2gyk: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2gyk.jpg|left|200px]]<br /><applet load="2gyk" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2gyk, resolution 1.600&Aring;" />
'''Crystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity protein, IMME9 (D51A)'''<br />


==Overview==
==Crystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity protein, IMME9 (D51A)==
The crystal structure of the cytotoxic endonuclease domain from the, bacterial toxin colicin E9 in complex with its cognate immunity protein, Im9 reveals that the inhibitor does not bind at the active site, the core, of which comprises the HNH motif found in intron-encoded homing, endonucleases, but rather at an adjacent position leaving the active site, exposed yet unable to bind DNA because of steric and electrostatic clashes, with incoming substrate. Although its mode of action is unorthodox, Im9 is, a remarkably effective inhibitor since it folds within milliseconds and, then associates with its target endonuclease at the rate of diffusion to, form an inactive complex with sub-femtomolar binding affinity. This, hyperefficient mechanism of inhibition could be well suited to other toxic, enzyme systems, particularly where the substrate is a polymer extending, beyond the boundaries of the active site.
<StructureSection load='2gyk' size='340' side='right'caption='[[2gyk]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2gyk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GYK 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]] 1.6&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2gyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gyk OCA], [https://pdbe.org/2gyk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gyk RCSB], [https://www.ebi.ac.uk/pdbsum/2gyk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gyk ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/IMM9_ECOLX IMM9_ECOLX] This protein is able to protect a cell, which harbors the plasmid ColE9 encoding colicin E9, against colicin E9, it binds specifically to the DNase-type colicin and inhibits its bactericidal activity.
== 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/gy/2gyk_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=2gyk ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2GYK 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 <scene name='pdbligand=ZN:'>ZN</scene> and <scene name='pdbligand=PO4:'>PO4</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Deoxyribonuclease_I Deoxyribonuclease I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.1 3.1.21.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GYK OCA].
*[[Colicin 3D structures|Colicin 3D structures]]
 
*[[Colicin immunity protein 3D structures|Colicin immunity protein 3D structures]]
==Reference==
__TOC__
Structural and mechanistic basis of immunity toward endonuclease colicins., Kleanthous C, Kuhlmann UC, Pommer AJ, Ferguson N, Radford SE, Moore GR, James R, Hemmings AM, Nat Struct Biol. 1999 Mar;6(3):243-52. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10074943 10074943]
</StructureSection>
[[Category: Deoxyribonuclease I]]
[[Category: Escherichia coli K-12]]
[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Protein complex]]
[[Category: Hemmings AM]]
[[Category: Hemmings, A.M.]]
[[Category: Kolade OO]]
[[Category: Kolade, O.O.]]
[[Category: Kuhlmann UC]]
[[Category: Kuhlmann, U.C.]]
[[Category: Santi PS]]
[[Category: Santi, P.S.]]
[[Category: PO4]]
[[Category: ZN]]
[[Category: 4-helix bundle]]
[[Category: dnase domain]]
[[Category: hnh-motif]]
[[Category: protein-protein complex]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 15:15:53 2008''

Latest revision as of 12:48, 30 August 2023

Crystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity protein, IMME9 (D51A)Crystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity protein, IMME9 (D51A)

Structural highlights

2gyk is a 4 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.6Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

IMM9_ECOLX This protein is able to protect a cell, which harbors the plasmid ColE9 encoding colicin E9, against colicin E9, it binds specifically to the DNase-type colicin and inhibits its bactericidal activity.

Evolutionary Conservation

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

See Also

2gyk, resolution 1.60Å

Drag the structure with the mouse to rotate

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

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2gyk&oldid=3850624"