2dfx: Difference between revisions

Revision as of 00:20, 4 May 2008

Related:

Structural annotation:
Resources:	UniProt : P18000, P13476

Functional annotation:
Biological process:	cytolysis defense response to bacterium bacteriocin immunity
Molecular function:	receptor binding nuclease activity endonuclease activity hydrolase activity

Evolutionary conservation:

Toggle Conservation Colors:

Rows = identical sequences:

Further Information:

Caveats,

Explanation,
Complete Results at ConSurfDB

Resources:

FirstGlance, OCA, PDBsum, RCSB

Coordinates:

save as pdb, mmCIF, xml

Crystal structure of the carboxy terminal domain of colicin E5 complexed with its inhibitor

OverviewOverview

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.

About this StructureAbout this Structure

2DFX is a Protein complex structure of sequences from Escherichia coli. Full crystallographic information is available from OCA.

ReferenceReference

Structural basis for sequence-dependent recognition of colicin E5 tRNase by mimicking the mRNA-tRNA interaction., Yajima S, Inoue S, Ogawa T, Nonaka T, Ohsawa K, Masaki H, Nucleic Acids Res. 2006;34(21):6074-82. Epub 2006 Nov 11. PMID:17099236 Page seeded by OCA on Sun May 4 00:20:33 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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 [[Image:2dfx.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 2dfx |SIZE=350|CAPTION= <scene name='initialview01'>2dfx</scene>, resolution 1.9&Aring;
+The line below this paragraph, containing "STRUCTURE_2dfx", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND=
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY=
+or leave the SCENE parameter empty for the default display.
-|GENE=
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-|DOMAIN=
+{{STRUCTURE_2dfx|  PDB=2dfx  |  SCENE=  }}
-|RELATEDENTRY=[[2djh|2DJH]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfx OCA], [http://www.ebi.ac.uk/pdbsum/2dfx PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dfx RCSB]</span>
-}}
 '''Crystal structure of the carboxy terminal domain of colicin E5 complexed with its inhibitor'''
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 [[Category: Ohsawa, K.]]
 [[Category: Yajima, S.]]
-[[Category: alpha/beta protein]]
+[[Category: Alpha/beta protein]]
-[[Category: protein-inhibitor protein complex]]
+[[Category: Protein-inhibitor protein complex]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 00:20:33 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:34:10 2008''