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PDBsum entry 3oj4
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Ligase/protein binding
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PDB id
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3oj4
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Contents |
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* Residue conservation analysis
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PDB id:
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Ligase/protein binding
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Title:
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Crystal structure of the a20 znf4, ubiquitin and ubch5a complex
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Structure:
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Ubiquitin-conjugating enzyme e2 d1. Chain: a, d. Fragment: ubiquitin-conjugating enzyme e2 d1. Synonym: ubiquitin-protein ligase d1, ubiquitin carrier protein d1, ubch5, ubiquitin-conjugating enzyme e2-17 kda 1, ubiquitin- conjugating enzyme e2(17)kb 1, ubc4/5 homolog, stimulator of fe transport, sft. Engineered: yes. Ubiquitin.
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Gene: ube2d1, sft, ubc5a, ubch5, ubch5a. Expressed in: escherichia coli. Expression_system_taxid: 469008. Gene: ubb. Gene: tnfaip3, otud7c.
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Resolution:
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3.40Å
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R-factor:
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0.284
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R-free:
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0.319
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Authors:
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I.Bosanac,S.G.Hymowitz
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Key ref:
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I.Bosanac
et al.
(2010).
Ubiquitin binding to A20 ZnF4 is required for modulation of NF-κB signaling.
Mol Cell,
40,
548-557.
PubMed id:
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Date:
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20-Aug-10
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Release date:
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08-Dec-10
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PROCHECK
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Headers
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References
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P51668
(UB2D1_HUMAN) -
Ubiquitin-conjugating enzyme E2 D1 from Homo sapiens
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Seq:
Struc:
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147 a.a.
147 a.a.
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Enzyme class 1:
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Chains A, D:
E.C.2.3.2.23
- E2 ubiquitin-conjugating enzyme.
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Reaction:
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S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L- cysteine
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Enzyme class 2:
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Chains A, D:
E.C.2.3.2.24
- (E3-independent) E2 ubiquitin-conjugating enzyme.
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Reaction:
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S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E1 ubiquitin-activating enzyme]-L-cysteine + N6- monoubiquitinyl-[acceptor protein]-L-lysine
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Enzyme class 3:
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Chains C, F:
E.C.2.3.2.-
- ?????
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Enzyme class 4:
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Chains C, F:
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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Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
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Mol Cell
40:548-557
(2010)
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PubMed id:
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Ubiquitin binding to A20 ZnF4 is required for modulation of NF-κB signaling.
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I.Bosanac,
I.E.Wertz,
B.Pan,
C.Yu,
S.Kusam,
C.Lam,
L.Phu,
Q.Phung,
B.Maurer,
D.Arnott,
D.S.Kirkpatrick,
V.M.Dixit,
S.G.Hymowitz.
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ABSTRACT
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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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A.Ma,
and
B.A.Malynn
(2012).
A20: linking a complex regulator of ubiquitylation to immunity and human disease.
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Nat Rev Immunol,
12,
774-785.
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A.Plechanovová,
E.G.Jaffray,
M.H.Tatham,
J.H.Naismith,
and
R.T.Hay
(2012).
Structure of a RING E3 ligase and ubiquitin-loaded E2 primed for catalysis.
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Nature,
489,
115-120.
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PDB code:
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J.D.Licchesi,
J.Mieszczanek,
T.E.Mevissen,
T.J.Rutherford,
M.Akutsu,
S.Virdee,
F.El Oualid,
J.W.Chin,
H.Ovaa,
M.Bienz,
and
D.Komander
(2012).
An ankyrin-repeat ubiquitin-binding domain determines TRABID's specificity for atypical ubiquitin chains.
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Nat Struct Mol Biol,
19,
62-71.
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PDB code:
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X.Jiang,
and
Z.J.Chen
(2012).
The role of ubiquitylation in immune defence and pathogen evasion.
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Nat Rev Immunol,
12,
35-48.
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D.Vucic,
V.M.Dixit,
and
I.E.Wertz
(2011).
Ubiquitylation in apoptosis: a post-translational modification at the edge of life and death.
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Nat Rev Mol Cell Biol,
12,
439-452.
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I.Bosanac,
L.Phu,
B.Pan,
I.Zilberleyb,
B.Maurer,
V.M.Dixit,
S.G.Hymowitz,
and
D.S.Kirkpatrick
(2011).
Modulation of K11-linkage formation by variable loop residues within UbcH5A.
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J Mol Biol,
408,
420-431.
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PDB code:
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B.A.Malynn,
and
A.Ma
(2010).
Ubiquitin makes its mark on immune regulation.
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Immunity,
33,
843-852.
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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
