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Ubiquitin conjugation
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PDB id
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1ayz
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* Residue conservation analysis
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Enzyme class:
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E.C.6.3.2.19
- Ubiquitin--protein ligase.
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Reaction:
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ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine
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ATP
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+
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ubiquitin
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+
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protein lysine
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=
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AMP
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+
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diphosphate
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+
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protein N-ubiquityllysine
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Gene Ontology (GO) functional annotation
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Cellular component
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proteasome complex
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4 terms
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Biological process
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response to DNA damage stimulus
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22 terms
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Biochemical function
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nucleotide binding
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6 terms
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DOI no:
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J Biol Chem
273:6271-6276
(1998)
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PubMed id:
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Crystal structure of the Saccharomyces cerevisiae ubiquitin-conjugating enzyme Rad6 at 2.6 A resolution.
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D.K.Worthylake,
S.Prakash,
L.Prakash,
C.P.Hill.
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ABSTRACT
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The Saccharomyces cerevisiae ubiquitin-conjugating enzyme (UBC) Rad6 is required
for several functions, including the repair of UV damaged DNA, damage-induced
mutagenesis, sporulation, and the degradation of cellular proteins that possess
destabilizing N-terminal residues. Rad6 mediates its role in N-end
rule-dependent protein degradation via interaction with the ubiquitin-protein
ligase Ubr1 and in DNA repair via interactions with the DNA binding protein
Rad18. We report here the crystal structure of Rad6 refined at 2.6 A resolution
to an R factor of 21.3%. The protein adopts an alpha/beta fold that is very
similar to other UBC structures. An apparent difference at the functionally
important first helix, however, has prompted a reassessment of previously
reported structures. The active site cysteine lies in a cleft formed by a coil
region that includes the 310 helix and a loop that is in different conformations
for the three molecules in the asymmetric unit. Residues important for Rad6
interaction with Ubr1 and Rad18 are on the opposite side of the structure from
the active site, indicating that this part of the UBC surface participates in
protein-protein interactions that define Rad6 substrate specificity.
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Selected figure(s)
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Figure 1.
Fig. 1. Electron density map calculated using density
modified single isomorphous replacement phases displayed with
the refined^ structure. 20.0-3.0 Å data were used in the
map calculation, and the map is contoured at 1.3  . Dashed
white lines indicate^ hydrogen bonding interactions of Asp-12,
Arg-8, and Tyr-63. The^ figure was made using the program O (25).
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Figure 2.
Fig. 2. Ribbon representation of Rad6. A, active site
cysteine shown in green. Residues 24-29, 32-41, 52-58, and 69-72
constitute^ the sheet (strands 1-4 in yellow) and residues 4-19,
102-113, 124-132, and 134-152 are in an  -helical
conformation (helices 1-4 in blue, maroon, cyan, and orange).
Residues 90-92 are in a 3[10] helical conformation (magenta). B,
colored to indicate N- and C-terminal binding determinants for
Ubr1 (blue and cyan) and^ Rad18 (orange and yellow). The loop
that forms the roof of the^ active site and is in different
conformations in the asymmetric^ unit (residues 115-121) is
indicated in red. Secondary structure^ was determined using the
program PROMOTIF (37). The figure was made using the programs
MOLSCRIPT (38) and RASTER 3D (39).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(1998,
273,
6271-6276)
copyright 1998.
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Figures were
selected
by an automated process.
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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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H.Walden
(2010).
Selenium incorporation using recombinant techniques.
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Acta Crystallogr D Biol Crystallogr, 66,
352-357.
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T.Ju,
W.Bocik,
A.Majumdar,
and
J.R.Tolman
(2010).
Solution structure and dynamics of human ubiquitin conjugating enzyme Ube2g2.
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Proteins, 78,
1291-1301.
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PDB code:
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B.A.Schulman,
and
J.W.Harper
(2009).
Ubiquitin-like protein activation by E1 enzymes: the apex for downstream signalling pathways.
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Nat Rev Mol Cell Biol, 10,
319-331.
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S.Barik
(2008).
An intronic microRNA silences genes that are functionally antagonistic to its host gene.
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Nucleic Acids Res, 36,
5232-5241.
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M.G.Malkowski,
E.Quartley,
A.E.Friedman,
J.Babulski,
Y.Kon,
J.Wolfley,
M.Said,
J.R.Luft,
E.M.Phizicky,
G.T.DeTitta,
and
E.J.Grayhack
(2007).
Blocking S-adenosylmethionine synthesis in yeast allows selenomethionine incorporation and multiwavelength anomalous dispersion phasing.
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Proc Natl Acad Sci U S A, 104,
6678-6683.
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PDB code:
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S.Lall
(2007).
Primers on chromatin.
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Nat Struct Mol Biol, 14,
1110-1115.
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A.Wood,
J.Schneider,
J.Dover,
M.Johnston,
and
A.Shilatifard
(2005).
The Bur1/Bur2 complex is required for histone H2B monoubiquitination by Rad6/Bre1 and histone methylation by COMPASS.
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Mol Cell, 20,
589-599.
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C.Dominguez,
A.M.Bonvin,
G.S.Winkler,
F.M.van Schaik,
H.T.Timmers,
and
R.Boelens
(2004).
Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches.
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Structure, 12,
633-644.
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PDB code:
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H.Oku,
T.Ohyama,
A.Hiroki,
K.Yamada,
K.Fukuyama,
H.Kawaguchi,
and
R.Katakai
(2004).
Addition of a peptide fragment on an alpha-helical depsipeptide induces alpha/3(10)-conjugated helix: synthesis, crystal structure, and CD spectra of Boc-Leu-Leu-Ala-(Leu-Leu-Lac)3-Leu-Leu-OEt.
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| |
Biopolymers, 75,
242-254.
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B.R.Wong,
F.Parlati,
K.Qu,
S.Demo,
T.Pray,
J.Huang,
D.G.Payan,
and
M.K.Bennett
(2003).
Drug discovery in the ubiquitin regulatory pathway.
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Drug Discov Today, 8,
746-754.
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P.Y.Wu,
M.Hanlon,
M.Eddins,
C.Tsui,
R.S.Rogers,
J.P.Jensen,
M.J.Matunis,
A.M.Weissman,
A.M.Weisman,
A.M.Weissman,
C.Wolberger,
C.P.Wolberger,
and
C.M.Pickart
(2003).
A conserved catalytic residue in the ubiquitin-conjugating enzyme family.
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EMBO J, 22,
5241-5250.
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B.Sarcevic,
A.Mawson,
R.T.Baker,
and
R.L.Sutherland
(2002).
Regulation of the ubiquitin-conjugating enzyme hHR6A by CDK-mediated phosphorylation.
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| |
EMBO J, 21,
2009-2018.
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|
|
O.Pornillos,
S.L.Alam,
R.L.Rich,
D.G.Myszka,
D.R.Davis,
and
W.I.Sundquist
(2002).
Structure and functional interactions of the Tsg101 UEV domain.
|
| |
EMBO J, 21,
2397-2406.
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PDB codes:
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T.R.Pray,
F.Parlati,
J.Huang,
B.R.Wong,
D.G.Payan,
M.K.Bennett,
S.D.Issakani,
S.Molineaux,
and
S.D.Demo
(2002).
Cell cycle regulatory E3 ubiquitin ligases as anticancer targets.
|
| |
Drug Resist Updat, 5,
249-258.
|
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|
|
A.P.VanDemark,
R.M.Hofmann,
C.Tsui,
C.M.Pickart,
and
C.Wolberger
(2001).
Molecular insights into polyubiquitin chain assembly: crystal structure of the Mms2/Ubc13 heterodimer.
|
| |
Cell, 105,
711-720.
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PDB codes:
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C.M.Pickart
(2001).
Mechanisms underlying ubiquitination.
|
| |
Annu Rev Biochem, 70,
503-533.
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|
|
C.Ptak,
C.Gwozd,
J.T.Huzil,
T.J.Gwozd,
G.Garen,
and
M.J.Ellison
(2001).
Creation of a pluripotent ubiquitin-conjugating enzyme.
|
| |
Mol Cell Biol, 21,
6537-6548.
|
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|
|
D.Sleep,
C.Finnis,
A.Turner,
and
L.Evans
(2001).
Yeast 2 microm plasmid copy number is elevated by a mutation in the nuclear gene UBC4.
|
| |
Yeast, 18,
403-421.
|
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|
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P.Leng,
P.E.Sudbery,
and
A.J.Brown
(2000).
Rad6p represses yeast-hypha morphogenesis in the human fungal pathogen Candida albicans.
|
| |
Mol Microbiol, 35,
1264-1275.
|
|
|
|
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|
|
F.Jiang,
and
R.Basavappa
(1999).
Crystal structure of the cyclin-specific ubiquitin-conjugating enzyme from clam, E2-C, at 2.0 A resolution.
|
| |
Biochemistry, 38,
6471-6478.
|
|
|
PDB code:
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Y.Xie,
and
A.Varshavsky
(1999).
The E2-E3 interaction in the N-end rule pathway: the RING-H2 finger of E3 is required for the synthesis of multiubiquitin chain.
|
| |
EMBO J, 18,
6832-6844.
|
|
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|
|
L.D.Mastrandrea,
E.M.Kasperek,
E.G.Niles,
and
C.M.Pickart
(1998).
Core domain mutation (S86Y) selectively inactivates polyubiquitin chain synthesis catalyzed by E2-25K.
|
| |
Biochemistry, 37,
9784-9792.
|
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|
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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
