1tfk: Difference between revisions

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New page: left|200px<br /><applet load="1tfk" size="450" color="white" frame="true" align="right" spinBox="true" caption="1tfk, resolution 2.10Å" /> '''Ribonuclease from Es...
 
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[[Image:1tfk.gif|left|200px]]<br /><applet load="1tfk" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1tfk, resolution 2.10&Aring;" />
'''Ribonuclease from Escherichia coli complexed with its inhibtor protein'''<br />


==Overview==
==Ribonuclease from Escherichia coli complexed with its inhibtor protein==
Colicin D is a plasmid-encoded proteinaceous toxin which kills sensitive, Escherichia coli. Toxicity stems from ribonuclease activity that targets, exclusively four isoacceptors of tRNA(Arg) with a cleavage position, between 38 and 39 of the corresponding anticodons. Since no other tRNAs, with the same sequences at 38 and 39 as tRNA(Arg)s are cleaved, colicin D, should be capable of recognizing some higher order structure of tRNAs. We, report here two crystal structures of catalytic domains of colicin D which, have different N-terminal lengths, both complexed with its cognate, inhibitor protein, ImmD. A row of positive charge patches is found on the, surface of the catalytic domain, suggestive of the binding site of the, tRNAs. This finding, together with our refined tRNase activity, experiments, indicates that the catalytic domain starting at position 595, has activity almost equivalent to that of colicin D.
<StructureSection load='1tfk' size='340' side='right'caption='[[1tfk]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1tfk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TFK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TFK FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1tfk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tfk OCA], [https://pdbe.org/1tfk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tfk RCSB], [https://www.ebi.ac.uk/pdbsum/1tfk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tfk ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/CEAD_ECOLX CEAD_ECOLX] Colicins are polypeptide toxins produced by and active against E.coli and closely related bacteria.  Colicin D inhibits protein synthesis.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tf/1tfk_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1tfk ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1TFK is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with MES as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1TFK OCA].
*[[Colicin 3D structures|Colicin 3D structures]]
 
*[[Colicin immunity protein 3D structures|Colicin immunity protein 3D structures]]
==Reference==
__TOC__
Relation between tRNase activity and the structure of colicin D according to X-ray crystallography., Yajima S, Nakanishi K, Takahashi K, Ogawa T, Hidaka M, Kezuka Y, Nonaka T, Ohsawa K, Masaki H, Biochem Biophys Res Commun. 2004 Sep 24;322(3):966-73. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15336558 15336558]
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: Hidaka, M.]]
[[Category: Hidaka M]]
[[Category: Kezuka, Y.]]
[[Category: Kezuka Y]]
[[Category: Masaki, H.]]
[[Category: Masaki H]]
[[Category: Nakanishi, K.]]
[[Category: Nakanishi K]]
[[Category: Nonaka, T.]]
[[Category: Nonaka T]]
[[Category: Ogawa, T.]]
[[Category: Ogawa T]]
[[Category: Ohsawa, K.]]
[[Category: Ohsawa K]]
[[Category: Takahashi, K.]]
[[Category: Takahashi K]]
[[Category: Yajima, S.]]
[[Category: Yajima S]]
[[Category: MES]]
[[Category: protein-protein complex]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 03:13:30 2007''

Latest revision as of 11:39, 14 February 2024

Ribonuclease from Escherichia coli complexed with its inhibtor proteinRibonuclease from Escherichia coli complexed with its inhibtor protein

Structural highlights

1tfk is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.1Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CEAD_ECOLX Colicins are polypeptide toxins produced by and active against E.coli and closely related bacteria. Colicin D inhibits protein synthesis.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1tfk, resolution 2.10Å

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OCA
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