 |
PDBsum entry 1j8c
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Structural genomics
|
PDB id
|
|
|
|
1j8c
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Biochemistry
41:1767-1777
(2002)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Structural studies of the interaction between ubiquitin family proteins and proteasome subunit S5a.
|
|
K.J.Walters,
M.F.Kleijnen,
A.M.Goh,
G.Wagner,
P.M.Howley.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
The 26S proteasome is essential for the proteolysis of proteins that have been
covalently modified by the attachment of polyubiquitinated chains. Although the
20S core particle performs the degradation, the 19S regulatory cap complex is
responsible for recognition of polyubiquitinated substrates. We have focused on
how the S5a component of the 19S complex interacts with different ubiquitin-like
(ubl) modules, to advance our understanding of how polyubiquitinated proteins
are targeted to the proteasome. To achieve this, we have determined the solution
structure of the ubl domain of hPLIC-2 and obtained a structural model of hHR23a
by using NMR spectroscopy and homology modeling. We have also compared the S5a
binding properties of ubiquitin, SUMO-1, and the ubl domains of hPLIC-2 and
hHR23a and have identified the residues on their respective S5a contact
surfaces. We provide evidence that the S5a-binding surface on the ubl domain of
hPLIC-2 is required for its interaction with the proteasome. This study provides
structural insights into protein recognition by the proteasome, and illustrates
how the protein surface of a commonly utilized fold has highly evolved for
various biological roles.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
J.Godek,
I.Sargiannidou,
S.Patel,
L.Hurd,
V.L.Rothman,
and
G.P.Tuszynski
(2011).
Angiocidin inhibits breast cancer proliferation through activation of epidermal growth factor receptor and nuclear factor kappa (NF-ĸB).
|
| |
Exp Mol Pathol,
90,
244-251.
|
|
|
|
|
|
|
N.Kettern,
C.Rogon,
A.Limmer,
H.Schild,
and
J.Höhfeld
(2011).
The Hsc/Hsp70 Co-Chaperone Network Controls Antigen Aggregation and Presentation during Maturation of Professional Antigen Presenting Cells.
|
| |
PLoS One,
6,
e16398.
|
|
|
|
|
|
|
M.Markaki,
and
N.Tavernarakis
(2010).
Modeling human diseases in Caenorhabditis elegans.
|
| |
Biotechnol J,
5,
1261-1276.
|
|
|
|
|
|
|
N.G.Sgourakis,
M.M.Patel,
A.E.Garcia,
G.I.Makhatadze,
and
S.A.McCallum
(2010).
Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain.
|
| |
J Mol Biol,
396,
1128-1144.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
N.Pashkova,
L.Gakhar,
S.C.Winistorfer,
L.Yu,
S.Ramaswamy,
and
R.C.Piper
(2010).
WD40 repeat propellers define a ubiquitin-binding domain that regulates turnover of F box proteins.
|
| |
Mol Cell,
40,
433-443.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
R.Ricco,
and
D.Kanduc
(2010).
Hepatitis B virus and Homo sapiens proteome-wide analysis: A profusion of viral peptide overlaps in neuron-specific human proteins.
|
| |
Biologics,
4,
75-81.
|
|
|
|
|
|
|
S.S.Safadi,
and
G.S.Shaw
(2010).
Differential interaction of the E3 ligase parkin with the proteasomal subunit S5a and the endocytic protein Eps15.
|
| |
J Biol Chem,
285,
1424-1434.
|
|
|
|
|
|
|
A.Navon,
and
A.Ciechanover
(2009).
The 26 S proteasome: from basic mechanisms to drug targeting.
|
| |
J Biol Chem,
284,
33713-33718.
|
|
|
|
|
|
|
D.Finley
(2009).
Recognition and processing of ubiquitin-protein conjugates by the proteasome.
|
| |
Annu Rev Biochem,
78,
477-513.
|
|
|
|
|
|
|
E.N.N'Diaye,
K.K.Kajihara,
I.Hsieh,
H.Morisaki,
J.Debnath,
and
E.J.Brown
(2009).
PLIC proteins or ubiquilins regulate autophagy-dependent cell survival during nutrient starvation.
|
| |
EMBO Rep,
10,
173-179.
|
|
|
|
|
|
|
I.Dikic,
S.Wakatsuki,
and
K.J.Walters
(2009).
Ubiquitin-binding domains - from structures to functions.
|
| |
Nat Rev Mol Cell Biol,
10,
659-671.
|
|
|
|
|
|
|
I.Ziv,
O.Kleifeld,
and
M.Glickman
(2009).
Nonconformity in ubiquitin compliance.
|
| |
EMBO J,
28,
1825-1827.
|
|
|
|
|
|
|
N.Zhang,
Q.Wang,
A.Ehlinger,
L.Randles,
J.W.Lary,
Y.Kang,
A.Haririnia,
A.J.Storaska,
J.L.Cole,
D.Fushman,
and
K.J.Walters
(2009).
Structure of the s5a:k48-linked diubiquitin complex and its interactions with rpn13.
|
| |
Mol Cell,
35,
280-290.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
S.H.Kim,
Y.Shi,
K.A.Hanson,
L.M.Williams,
R.Sakasai,
M.J.Bowler,
and
R.S.Tibbetts
(2009).
Potentiation of Amyotrophic Lateral Sclerosis (ALS)-associated TDP-43 Aggregation by the Proteasome-targeting Factor, Ubiquilin 1.
|
| |
J Biol Chem,
284,
8083-8092.
|
|
|
|
|
|
|
V.Su,
and
A.F.Lau
(2009).
Ubiquitin-like and ubiquitin-associated domain proteins: significance in proteasomal degradation.
|
| |
Cell Mol Life Sci,
66,
2819-2833.
|
|
|
|
|
|
|
E.N.N'Diaye,
A.C.Hanyaloglu,
K.K.Kajihara,
M.A.Puthenveedu,
P.Wu,
M.von Zastrow,
and
E.J.Brown
(2008).
The ubiquitin-like protein PLIC-2 is a negative regulator of G protein-coupled receptor endocytosis.
|
| |
Mol Biol Cell,
19,
1252-1260.
|
|
|
|
|
|
|
K.Husnjak,
S.Elsasser,
N.Zhang,
X.Chen,
L.Randles,
Y.Shi,
K.Hofmann,
K.J.Walters,
D.Finley,
and
I.Dikic
(2008).
Proteasome subunit Rpn13 is a novel ubiquitin receptor.
|
| |
Nature,
453,
481-488.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
Y.Matiuhin,
D.S.Kirkpatrick,
I.Ziv,
W.Kim,
A.Dakshinamurthy,
O.Kleifeld,
S.P.Gygi,
N.Reis,
and
M.H.Glickman
(2008).
Extraproteasomal Rpn10 restricts access of the polyubiquitin-binding protein Dsk2 to proteasome.
|
| |
Mol Cell,
32,
415-425.
|
|
|
|
|
|
|
B.C.Dickinson,
R.Varadan,
and
D.Fushman
(2007).
Effects of cyclization on conformational dynamics and binding properties of Lys48-linked di-ubiquitin.
|
| |
Protein Sci,
16,
369-378.
|
|
|
|
|
|
|
N.Ghaboosi,
and
R.J.Deshaies
(2007).
A conditional yeast E1 mutant blocks the ubiquitin-proteasome pathway and reveals a role for ubiquitin conjugates in targeting Rad23 to the proteasome.
|
| |
Mol Biol Cell,
18,
1953-1963.
|
|
|
|
|
|
|
X.Zhu,
R.Ménard,
and
T.Sulea
(2007).
High incidence of ubiquitin-like domains in human ubiquitin-specific proteases.
|
| |
Proteins,
69,
1-7.
|
|
|
|
|
|
|
Y.Kang,
N.Zhang,
D.M.Koepp,
and
K.J.Walters
(2007).
Ubiquitin receptor proteins hHR23a and hPLIC2 interact.
|
| |
J Mol Biol,
365,
1093-1101.
|
|
|
|
|
|
|
Y.Tayama,
H.Kawahara,
R.Minami,
M.Shimada,
and
H.Yokosawa
(2007).
Association of Rpn10 with high molecular weight complex is enhanced during retinoic acid-induced differentiation of neuroblastoma cells.
|
| |
Mol Cell Biochem,
306,
53-57.
|
|
|
|
|
|
|
A.V.Thomas,
L.Herl,
R.Spoelgen,
M.Hiltunen,
P.B.Jones,
R.E.Tanzi,
B.T.Hyman,
and
O.Berezovska
(2006).
Interaction between presenilin 1 and ubiquilin 1 as detected by fluorescence lifetime imaging microscopy and a high-throughput fluorescent plate reader.
|
| |
J Biol Chem,
281,
26400-26407.
|
|
|
|
|
|
|
E.D.Lowe,
N.Hasan,
J.F.Trempe,
L.Fonso,
M.E.Noble,
J.A.Endicott,
L.N.Johnson,
and
N.R.Brown
(2006).
Structures of the Dsk2 UBL and UBA domains and their complex.
|
| |
Acta Crystallogr D Biol Crystallogr,
62,
177-188.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
F.Ferron,
S.Longhi,
B.Canard,
and
D.Karlin
(2006).
A practical overview of protein disorder prediction methods.
|
| |
Proteins,
65,
1.
|
|
|
|
|
|
|
L.Fallon,
C.M.Bélanger,
A.T.Corera,
M.Kontogiannea,
E.Regan-Klapisz,
F.Moreau,
J.Voortman,
M.Haber,
G.Rouleau,
T.Thorarinsdottir,
A.Brice,
P.M.van Bergen En Henegouwen,
and
E.A.Fon
(2006).
A regulated interaction with the UIM protein Eps15 implicates parkin in EGF receptor trafficking and PI(3)K-Akt signalling.
|
| |
Nat Cell Biol,
8,
834-842.
|
|
|
|
|
|
|
R.Heir,
C.Ablasou,
E.Dumontier,
M.Elliott,
C.Fagotto-Kaufmann,
and
F.K.Bedford
(2006).
The UBL domain of PLIC-1 regulates aggresome formation.
|
| |
EMBO Rep,
7,
1252-1258.
|
|
|
|
|
|
|
Y.G.Chang,
A.X.Song,
Y.G.Gao,
Y.H.Shi,
X.J.Lin,
X.T.Cao,
D.H.Lin,
and
H.Y.Hu
(2006).
Solution structure of the ubiquitin-associated domain of human BMSC-UbP and its complex with ubiquitin.
|
| |
Protein Sci,
15,
1248-1259.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
B.E.Riley,
H.Y.Zoghbi,
and
H.T.Orr
(2005).
SUMOylation of the polyglutamine repeat protein, ataxin-1, is dependent on a functional nuclear localization signal.
|
| |
J Biol Chem,
280,
21942-21948.
|
|
|
|
|
|
|
G.Nicastro,
R.P.Menon,
L.Masino,
P.P.Knowles,
N.Q.McDonald,
and
A.Pastore
(2005).
The solution structure of the Josephin domain of ataxin-3: structural determinants for molecular recognition.
|
| |
Proc Natl Acad Sci U S A,
102,
10493-10498.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
I.H.Henn,
J.M.Gostner,
P.Lackner,
J.Tatzelt,
and
K.F.Winklhofer
(2005).
Pathogenic mutations inactivate parkin by distinct mechanisms.
|
| |
J Neurochem,
92,
114-122.
|
|
|
|
|
|
|
L.Kaplun,
R.Tzirkin,
A.Bakhrat,
N.Shabek,
Y.Ivantsiv,
and
D.Raveh
(2005).
The DNA damage-inducible UbL-UbA protein Ddi1 participates in Mec1-mediated degradation of Ho endonuclease.
|
| |
Mol Cell Biol,
25,
5355-5362.
|
|
|
|
|
|
|
R.Farràs,
G.Bossis,
E.Andermarcher,
I.Jariel-Encontre,
and
M.Piechaczyk
(2005).
Mechanisms of delivery of ubiquitylated proteins to the proteasome: new target for anti-cancer therapy?
|
| |
Crit Rev Oncol Hematol,
54,
31-51.
|
|
|
|
|
|
|
T.Hara,
T.Kamura,
S.Kotoshiba,
H.Takahashi,
K.Fujiwara,
I.Onoyama,
M.Shirakawa,
N.Mizushima,
and
K.I.Nakayama
(2005).
Role of the UBL-UBA protein KPC2 in degradation of p27 at G1 phase of the cell cycle.
|
| |
Mol Cell Biol,
25,
9292-9303.
|
|
|
|
|
|
|
Y.Kikukawa,
R.Minami,
M.Shimada,
M.Kobayashi,
K.Tanaka,
H.Yokosawa,
and
H.Kawahara
(2005).
Unique proteasome subunit Xrpn10c is a specific receptor for the antiapoptotic ubiquitin-like protein Scythe.
|
| |
FEBS J,
272,
6373-6386.
|
|
|
|
|
|
|
B.E.Riley,
Y.Xu,
H.Y.Zoghbi,
and
H.T.Orr
(2004).
The effects of the polyglutamine repeat protein ataxin-1 on the UbL-UBA protein A1Up.
|
| |
J Biol Chem,
279,
42290-42301.
|
|
|
|
|
|
|
I.Kim,
K.Mi,
and
H.Rao
(2004).
Multiple interactions of rad23 suggest a mechanism for ubiquitylated substrate delivery important in proteolysis.
|
| |
Mol Biol Cell,
15,
3357-3365.
|
|
|
|
|
|
|
K.Fujiwara,
T.Tenno,
K.Sugasawa,
J.G.Jee,
I.Ohki,
C.Kojima,
H.Tochio,
H.Hiroaki,
F.Hanaoka,
and
M.Shirakawa
(2004).
Structure of the ubiquitin-interacting motif of S5a bound to the ubiquitin-like domain of HR23B.
|
| |
J Biol Chem,
279,
4760-4767.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.J.May,
S.E.Larsen,
J.H.Shim,
L.A.Madge,
and
S.Ghosh
(2004).
A novel ubiquitin-like domain in IkappaB kinase beta is required for functional activity of the kinase.
|
| |
J Biol Chem,
279,
45528-45539.
|
|
|
|
|
|
|
M.S.Hipp,
S.Raasi,
M.Groettrup,
and
G.Schmidtke
(2004).
NEDD8 ultimate buster-1L interacts with the ubiquitin-like protein FAT10 and accelerates its degradation.
|
| |
J Biol Chem,
279,
16503-16510.
|
|
|
|
|
|
|
M.Urushitani,
J.Kurisu,
M.Tateno,
S.Hatakeyama,
K.Nakayama,
S.Kato,
and
R.Takahashi
(2004).
CHIP promotes proteasomal degradation of familial ALS-linked mutant SOD1 by ubiquitinating Hsp/Hsc70.
|
| |
J Neurochem,
90,
231-244.
|
|
|
|
|
|
|
R.Hartmann-Petersen,
and
C.Gordon
(2004).
Integral UBL domain proteins: a family of proteasome interacting proteins.
|
| |
Semin Cell Dev Biol,
15,
247-259.
|
|
|
|
|
|
|
S.L.Miller,
E.Malotky,
and
J.P.O'Bryan
(2004).
Analysis of the role of ubiquitin-interacting motifs in ubiquitin binding and ubiquitylation.
|
| |
J Biol Chem,
279,
33528-33537.
|
|
|
|
|
|
|
T.D.Mueller,
M.Kamionka,
and
J.Feigon
(2004).
Specificity of the interaction between ubiquitin-associated domains and ubiquitin.
|
| |
J Biol Chem,
279,
11926-11936.
|
|
|
|
|
|
|
B.Wang,
S.L.Alam,
H.H.Meyer,
M.Payne,
T.L.Stemmler,
D.R.Davis,
and
W.I.Sundquist
(2003).
Structure and ubiquitin interactions of the conserved zinc finger domain of Npl4.
|
| |
J Biol Chem,
278,
20225-20234.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
E.N.N'Diaye,
and
E.J.Brown
(2003).
The ubiquitin-related protein PLIC-1 regulates heterotrimeric G protein function through association with Gbetagamma.
|
| |
J Cell Biol,
163,
1157-1165.
|
|
|
|
|
|
|
E.Sakata,
Y.Yamaguchi,
E.Kurimoto,
J.Kikuchi,
S.Yokoyama,
S.Yamada,
H.Kawahara,
H.Yokosawa,
N.Hattori,
Y.Mizuno,
K.Tanaka,
and
K.Kato
(2003).
Parkin binds the Rpn10 subunit of 26S proteasomes through its ubiquitin-like domain.
|
| |
EMBO Rep,
4,
301-306.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
K.A.Swanson,
R.S.Kang,
S.D.Stamenova,
L.Hicke,
and
I.Radhakrishnan
(2003).
Solution structure of Vps27 UIM-ubiquitin complex important for endosomal sorting and receptor downregulation.
|
| |
EMBO J,
22,
4597-4606.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
K.J.Walters,
P.J.Lech,
A.M.Goh,
Q.Wang,
and
P.M.Howley
(2003).
DNA-repair protein hHR23a alters its protein structure upon binding proteasomal subunit S5a.
|
| |
Proc Natl Acad Sci U S A,
100,
12694-12699.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
K.S.Ryu,
K.J.Lee,
S.H.Bae,
B.K.Kim,
K.A.Kim,
and
B.S.Choi
(2003).
Binding surface mapping of intra- and interdomain interactions among hHR23B, ubiquitin, and polyubiquitin binding site 2 of S5a.
|
| |
J Biol Chem,
278,
36621-36627.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
L.Gao,
H.Tu,
S.T.Shi,
K.J.Lee,
M.Asanaka,
S.B.Hwang,
and
M.M.Lai
(2003).
Interaction with a ubiquitin-like protein enhances the ubiquitination and degradation of hepatitis C virus RNA-dependent RNA polymerase.
|
| |
J Virol,
77,
4149-4159.
|
|
|
|
|
|
|
M.F.Kleijnen,
R.M.Alarcon,
and
P.M.Howley
(2003).
The ubiquitin-associated domain of hPLIC-2 interacts with the proteasome.
|
| |
Mol Biol Cell,
14,
3868-3875.
|
|
|
|
|
|
|
M.Grynberg,
L.Jaroszewski,
and
A.Godzik
(2003).
Domain analysis of the tubulin cofactor system: a model for tubulin folding and dimerization.
|
| |
BMC Bioinformatics,
4,
46.
|
|
|
|
|
|
|
M.Seeger,
R.Hartmann-Petersen,
C.R.Wilkinson,
M.Wallace,
I.Samejima,
M.S.Taylor,
and
C.Gordon
(2003).
Interaction of the anaphase-promoting complex/cyclosome and proteasome protein complexes with multiubiquitin chain-binding proteins.
|
| |
J Biol Chem,
278,
16791-16796.
|
|
|
|
|
|
|
P.S.Bilodeau,
S.C.Winistorfer,
W.R.Kearney,
A.D.Robertson,
and
R.C.Piper
(2003).
Vps27-Hse1 and ESCRT-I complexes cooperate to increase efficiency of sorting ubiquitinated proteins at the endosome.
|
| |
J Cell Biol,
163,
237-243.
|
|
|
|
|
|
|
Q.Wang,
A.M.Goh,
P.M.Howley,
and
K.J.Walters
(2003).
Ubiquitin recognition by the DNA repair protein hHR23a.
|
| |
Biochemistry,
42,
13529-13535.
|
|
|
|
|
|
|
R.D.Fisher,
B.Wang,
S.L.Alam,
D.S.Higginson,
H.Robinson,
W.I.Sundquist,
and
C.P.Hill
(2003).
Structure and ubiquitin binding of the ubiquitin-interacting motif.
|
| |
J Biol Chem,
278,
28976-28984.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
R.Hartmann-Petersen,
M.Seeger,
and
C.Gordon
(2003).
Transferring substrates to the 26S proteasome.
|
| |
Trends Biochem Sci,
28,
26-31.
|
|
|
|
|
|
|
S.C.Upadhya,
and
A.N.Hegde
(2003).
A potential proteasome-interacting motif within the ubiquitin-like domain of parkin and other proteins.
|
| |
Trends Biochem Sci,
28,
280-283.
|
|
|
|
|
|
|
S.Glockzin,
F.X.Ogi,
A.Hengstermann,
M.Scheffner,
and
C.Blattner
(2003).
Involvement of the DNA repair protein hHR23 in p53 degradation.
|
| |
Mol Cell Biol,
23,
8960-8969.
|
|
|
|
|
|
|
S.Raasi,
and
C.M.Pickart
(2003).
Rad23 ubiquitin-associated domains (UBA) inhibit 26 S proteasome-catalyzed proteolysis by sequestering lysine 48-linked polyubiquitin chains.
|
| |
J Biol Chem,
278,
8951-8959.
|
|
|
|
|
|
|
T.D.Mueller,
and
J.Feigon
(2003).
Structural determinants for the binding of ubiquitin-like domains to the proteasome.
|
| |
EMBO J,
22,
4634-4645.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
S.Alberti,
J.Demand,
C.Esser,
N.Emmerich,
H.Schild,
and
J.Hohfeld
(2002).
Ubiquitylation of BAG-1 suggests a novel regulatory mechanism during the sorting of chaperone substrates to the proteasome.
|
| |
J Biol Chem,
277,
45920-45927.
|
|
|
|
|
|
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.
|
|
Links
