PDBsum entry 2jjr

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protein ligands links
Hydrolase PDB id
Protein chain
247 a.a. *
SO4 ×5
PEG ×5
Waters ×164
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: V232k, n236d-trichosanthin
Structure: Ribosome-inactivating protein alpha- trichosanthin. Chain: a. Synonym: trichosanthin mutant v232k n236d, rrna n-glycosidase, alpha-tcs. Engineered: yes. Mutation: yes
Source: Trichosanthes kirilowii. Mongolian snake-gourd. Organism_taxid: 3677. Expressed in: escherichia coli. Expression_system_taxid: 511693. Expression_system_variant: (de3)plyss.
2.30Å     R-factor:   0.186     R-free:   0.214
Authors: P.H.Too,M.K.Ma,A.N.Mak,C.K.Tung,G.Zhu,S.W.Au,K.B.Wong, P.C.Shaw
Key ref: 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: 19073700
21-Apr-08     Release date:   30-Dec-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P09989  (RIPT_TRIKI) -  Ribosome-inactivating protein alpha-trichosanthin
289 a.a.
247 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - rRNA N-glycosylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   4 terms 
  Biochemical function     hydrolase activity     2 terms  


Nucleic Acids Res 37:602-610 (2009)
PubMed id: 19073700  
The C-terminal fragment of the ribosomal P protein complexed to trichosanthin reveals the interaction between the ribosome-inactivating protein and the ribosome.
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.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21264238 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.
  PLoS One, 6, e15916.  
21455295 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.
  PLoS One, 6, e17883.  
20385603 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.
  Nucleic Acids Res, 38, 5206-5216.
PDB code: 2w1o
20558598 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.
  Nucleic Acids Res, 38, 6803-6812.  
19292477 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.
  Biochemistry, 48, 3853-3863.  
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