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PDBsum entry 2jdl
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Contents |
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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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Structure of c-terminal region of acidic p2 ribosomal protein complexed with trichosanthin
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Structure:
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Ribosome-inactivating protein alpha-trichosanthin. Chain: a, b. Fragment: residues 25-270. Synonym: rrna n-glycosidase, alpha-tcs, trichosanthin. Engineered: yes. Acidic ribosomal protein p2. Chain: c, d. Engineered: yes
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Source:
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Trichosanthes kirilowii. Mongolian snake-gourd. Organism_taxid: 3677. Expressed in: escherichia coli. Expression_system_taxid: 511693. Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606
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Resolution:
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2.20Å
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R-factor:
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0.167
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R-free:
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0.238
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Authors:
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P.H.Too,A.N.Mak,G.Zhu,S.W.Au,K.B.Wong,P.C.Shaw
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Key ref:
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P.H.Too
et al.
(2009).
The C-terminal fragment of the ribosomal P protein complexed to trichosanthin reveals the interaction between the ribosome-inactivating protein and the ribosome.
Nucleic Acids Res,
37,
602-610.
PubMed id:
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Date:
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11-Jan-07
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Release date:
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05-Feb-08
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PROCHECK
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Headers
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References
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P09989
(RIPT_TRIKI) -
Ribosome-inactivating protein alpha-trichosanthin from Trichosanthes kirilowii
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Seq:
Struc:
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289 a.a.
247 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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Enzyme class:
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E.C.3.2.2.22
- rRNA N-glycosylase.
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Reaction:
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Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
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Nucleic Acids Res
37:602-610
(2009)
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PubMed id:
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The C-terminal fragment of the ribosomal P protein complexed to trichosanthin reveals the interaction between the ribosome-inactivating protein and the ribosome.
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P.H.Too,
M.K.Ma,
A.N.Mak,
Y.T.Wong,
C.K.Tung,
G.Zhu,
S.W.Au,
K.B.Wong,
P.C.Shaw.
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ABSTRACT
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Ribosome-inactivating proteins (RIPs) inhibit protein synthesis by enzymatically
depurinating a specific adenine residue at the sarcin-ricin loop of the 28S
rRNA, which thereby prevents the binding of elongation factors to the GTPase
activation centre of the ribosome. Here, we present the 2.2 A crystal structure
of trichosanthin (TCS) complexed to the peptide SDDDMGFGLFD, which corresponds
to the conserved C-terminal elongation factor binding domain of the ribosomal P
protein. The N-terminal region of this peptide interacts with Lys173, Arg174 and
Lys177 in TCS, while the C-terminal region is inserted into a hydrophobic
pocket. The interaction with the P protein contributes to the
ribosome-inactivating activity of TCS. This 11-mer C-terminal P peptide can be
docked with selected important plant and bacterial RIPs, indicating that a
similar interaction may also occur with other RIPs.
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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.Shapira,
M.Gal-Tanamy,
L.Nahary,
D.Litvak-Greenfeld,
R.Zemel,
R.Tur-Kaspa,
and
I.Benhar
(2011).
Engineered toxins "zymoxins" are activated by the HCV NS3 protease by removal of an inhibitory protein domain.
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PLoS One,
6,
e15916.
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Y.P.Pang,
J.G.Park,
S.Wang,
A.Vummenthala,
R.K.Mishra,
J.E.McLaughlin,
R.Di,
J.N.Kahn,
N.E.Tumer,
L.Janosi,
J.Davis,
and
C.B.Millard
(2011).
Small-molecule inhibitor leads of ribosome-inactivating proteins developed using the doorstop approach.
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PLoS One,
6,
e17883.
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K.M.Lee,
C.W.Yu,
D.S.Chan,
T.Y.Chiu,
G.Zhu,
K.H.Sze,
P.C.Shaw,
and
K.B.Wong
(2010).
Solution structure of the dimerization domain of ribosomal protein P2 provides insights for the structural organization of eukaryotic stalk.
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Nucleic Acids Res,
38,
5206-5216.
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PDB code:
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S.K.Law,
R.R.Wang,
A.N.Mak,
K.B.Wong,
Y.T.Zheng,
and
P.C.Shaw
(2010).
A switch-on mechanism to activate maize ribosome-inactivating protein for targeting HIV-infected cells.
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Nucleic Acids Res,
38,
6803-6812.
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X.P.Li,
J.C.Chiou,
M.Remacha,
J.P.Ballesta,
and
N.E.Tumer
(2009).
A two-step binding model proposed for the electrostatic interactions of ricin a chain with ribosomes.
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Biochemistry,
48,
3853-3863.
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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
