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- SASDFQ3: Complex with 1H histone acetyltransferase Rtt109 and histones H3 ... -

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Basic information

Entry
Database: SASBDB / ID: SASDFQ3
SampleComplex with 1H histone acetyltransferase Rtt109 and histones H3 and H4, 2H histone chaperones Asf1 and Vps75 (1H Rtt109-H3:H4, 2H Asf1-Vps75) acquired in 42% v/v D2O
  • Vacuolar protein sorting-associated protein 75 (1-225 aa)Vacuole (protein), Vps75 1-225, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
  • Histone acetyltransferase RTT109 (protein), Rtt109, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
  • Histone chaperone ASF1 (protein), Asf1
  • Histone H3.2 (35-135 aa) (protein), H3 (35-135), Xenopus laevis
  • Histone H4 (protein), H4, Xenopus laevis
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 ...: / : / 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 / peptidyl-lysine acetylation / replication-born double-strand break repair via sister chromatid exchange / histone H3 acetyltransferase activity / retrotransposon silencing / DNA replication-dependent chromatin assembly / nucleosome disassembly / histone H3K27 acetyltransferase activity / : / silent mating-type cassette heterochromatin formation / peptide-lysine-N-acetyltransferase activity / protein acetylation / subtelomeric heterochromatin formation / negative regulation of DNA damage checkpoint / regulation of DNA repair / histone acetyltransferase / positive regulation of transcription elongation by RNA polymerase II / regulation of protein phosphorylation / nucleosome assembly / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / nucleosome / 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
Histone acetyltransferase Rtt109 / Rtt109-type histone acetyltransferase (HAT) domain profile. / Histone deposition protein Asf1 / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Histone acetyltransferase Rtt109/CBP ...Histone acetyltransferase Rtt109 / Rtt109-type histone acetyltransferase (HAT) domain profile. / Histone deposition protein Asf1 / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone chaperone ASF1 / Vacuolar protein sorting-associated protein 75 / Histone H4 / Histone H3.2 / Histone acetyltransferase RTT109
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Xenopus laevis (African clawed frog)
CitationJournal: 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
  • Nataliya Danilenko (Leibniz University of Hannover, Germany)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Models

Model #2828
Type: atomic / Chi-square value: 4.123 / P-value: 0.000198
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: Complex with 1H histone acetyltransferase Rtt109 and histones H3 and H4, 2H histone chaperones Asf1 and Vps75 (1H Rtt109-H3:H4, 2H Asf1-Vps75) acquired in 42% v/v D2O
Specimen concentration: 4.7 mg/ml / Entity id: 1488 / 1489 / 1490 / 1491 / 1492
BufferName: 50 mM citrate, 150 mM NaCl, 5 mM BME, 42% D2O / pH: 6.5
Entity #1488Name: 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 #1489Name: 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 #1490Name: 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 #1491Name: 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 #1492Name: 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

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Experimental information

BeamInstrument name: FRM2 KWS1 / City: Munich / 国: Germany / Type of source: neutron source / Wavelength: 0.5 Å / Dist. spec. to detc.: 4 mm
DetectorName: 6Li-Scintillator 1 mm thickness + photomultiplier / Type: SANS / Pixsize x: 5.3 mm
Scan
Title: Complex with 1H histone acetyltransferase Rtt109 and histones H3 and H4, 2H histone chaperones Asf1 and Vps75 (1H Rtt109-H3:H4, 2H Asf1-Vps75) acquired in 42% v/v D2O
Measurement date: Mar 5, 2017 / Storage temperature: 25 °C / Cell temperature: 25 °C / Exposure time: 7200 sec. / Number of frames: 1 / Unit: 1/A /
MinMax
Q0.0127 0.3923
Distance distribution function P(R)
Sofotware P(R): GNOM 4.6 / Number of points: 94 /
MinMax
Q0.01446 0.3923
P(R) point1 94
R0 110
Result
Experimental MW: 146 kDa / Type of curve: single_conc
P(R)GuinierGuinier error
Forward scattering, I00.2503 0.25 0.00092
Radius of gyration, Rg3.66 nm3.499 nm0.046

MinMax
D-11
Guinier point1 12

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