6tbm

From Proteopedia

(Difference between revisions)

Revision as of 06:28, 11 April 2020

Structure of SAGA bound to TBP, including Spt8 and DUB

6tbm, resolution 20.00Å

Structural highlights

6tbm is a 18 chain structure with sequence from [1], Komagataella phaffii (strain gs115 / atcc 20864) and Komagataella phaffii gs115. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	6tb4
Activity:	Ubiquitinyl hydrolase 1, with EC number 3.4.19.12
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[C4QXP2_KOMPG] Functions as a component of the DNA-binding general transcription factor complex TFIID and the transcription regulatory histone acetylation (HAT) complexes SAGA and SLIK. Binding of TFIID to a promoter (with or without TATA element) is the initial step in preinitiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification (histone acetylation), facilitation of DNA opening and initiation of transcription. SAGA is required for recruitment of the basal transcription machinery. SLIK is proposed to have partly overlapping functions with SAGA.[PIRNR:PIRNR017246] [C4R2D9_KOMPG] Functions as component of the transcription regulatory histone acetylation (HAT) complex SAGA. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction and promoter selectivity, interaction with transcription activators, and chromatin modification through histone acetylation and deubiquitination. SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). Involved in transcriptional regulation of a subset of SAGA-regulated genes. Within the SAGA complex, participates in a subcomplex, that specifically deubiquitinates histones H2B.[RuleBase:RU261113] [C4R1P1_KOMPG] Involved in mRNA export coupled transcription activation by association with both the TREX-2 and the SAGA complexes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction and promoter selectivity, interaction with transcription activators, and chromatin modification through histone acetylation and deubiquitination. Within the SAGA complex, participates to a subcomplex required for deubiquitination of H2B and for the maintenance of steady-state H3 methylation levels. The TREX-2 complex functions in docking export-competent ribonucleoprotein particles (mRNPs) to the nuclear entrance of the nuclear pore complex (nuclear basket). TREX-2 participates in mRNA export and accurate chromatin positioning in the nucleus by tethering genes to the nuclear periphery. May also be involved in cytoplasmic mRNA decay by interaction with components of P-bodies.[HAMAP-Rule:MF_03046]

Publication Abstract from PubMed

SAGA (Spt-Ada-Gcn5-acetyltransferase) is a 19-subunit complex that stimulates transcription via two chromatin-modifying enzymatic modules and by delivering the TATA box binding protein (TBP) to nucleate the pre-initiation complex on DNA, a pivotal event in the expression of protein-encoding genes(1). Here we present the structure of yeast SAGA with bound TBP. The core of the complex is resolved at 3.5 A resolution (0.143 Fourier shell correlation). The structure reveals the intricate network of interactions that coordinate the different functional domains of SAGA and resolves an octamer of histone-fold domains at the core of SAGA. This deformed octamer deviates considerably from the symmetrical analogue in the nucleosome and is precisely tuned to establish a peripheral site for TBP, where steric hindrance represses binding of spurious DNA. Complementary biochemical analysis points to a mechanism for TBP delivery and release from SAGA that requires transcription factor IIA and whose efficiency correlates with the affinity of DNA to TBP. We provide the foundations for understanding the specific delivery of TBP to gene promoters and the multiple roles of SAGA in regulating gene expression.

Structure of SAGA and mechanism of TBP deposition on gene promoters.,Papai G, Frechard A, Kolesnikova O, Crucifix C, Schultz P, Ben-Shem A Nature. 2020 Jan;577(7792):711-716. doi: 10.1038/s41586-020-1944-2. Epub 2020 Jan, 22. PMID:31969704^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Papai G, Frechard A, Kolesnikova O, Crucifix C, Schultz P, Ben-Shem A. Structure of SAGA and mechanism of TBP deposition on gene promoters. Nature. 2020 Jan;577(7792):711-716. doi: 10.1038/s41586-020-1944-2. Epub 2020 Jan, 22. PMID:31969704 doi:http://dx.doi.org/10.1038/s41586-020-1944-2

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6tbm"

@@ Line 3: / Line 3: @@
 <SX load='6tbm' size='340' side='right' viewer='molstar' caption='[[6tbm]], [[Resolution|resolution]] 20.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6tbm]] is a 18 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/Komagataella_phaffii_(strain_gs115_/_atcc_20864) Komagataella phaffii (strain gs115 / atcc 20864)] and [http://en.wikipedia.org/wiki/Komagataella_phaffii_gs115 Komagataella phaffii gs115]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6TBM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6tbm]] is a 18 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/Komagataella_phaffii_(strain_gs115_/_atcc_20864) Komagataella phaffii (strain gs115 / atcc 20864)] and [http://en.wikipedia.org/wiki/Komagataella_phaffii_gs115 Komagataella phaffii gs115]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TBM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TBM FirstGlance]. <br>
 </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLZ:AMINO-ACETALDEHYDE'>GLZ</scene>, <scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6tb4|6tb4]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitinyl_hydrolase_1 Ubiquitinyl hydrolase 1], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.19.12 3.4.19.12] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6tbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tbm OCA], [http://pdbe.org/6tbm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tbm RCSB], [http://www.ebi.ac.uk/pdbsum/6tbm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tbm ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6tbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tbm OCA], [http://pdbe.org/6tbm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tbm RCSB], [http://www.ebi.ac.uk/pdbsum/6tbm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tbm ProSAT]</span></td></tr>
 </table>
 == Function ==

6tbm

From Proteopedia

Revision as of 06:28, 11 April 2020

Structure of SAGA bound to TBP, including Spt8 and DUB

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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