2djh: Difference between revisions
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|PDB= 2djh |SIZE=350|CAPTION= <scene name='initialview01'>2djh</scene>, resolution 1.90Å | |PDB= 2djh |SIZE=350|CAPTION= <scene name='initialview01'>2djh</scene>, resolution 1.90Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=3PD:2-AMINO-9-(2-DEOXY-3-O-PHOSPHONOPENTOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE'>3PD</scene> | |LIGAND= <scene name='pdbligand=3PD:2-AMINO-9-(2-DEOXY-3-O-PHOSPHONOPENTOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE'>3PD</scene>, <scene name='pdbligand=UM3:2'-DEOXYURIDINE+3'-MONOPHOSPHATE'>UM3</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY=[[2dfx|2DFX]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2djh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2djh OCA], [http://www.ebi.ac.uk/pdbsum/2djh PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2djh RCSB]</span> | |||
}} | }} | ||
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[[Category: Ohsawa, K.]] | [[Category: Ohsawa, K.]] | ||
[[Category: Yajima, S.]] | [[Category: Yajima, S.]] | ||
[[Category: alpha/beta protein]] | [[Category: alpha/beta protein]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:35:25 2008'' | ||
Revision as of 02:35, 31 March 2008
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| , resolution 1.90Å | |||||||
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| Ligands: | , | ||||||
| Related: | 2DFX
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of the carboxy-terminal ribonuclease domain of Colicin E5
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
2DJH is a Single protein structure of sequence 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
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