |   -         -         -       176       186       196       206       216  |    226       236       246       256  |    266       276       286   |   296       306       316       326   |   336       346       356       366       376       386    |  396        
                            |||||                                                                                                                                          142                              175                                         219-MSE                                 259-MSE                        290-ALY                                 330-MSE                                                      391-MSE         
                           1D||||                                                                                                                                                                                                                                                                                                                                                                                                                   
                            1C|||                                                                                                                                                                                                                                                                                                                                                                                                                   
                             1B||                                                                                                                                                                                                                                                                                                                                                                                                                   
                              1A-MSE                                                                                                                                                                                                                                                                                                                                                                                                                
                                1-MSE                                                                                                                                                                                                                                                                                                                                                                                                               

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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 2ZFN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZFN)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (14, 14)

Asymmetric/Biological 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RT109_YEAST | Q077942rim 3cz7 3q33 3q35 3q66 3q68 3qm0

(-) Related Entries Specified in the PDB File

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