[English] 日本語
Yorodumi- SASDFL3: All 1H histone acetyltransferase Rtt109 complex with histones H3 ... -
+Open data
-Basic information
Entry | Database: SASBDB / ID: SASDFL3 |
---|---|
Sample | All 1H histone acetyltransferase Rtt109 complex with histones H3 and H4 and histone chaperones Asf1 and Vps75 (acquired in 100% v/v D2O)
|
Function / homology | Function and homology information : / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / histone H3K23 acetyltransferase activity / histone H3K56 acetyltransferase activity / H3 histone acetyltransferase complex / DNA replication-dependent chromatin disassembly / histone H3K14 acetyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K9 acetyltransferase activity / maintenance of rDNA ...: / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / histone H3K23 acetyltransferase activity / histone H3K56 acetyltransferase activity / H3 histone acetyltransferase complex / DNA replication-dependent chromatin disassembly / histone H3K14 acetyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K9 acetyltransferase activity / maintenance of rDNA / acetyltransferase activator activity / replication-born double-strand break repair via sister chromatid exchange / retrotransposon silencing / DNA replication-dependent chromatin assembly / nucleosome disassembly / histone H3 acetyltransferase activity / : / histone H3K27 acetyltransferase activity / silent mating-type cassette heterochromatin formation / peptide-lysine-N-acetyltransferase activity / negative regulation of DNA damage checkpoint / subtelomeric heterochromatin formation / regulation of DNA repair / histone acetyltransferase / positive regulation of transcription elongation by RNA polymerase II / regulation of protein phosphorylation / protein modification process / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / nucleosome / nucleosome assembly / protein transport / chromatin organization / histone binding / regulation of gene expression / chromosome, telomeric region / protein heterodimerization activity / DNA damage response / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function |
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Xenopus laevis (African clawed frog) |
Citation | Journal: Nat Commun / Year: 2019 Title: Histone chaperone exploits intrinsic disorder to switch acetylation specificity. Authors: Nataliya Danilenko / Lukas Lercher / John Kirkpatrick / Frank Gabel / Luca Codutti / Teresa Carlomagno / Abstract: Histones, the principal protein components of chromatin, contain long disordered sequences, which are extensively post-translationally modified. Although histone chaperones are known to control both ...Histones, the principal protein components of chromatin, contain long disordered sequences, which are extensively post-translationally modified. Although histone chaperones are known to control both the activity and specificity of histone-modifying enzymes, the mechanisms promoting modification of highly disordered substrates, such as lysine-acetylation within the N-terminal tail of histone H3, are not understood. Here, to understand how histone chaperones Asf1 and Vps75 together promote H3 K9-acetylation, we establish the solution structural model of the acetyltransferase Rtt109 in complex with Asf1 and Vps75 and the histone dimer H3:H4. We show that Vps75 promotes K9-acetylation by engaging the H3 N-terminal tail in fuzzy electrostatic interactions with its disordered C-terminal domain, thereby confining the H3 tail to a wide central cavity faced by the Rtt109 active site. These fuzzy interactions between disordered domains achieve localization of lysine residues in the H3 tail to the catalytic site with minimal loss of entropy, and may represent a common mechanism of enzymatic reactions involving highly disordered substrates. |
Contact author |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Data source
SASBDB page | SASDFL3 |
---|
-Related structure data
-External links
Related items in Molecule of the Month |
---|
-Models
Model #2824 | Type: atomic / Chi-square value: 27.844 / P-value: 0.000870 Search similar-shape structures of this assembly by Omokage search (details) |
---|
-Sample
Sample | Name: All 1H histone acetyltransferase Rtt109 complex with histones H3 and H4 and histone chaperones Asf1 and Vps75 (acquired in 100% v/v D2O) Specimen concentration: 2.35 mg/ml / Entity id: 1488 / 1489 / 1490 / 1491 / 1492 |
---|---|
Buffer | Name: 50 mM citrate, 150 mM NaCl, 5 mM BME, 100% D2O / pH: 6.5 |
Entity #1488 | Name: Vps75 1-225 / Type: protein Description: Vacuolar protein sorting-associated protein 75 (1-225 aa)Vacuole Formula weight: 26.554 / Num. of mol.: 2 Source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) References: UniProt: P53853 Sequence: MMSDQENENE HAKAFLGLAK CEEEVDAIER EVELYRLNKM KPVYEKRDAY IDEIAEFWKI VLSQHVSFAN YIRASDFKYI DTIDKIKVEW LALESEMYDT RDFSITFHFH GIEGDFKEQQ VTKVFQIKKG KDDQEDGILT SEPVPIEWPQ SYDSINPDLI KDKRSPEGKK ...Sequence: MMSDQENENE HAKAFLGLAK CEEEVDAIER EVELYRLNKM KPVYEKRDAY IDEIAEFWKI VLSQHVSFAN YIRASDFKYI DTIDKIKVEW LALESEMYDT RDFSITFHFH GIEGDFKEQQ VTKVFQIKKG KDDQEDGILT SEPVPIEWPQ SYDSINPDLI KDKRSPEGKK KYRQGMKTIF GWFRWTGLKP GKEFPHGDSL ASLFSEEIYP FCVKYYAEAQ RDLED |
Entity #1489 | Name: Rtt109 / Type: protein / Description: Histone acetyltransferase RTT109 / Formula weight: 50.095 / Num. of mol.: 1 Source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) References: UniProt: Q07794 Sequence: MSLNDFLSSV LPVSEQFEYL SLQSIPLETH AVVTPNKDDK RVPKSTIKTQ HFFSLFHQGK VFFSLEVYVY VTLWDEADAE RLIFVSKADT NGYCNTRVSV RDITKIILEF ILSIDPNYYL QKVKPAIRSY KKISPELISA ASTPARTLRI LARRLKQSGS TVLKEIESPR ...Sequence: MSLNDFLSSV LPVSEQFEYL SLQSIPLETH AVVTPNKDDK RVPKSTIKTQ HFFSLFHQGK VFFSLEVYVY VTLWDEADAE RLIFVSKADT NGYCNTRVSV RDITKIILEF ILSIDPNYYL QKVKPAIRSY KKISPELISA ASTPARTLRI LARRLKQSGS TVLKEIESPR FQQDLYLSFT CPREILTKIC LFTRPASQYL FPDSSKNSKK HILNGEELMK WWGFILDRLL IECFQNDTQA KLRIPGEDPA RVRSYLRGMK YPLWQVGDIF TSKENSLAVY NIPLFPDDPK ARFIHQLAEE DRLLKVSLSS FWIELQERQE FKLSVTSSVM GISGYSLATP SLFPSSADVI VPKSRKQFRA IKKYITGEEY DTEEGAIEAF TNIRDFLLLR MATNLQSLTG KREHRERNQP VPASNINTLA ITMLKPRKKA KALPKT |
Entity #1490 | Name: Asf1 / Type: protein / Description: Histone chaperone ASF1 / Formula weight: 19.125 / Num. of mol.: 1 / References: UniProt: P32447 Sequence: MSIVSLLGIK VLNNPAKFTD PYEFEITFEC LESLKHDLEW KLTYVGSSRS LDHDQELDSI LVGPVPVGVN KFVFSADPPS AELIPASELV SVTVILLSCS YDGREFVRVG YYVNNEYDEE ELRENPPAKV QVDHIVRNIL AEKPRVTRFN IVWDNENEGD LYPPEQPGV |
Entity #1491 | Name: H3 (35-135) / Type: protein / Description: Histone H3.2 (35-135 aa) / Formula weight: 11.747 / Num. of mol.: 1 / Source: Xenopus laevis / References: UniProt: P84233 Sequence: VKKPHRYRPG TVALREIRRY QKSTELLIRK LPFQRLVREI AQDFKTDLRF QSAAIGALQE ASEAYLVGLF EDTNLCAIHA KRVTIMPKDI QLARRIRGER A |
Entity #1492 | Name: H4 / Type: protein / Description: Histone H4 / Formula weight: 11.367 / Num. of mol.: 1 / Source: Xenopus laevis / References: UniProt: P62799 Sequence: MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGG |
-Experimental information
Beam | Instrument name: FRM2 KWS1 / City: Munich / 国: Germany / Type of source: neutron source / Wavelength: 0.5 Å / Dist. spec. to detc.: 4 mm | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Detector | Name: 6Li-Scintillator 1 mm thickness + photomultiplier / Type: SANS / Pixsize x: 5.3 mm | |||||||||||||||||||||
Scan | Title: All 1H histone acetyltransferase Rtt109 complex with histones H3 and H4 and histone chaperones Asf1 and Vps75 (acquired in 100% v/v D2O) Measurement date: Mar 3, 2017 / Storage temperature: 25 °C / Cell temperature: 25 °C / Exposure time: 7200 sec. / Number of frames: 1 / Unit: 1/A /
| |||||||||||||||||||||
Distance distribution function P(R) | Sofotware P(R): GNOM 4.6 / Number of points: 89 /
| |||||||||||||||||||||
Result | Experimental MW: 145 kDa / Type of curve: single_conc
|