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PDBsum entry 1lcy
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* Residue conservation analysis
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PDB id:
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Hydrolase
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Title:
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Crystal structure of the mitochondrial serine protease htra2
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Structure:
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Htra2 serine protease. Chain: a. Engineered: yes. Mutation: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Biol. unit:
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Trimer (from
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Resolution:
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2.00Å
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R-factor:
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0.235
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R-free:
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0.274
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Authors:
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W.Li,S.M.Srinivasula,J.Chai,P.Li,J.W.Wu,Z.Zhang,E.S.Alnemri,Y.Shi
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Key ref:
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W.Li
et al.
(2002).
Structural insights into the pro-apoptotic function of mitochondrial serine protease HtrA2/Omi.
Nat Struct Biol,
9,
436-441.
PubMed id:
DOI:
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Date:
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07-Apr-02
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Release date:
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22-May-02
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PROCHECK
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Headers
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References
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O43464
(HTRA2_HUMAN) -
Serine protease HTRA2, mitochondrial from Homo sapiens
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Seq: Struc:
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458 a.a.
296 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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*
PDB and UniProt seqs differ
at 1 residue position (black
cross)
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DOI no:
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Nat Struct Biol
9:436-441
(2002)
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PubMed id:
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Structural insights into the pro-apoptotic function of mitochondrial serine protease HtrA2/Omi.
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W.Li,
S.M.Srinivasula,
J.Chai,
P.Li,
J.W.Wu,
Z.Zhang,
E.S.Alnemri,
Y.Shi.
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ABSTRACT
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HtrA2/Omi, a mitochondrial serine protease in mammals, is important in
programmed cell death. However, the underlining mechanism of HtrA2/Omi-mediated
apoptosis remains unclear. Analogous to the bacterial homolog HtrA (DegP), the
mature HtrA2 protein contains a central serine protease domain and a C-terminal
PDZ domain. The 2.0 A crystal structure of HtrA2/Omi reveals the formation of a
pyramid-shaped homotrimer mediated exclusively by the serine protease domains.
The peptide-binding pocket of the PDZ domain is buried in the intimate interface
between the PDZ and the protease domains. Mutational analysis reveals that the
monomeric HtrA2/Omi mutants are unable to induce cell death and are deficient in
protease activity. The PDZ domain modulates HtrA2/Omi-mediated cell death
activity by regulating its serine protease activity. These structural and
biochemical observations provide an important framework for deciphering the
mechanisms of HtrA2/Omi-mediated apoptosis.
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Selected figure(s)
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Figure 1.
Figure 1. Structure of HtrA2/Omi. a, Schematic representation
of the HtrA2/Omi monomer. The serine protease and the PDZ
domains are colored cyan and pink, respectively. The flexible
linker between the two domains is represented by a dotted line.
The position of the catalytic Ser 306 is highlighted in red. b,
A close-up view of the intramolecular hydrophobic contacts
between the protease and the PDZ domains. Residues from the
protease and the PDZ domains are shown in yellow and orange,
respectively. c, Superposition of the PDZ domains from HtrA2/Omi
(pink) and the membrane-associated protein syntrophin (green,
PDB entry 2PDZ)31. Strands 5/
6
from the serine protease domain and the syntrophin-bound peptide
are shown in cyan and dark blue, respectively. d, Sequence
alignment of the human HtrA proteins and their homolog in E.
coli. The alignment was generated by ClustalW32. The secondary
structural elements are indicated above the alignment. The
catalytic triad residues are boxed in red, and regions critical
for homotrimerization or intramolecular contacts are indicated
below the alignment. Conserved residues are boxed in yellow.
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Figure 2.
Figure 2. HtrA2/Omi forms a pyramid-shaped homotrimer. a, The
HtrA2/Omi trimer is viewed either along (left) or perpendicular
to (right) the three-fold symmetry axis. Trimerization is
mediated exclusively by the serine protease domain. The
N-terminal IAP-binding tetrapeptide motif is located at the top
of the pyramid, and the PDZ domain is at the base. b, Surface
representation of the HtrA2/Omi structure. White arrows indicate
the positions of the catalytic Ser residues. c, A slice of
HtrA2/Omi structure to highlight the position of the catalytic
residue. The HtrA2/Omi surface is represented by color-coded
mesh, with the same scheme as in (a,b) and an orientation
similar to that in (a, right). d, A stereo view of part of the
trimerization interface. The three HtrA2/Omi monomers are
colored green, orange and blue, with their side chains in red.
Three aromatic residues from each monomer interdigitate to form
a tighly packed hydrophobic interface. The experimental electron
density, contoured at 1.5 ,
is shown in green around the three aromatic residues.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(2002,
9,
436-441)
copyright 2002.
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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.Malet,
F.Canellas,
J.Sawa,
J.Yan,
K.Thalassinos,
M.Ehrmann,
T.Clausen,
and
H.R.Saibil
(2012).
Newly folded substrates inside the molecular cage of the HtrA chaperone DegQ.
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Nat Struct Mol Biol,
19,
152-157.
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PDB codes:
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A.Finkelshtein,
N.Shlezinger,
O.Bunis,
and
A.Sharon
(2011).
Botrytis cinerea BcNma is involved in apoptotic cell death but not in stress adaptation.
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Fungal Genet Biol,
48,
621-630.
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A.L.Bulteau,
and
A.Bayot
(2011).
Mitochondrial proteases and cancer.
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Biochim Biophys Acta,
1807,
595-601.
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H.Schuhmann,
U.Mogg,
and
I.Adamska
(2011).
A new principle of oligomerization of plant DEG7 protease based on interactions of degenerated protease domains.
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Biochem J,
435,
167-174.
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I.P.de Castro,
L.M.Martins,
and
S.H.Loh
(2011).
Mitochondrial quality control and Parkinson's disease: a pathway unfolds.
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Mol Neurobiol,
43,
80-86.
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L.Truebestein,
A.Tennstaedt,
T.Mönig,
T.Krojer,
F.Canellas,
M.Kaiser,
T.Clausen,
and
M.Ehrmann
(2011).
Substrate-induced remodeling of the active site regulates human HTRA1 activity.
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Nat Struct Mol Biol,
18,
386-388.
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PDB codes:
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P.F.Huesgen,
H.Miranda,
X.Lam,
M.Perthold,
H.Schuhmann,
I.Adamska,
and
C.Funk
(2011).
Recombinant Deg/HtrA proteases from Synechocystis sp. PCC 6803 differ in substrate specificity, biochemical characteristics and mechanism.
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Biochem J,
435,
733-742.
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Q.Xu,
and
R.L.Dunbrack
(2011).
The protein common interface database (ProtCID)--a comprehensive database of interactions of homologous proteins in multiple crystal forms.
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Nucleic Acids Res,
39,
D761-D770.
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T.Clausen,
M.Kaiser,
R.Huber,
and
M.Ehrmann
(2011).
HTRA proteases: regulated proteolysis in protein quality control.
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Nat Rev Mol Cell Biol,
12,
152-162.
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T.Geppert,
B.Hoy,
S.Wessler,
and
G.Schneider
(2011).
Context-based identification of protein-protein interfaces and "hot-spot" residues.
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Chem Biol,
18,
344-353.
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K.Fan,
J.Zhang,
Q.Shang,
and
X.Tu
(2010).
1H, 13C and 15N resonance assignment of the PDZ domain of HtrA from Streptococcus pneumoniae.
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Biomol NMR Assign,
4,
79-82.
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L.Cesaro,
and
M.Salvi
(2010).
Mitochondrial tyrosine phosphoproteome: new insights from an up-to-date analysis.
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Biofactors,
36,
437-450.
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X.Sun,
M.Ouyang,
J.Guo,
J.Ma,
C.Lu,
Z.Adam,
and
L.Zhang
(2010).
The thylakoid protease Deg1 is involved in photosystem-II assembly in Arabidopsis thaliana.
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Plant J,
62,
240-249.
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X.Sun,
T.Fu,
N.Chen,
J.Guo,
J.Ma,
M.Zou,
C.Lu,
and
L.Zhang
(2010).
The stromal chloroplast Deg7 protease participates in the repair of photosystem II after photoinhibition in Arabidopsis.
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Plant Physiol,
152,
1263-1273.
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B.O.Cezairliyan,
and
R.T.Sauer
(2009).
Control of Pseudomonas aeruginosa AlgW protease cleavage of MucA by peptide signals and MucB.
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Mol Microbiol,
72,
368-379.
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D.Su,
Z.Su,
J.Wang,
S.Yang,
and
J.Ma
(2009).
UCF-101, a novel Omi/HtrA2 inhibitor, protects against cerebral ischemia/reperfusion injury in rats.
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Anat Rec (Hoboken),
292,
854-861.
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F.Johnson,
and
M.G.Kaplitt
(2009).
Novel mitochondrial substrates of omi indicate a new regulatory role in neurodegenerative disorders.
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PLoS One,
4,
e7100.
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J.Chien,
T.Ota,
G.Aletti,
R.Shridhar,
M.Boccellino,
L.Quagliuolo,
A.Baldi,
and
V.Shridhar
(2009).
Serine protease HtrA1 associates with microtubules and inhibits cell migration.
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Mol Cell Biol,
29,
4177-4187.
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J.Chien,
X.He,
and
V.Shridhar
(2009).
Identification of tubulins as substrates of serine protease HtrA1 by mixture-based oriented peptide library screening.
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J Cell Biochem,
107,
253-263.
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J.Kooistra,
J.Milojevic,
G.Melacini,
and
J.Ortega
(2009).
A new function of human HtrA2 as an amyloid-beta oligomerization inhibitor.
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J Alzheimers Dis,
17,
281-294.
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J.Sohn,
R.A.Grant,
and
R.T.Sauer
(2009).
OMP peptides activate the DegS stress-sensor protease by a relief of inhibition mechanism.
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Structure,
17,
1411-1421.
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PDB codes:
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M.I.Smith,
Y.Y.Huang,
and
M.Deshmukh
(2009).
Skeletal muscle differentiation evokes endogenous XIAP to restrict the apoptotic pathway.
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PLoS ONE,
4,
e5097.
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N.Padmanabhan,
L.Fichtner,
A.Dickmanns,
R.Ficner,
J.B.Schulz,
and
G.H.Braus
(2009).
The yeast HtrA orthologue Ynm3 is a protease with chaperone activity that aids survival under heat stress.
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Mol Biol Cell,
20,
68-77.
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S.Fulda
(2009).
Inhibitor of apoptosis proteins in hematological malignancies.
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Leukemia,
23,
467-476.
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E.V.Koonin,
Y.I.Wolf,
K.Nagasaki,
and
V.V.Dolja
(2008).
The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups.
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Nat Rev Microbiol,
6,
925-939.
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J.Jiang,
X.Zhang,
Y.Chen,
Y.Wu,
Z.H.Zhou,
Z.Chang,
and
S.F.Sui
(2008).
Activation of DegP chaperone-protease via formation of large cage-like oligomers upon binding to substrate proteins.
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Proc Natl Acad Sci U S A,
105,
11939-11944.
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J.R.Chao,
E.Parganas,
K.Boyd,
C.Y.Hong,
J.T.Opferman,
and
J.N.Ihle
(2008).
Hax1-mediated processing of HtrA2 by Parl allows survival of lymphocytes and neurons.
|
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Nature,
452,
98.
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J.Yun,
J.H.Cao,
M.W.Dodson,
I.E.Clark,
P.Kapahi,
R.B.Chowdhury,
and
M.Guo
(2008).
Loss-of-function analysis suggests that Omi/HtrA2 is not an essential component of the PINK1/PARKIN pathway in vivo.
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J Neurosci,
28,
14500-14510.
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L.Vande Walle,
M.Lamkanfi,
and
P.Vandenabeele
(2008).
The mitochondrial serine protease HtrA2/Omi: an overview.
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Cell Death Differ,
15,
453-460.
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M.S.Bhuiyan,
and
K.Fukunaga
(2008).
Activation of HtrA2, a mitochondrial serine protease mediates apoptosis: current knowledge on HtrA2 mediated myocardial ischemia/reperfusion injury.
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Cardiovasc Ther,
26,
224-232.
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O.Onder,
S.Turkarslan,
D.Sun,
and
F.Daldal
(2008).
Overproduction or absence of the periplasmic protease DegP severely compromises bacterial growth in the absence of the dithiol: disulfide oxidoreductase DsbA.
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Mol Cell Proteomics,
7,
875-890.
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R.Inagaki,
K.Tagawa,
M.L.Qi,
Y.Enokido,
H.Ito,
T.Tamura,
S.Shimizu,
K.Oyanagi,
N.Arai,
I.Kanazawa,
E.E.Wanker,
and
H.Okazawa
(2008).
Omi / HtrA2 is relevant to the selective vulnerability of striatal neurons in Huntington's disease.
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Eur J Neurosci,
28,
30-40.
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S.Launay,
E.Maubert,
N.Lebeurrier,
A.Tennstaedt,
M.Campioni,
F.Docagne,
C.Gabriel,
L.Dauphinot,
M.C.Potier,
M.Ehrmann,
A.Baldi,
and
D.Vivien
(2008).
HtrA1-dependent proteolysis of TGF-beta controls both neuronal maturation and developmental survival.
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Cell Death Differ,
15,
1408-1416.
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V.Bogaerts,
J.Theuns,
and
C.van Broeckhoven
(2008).
Genetic findings in Parkinson's disease and translation into treatment: a leading role for mitochondria?
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Genes Brain Behav,
7,
129-151.
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V.Bogaerts,
K.Nuytemans,
J.Reumers,
P.Pals,
S.Engelborghs,
B.Pickut,
E.Corsmit,
K.Peeters,
J.Schymkowitz,
P.P.De Deyn,
P.Cras,
F.Rousseau,
J.Theuns,
and
C.Van Broeckhoven
(2008).
Genetic variability in the mitochondrial serine protease HTRA2 contributes to risk for Parkinson disease.
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Hum Mutat,
29,
832-840.
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A.Jomaa,
D.Damjanovic,
V.Leong,
R.Ghirlando,
J.Iwanczyk,
and
J.Ortega
(2007).
The inner cavity of Escherichia coli DegP protein is not essential for molecular chaperone and proteolytic activity.
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J Bacteriol,
189,
706-716.
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E.S.Alnemri
(2007).
HtrA2 and Parkinson's disease: think PINK?
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Nat Cell Biol,
9,
1227-1229.
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H.J.Huttunen,
S.Y.Guénette,
C.Peach,
C.Greco,
W.Xia,
D.Y.Kim,
C.Barren,
R.E.Tanzi,
and
D.M.Kovacs
(2007).
HtrA2 regulates beta-amyloid precursor protein (APP) metabolism through endoplasmic reticulum-associated degradation.
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J Biol Chem,
282,
28285-28295.
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H.Plun-Favreau,
K.Klupsch,
N.Moisoi,
S.Gandhi,
S.Kjaer,
D.Frith,
K.Harvey,
E.Deas,
R.J.Harvey,
N.McDonald,
N.W.Wood,
L.M.Martins,
and
J.Downward
(2007).
The mitochondrial protease HtrA2 is regulated by Parkinson's disease-associated kinase PINK1.
|
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Nat Cell Biol,
9,
1243-1252.
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J.Sohn,
R.A.Grant,
and
R.T.Sauer
(2007).
Allosteric activation of DegS, a stress sensor PDZ protease.
|
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Cell,
131,
572-583.
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PDB codes:
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M.Challa,
S.Malladi,
B.J.Pellock,
D.Dresnek,
S.Varadarajan,
Y.W.Yin,
K.White,
and
S.B.Bratton
(2007).
Drosophila Omi, a mitochondrial-localized IAP antagonist and proapoptotic serine protease.
|
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EMBO J,
26,
3144-3156.
|
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N.Yan,
and
Y.Shi
(2007).
Allosteric activation of a bacterial stress sensor.
|
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Cell,
131,
441-443.
|
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P.F.Huesgen,
P.Scholz,
and
I.Adamska
(2007).
The serine protease HhoA from Synechocystis sp. strain PCC 6803: substrate specificity and formation of a hexameric complex are regulated by the PDZ domain.
|
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J Bacteriol,
189,
6611-6618.
|
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S.Fulda
(2007).
Inhibitor of apoptosis proteins as targets for anticancer therapy.
|
| |
Expert Rev Anticancer Ther,
7,
1255-1264.
|
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|
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S.Kuninaka,
S.I.Iida,
T.Hara,
M.Nomura,
H.Naoe,
T.Morisaki,
M.Nitta,
Y.Arima,
T.Mimori,
S.Yonehara,
and
H.Saya
(2007).
Serine protease Omi/HtrA2 targets WARTS kinase to control cell proliferation.
|
| |
Oncogene,
26,
2395-2406.
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S.T.Runyon,
Y.Zhang,
B.A.Appleton,
S.L.Sazinsky,
P.Wu,
B.Pan,
C.Wiesmann,
N.J.Skelton,
and
S.S.Sidhu
(2007).
Structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3.
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Protein Sci,
16,
2454-2471.
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PDB codes:
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X.Ma,
S.Kalakonda,
S.M.Srinivasula,
S.P.Reddy,
L.C.Platanias,
and
D.V.Kalvakolanu
(2007).
GRIM-19 associates with the serine protease HtrA2 for promoting cell death.
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Oncogene,
26,
4842-4849.
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Y.Zhang,
B.A.Appleton,
P.Wu,
C.Wiesmann,
and
S.S.Sidhu
(2007).
Structural and functional analysis of the ligand specificity of the HtrA2/Omi PDZ domain.
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Protein Sci,
16,
1738-1750.
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PDB code:
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F.Tong,
P.N.Black,
L.Bivins,
S.Quackenbush,
V.Ctrnacta,
and
C.C.DiRusso
(2006).
Direct interaction of Saccharomyces cerevisiae Faa1p with the Omi/HtrA protease orthologue Ynm3p alters lipid homeostasis.
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Mol Genet Genomics,
275,
330-343.
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F.Y.Li,
P.D.Jeffrey,
J.W.Yu,
and
Y.Shi
(2006).
Crystal structure of a viral FLIP: insights into FLIP-mediated inhibition of death receptor signaling.
|
| |
J Biol Chem,
281,
2960-2968.
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PDB code:
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L.N.Kinch,
K.Ginalski,
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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
codes are
shown on the right.
|
');
}
}
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