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PDBsum entry 3mhs
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Hydrolase/transcription regulator/protei
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PDB id
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3mhs
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Contents |
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455 a.a.
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91 a.a.
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93 a.a.
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76 a.a.
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86 a.a.
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* Residue conservation analysis
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PDB id:
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| Name: |
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Hydrolase/transcription regulator/protei
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Title:
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Structure of the saga ubp8/sgf11/sus1/sgf73 dub module bound to ubiquitin aldehyde
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Structure:
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Ubiquitin carboxyl-terminal hydrolase 8. Chain: a. Synonym: ubiquitin thioesterase 8, ubiquitin-specific-processing protease 8, deubiquitinating enzyme 8. Engineered: yes. Protein sus1. Chain: b. Engineered: yes. Saga-associated factor 11.
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Source:
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Saccharomyces cerevisiae. Brewer's yeast,lager beer yeast,yeast. Organism_taxid: 4932. Gene: ubp8, ymr223w, ym9959.05. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: sus1, ybr111w-a. Gene: sgf11, ypl047w. Homo sapiens.
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Resolution:
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1.89Å
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R-factor:
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0.161
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R-free:
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0.208
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Authors:
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N.L.Samara,A.B.Datta,C.E.Berndsen,X.Zhang,T.Yao,R.E.Cohen,C.Wolberger
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Key ref:
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N.L.Samara
et al.
(2010).
Structural insights into the assembly and function of the SAGA deubiquitinating module.
Science,
328,
1025-1029.
PubMed id:
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Date:
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08-Apr-10
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Release date:
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21-Apr-10
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PROCHECK
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Headers
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References
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P50102
(UBP8_YEAST) -
Ubiquitin carboxyl-terminal hydrolase 8 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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Seq:
Struc:
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471 a.a.
455 a.a.
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Q6WNK7
(SUS1_YEAST) -
Transcription and mRNA export factor SUS1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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Seq:
Struc:
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96 a.a.
91 a.a.
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Q03067
(SGF11_YEAST) -
SAGA-associated factor 11 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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Seq:
Struc:
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99 a.a.
93 a.a.
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Enzyme class:
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Chain A:
E.C.3.4.19.12
- ubiquitinyl hydrolase 1.
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Reaction:
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Thiol-dependent hydrolysis of ester, thiolester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
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Science
328:1025-1029
(2010)
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PubMed id:
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Structural insights into the assembly and function of the SAGA deubiquitinating module.
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N.L.Samara,
A.B.Datta,
C.E.Berndsen,
X.Zhang,
T.Yao,
R.E.Cohen,
C.Wolberger.
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ABSTRACT
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SAGA is a transcriptional coactivator complex that is conserved across
eukaryotes and performs multiple functions during transcriptional activation and
elongation. One role is deubiquitination of histone H2B, and this activity
resides in a distinct subcomplex called the deubiquitinating module (DUBm),
which contains the ubiquitin-specific protease Ubp8, bound to Sgf11, Sus1, and
Sgf73. The deubiquitinating activity depends on the presence of all four DUBm
proteins. We report here the 1.90 angstrom resolution crystal structure of the
DUBm bound to ubiquitin aldehyde, as well as the 2.45 angstrom resolution
structure of the uncomplexed DUBm. The structure reveals an arrangement of
protein domains that gives rise to a highly interconnected complex, which is
stabilized by eight structural zinc atoms that are critical for enzymatic
activity. The structure suggests a model for how interactions with the other
DUBm proteins activate Ubp8 and allows us to speculate about how the DUBm binds
to monoubiquitinated histone H2B in nucleosomes.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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K.K.Lee,
M.E.Sardiu,
S.K.Swanson,
J.M.Gilmore,
M.Torok,
P.A.Grant,
L.Florens,
J.L.Workman,
and
M.P.Washburn
(2011).
Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes.
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Mol Syst Biol,
7,
503.
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K.Y.Huang,
G.A.Amodeo,
L.Tong,
and
A.McDermott
(2011).
The structure of human ubiquitin in 2-methyl-2,4-pentanediol: a new conformational switch.
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Protein Sci,
20,
630-639.
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PDB code:
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L.Frappier,
and
C.P.Verrijzer
(2011).
Gene expression control by protein deubiquitinases.
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Curr Opin Genet Dev,
21,
207-213.
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M.P.Luna-Vargas,
A.C.Faesen,
W.J.van Dijk,
M.Rape,
A.Fish,
and
T.K.Sixma
(2011).
Ubiquitin-specific protease 4 is inhibited by its ubiquitin-like domain.
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EMBO Rep,
12,
365-372.
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PDB code:
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J.Bonnet,
Y.H.Wang,
G.Spedale,
R.A.Atkinson,
C.Romier,
A.Hamiche,
W.W.Pijnappel,
H.T.Timmers,
L.Tora,
D.Devys,
and
B.Kieffer
(2010).
The structural plasticity of SCA7 domains defines their differential nucleosome-binding properties.
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EMBO Rep,
11,
612-618.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
