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PDBsum entry 2dfx
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protein Protein-protein interface(s) links
Hydrolase PDB id
2dfx

 

 

 

 

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Contents
Protein chains
92 a.a. *
106 a.a. *
Waters ×102
* Residue conservation analysis
PDB id:
2dfx
Name: Hydrolase
Title: Crystal structure of the carboxy terminal domain of colicin e5 complexed with its inhibitor
Structure: Colicin-e5. Chain: e. Fragment: c-terminal domain, residues 2-116. Synonym: fragment. Engineered: yes. Colicin-e5 immunity protein. Chain: i. Synonym: imme5, microcin-e5 immunity protein. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.90Å     R-factor:   0.179     R-free:   0.198
Authors: S.Yajima,S.Inoue,T.Ogawa,T.Nonaka,K.Ohsawa,H.Masaki
Key ref: S.Yajima et al. (2006). Structural basis for sequence-dependent recognition of colicin E5 tRNase by mimicking the mRNA-tRNA interaction. Nucleic Acids Res, 34, 6074-6082. PubMed id: 17099236
Date:
06-Mar-06     Release date:   23-Jan-07    
PROCHECK
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 Headers
 References

Protein chain
P18000  (CEA5_ECOLX) -  Colicin-E5 (Fragment) from Escherichia coli
Seq:
Struc: 		180 a.a.
92 a.a.
Protein chain
P13476  (IMM5_ECOLX) -  Colicin-E5 immunity protein from Escherichia coli
Seq:
Struc: 		83 a.a.
106 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain E: E.C.3.1.-.-
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
Nucleic Acids Res 34:6074-6082 (2006)
PubMed id: 17099236  
 
 
Structural basis for sequence-dependent recognition of colicin E5 tRNase by mimicking the mRNA-tRNA interaction.
S.Yajima, S.Inoue, T.Ogawa, T.Nonaka, K.Ohsawa, H.Masaki.
 
  ABSTRACT  
 
Colicin E5--a tRNase toxin--specifically cleaves QUN (Q: queuosine) anticodons of the Escherichia coli tRNAs for Tyr, His, Asn and Asp. Here, we report the crystal structure of the C-terminal ribonuclease domain (CRD) of E5 complexed with a substrate analog, namely, dGpdUp, at a resolution of 1.9 A. Thisstructure is the first to reveal the substrate recognition mechanism of sequence-specific ribonucleases. E5-CRD realized the strict recognition for both the guanine and uracil bases of dGpdUp forming Watson-Crick-type hydrogen bonds and ring stacking interactions, thus mimicking the codons of mRNAs to bind to tRNA anticodons. The docking model of E5-CRD with tRNA also suggests its substrate preference for tRNA over ssRNA. In addition, the structure of E5-CRD/dGpdUp along with the mutational analysis suggests that Arg33 may play an important role in the catalytic activity, and Lys25/Lys60 may also be involved without His in E5-CRD. Finally, the comparison of the structures of E5-CRD/dGpdUp and E5-CRD/ImmE5 (an inhibitor protein) complexes suggests that the binding mode of E5-CRD and ImmE5 mimics that of mRNA and tRNA; this may represent the evolutionary pathway of these proteins from the RNA-RNA interaction through the RNA-protein interaction of tRNA/E5-CRD.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20855293 B.Meineke, B.Schwer, R.Schaffrath, and S.Shuman (2011).
Determinants of eukaryal cell killing by the bacterial ribotoxin PrrC.
  Nucleic Acids Res, 39, 687-700.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
  20975905 L.C.Barbosa, S.S.Garrido, A.Garcia, D.B.Delfino, and R.Marchetto (2010).
Function inferences from a molecular structural model of bacterial ParE toxin.
  Bioinformation, 4, 438-440.  
20007328 R.Jain, and S.Shuman (2010).
Bacterial Hen1 is a 3' terminal RNA ribose 2'-O-methyltransferase component of a bacterial RNA repair cassette.
  RNA, 16, 316-323.  
19297318 G.Y.Li, Y.Zhang, M.Inouye, and M.Ikura (2009).
Inhibitory mechanism of Escherichia coli RelE-RelB toxin-antitoxin module involves a helix displacement near an mRNA interferase active site.
  J Biol Chem, 284, 14628-14636.
PDB codes: 2kc8 2kc9
19877125 M.Shigematsu, T.Ogawa, A.Kido, H.K.Kitamoto, M.Hidaka, and H.Masaki (2009).
Cellular and transcriptional responses of yeast to the cleavage of cytosolic tRNAs induced by colicin D.
  Yeast, 26, 663-673.  
19383764 N.Keppetipola, R.Jain, B.Meineke, M.Diver, and S.Shuman (2009).
Structure-activity relationships in Kluyveromyces lactis gamma-toxin, a eukaryal tRNA anticodon nuclease.
  RNA, 15, 1036-1044.  
19151102 T.Ogawa, M.Hidaka, K.Kohno, and H.Masaki (2009).
Colicin E5 ribonuclease domain cleaves Saccharomyces cerevisiae tRNAs leading to impairment of the cell growth.
  J Biochem, 145, 461-466.  
18096622 J.Lu, A.Esberg, B.Huang, and A.S.Byström (2008).
Kluyveromyces lactis gamma-toxin, a ribonuclease that recognizes the anticodon stem loop of tRNA.
  Nucleic Acids Res, 36, 1072-1080.  
17604307 D.Klaiman, M.Amitsur, S.Blanga-Kanfi, M.Chai, D.R.Davis, and G.Kaufmann (2007).
Parallel dimerization of a PrrC-anticodon nuclease region implicated in tRNALys recognition.
  Nucleic Acids Res, 35, 4704-4714.  
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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