3ckd: Difference between revisions

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New page: left|200px {{Structure |PDB= 3ckd |SIZE=350|CAPTION= <scene name='initialview01'>3ckd</scene>, resolution 2.65Å |SITE= <scene name='pdbsite=AC1:So4+Binding+Site+...
 
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[[Image:3ckd.jpg|left|200px]]


{{Structure
==Crystal structure of the C-terminal domain of the Shigella type III effector IpaH==
|PDB= 3ckd |SIZE=350|CAPTION= <scene name='initialview01'>3ckd</scene>, resolution 2.65&Aring;
<StructureSection load='3ckd' size='340' side='right'caption='[[3ckd]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
|SITE= <scene name='pdbsite=AC1:So4+Binding+Site+For+Residue+C+600'>AC1</scene>, <scene name='pdbsite=AC2:So4+Binding+Site+For+Residue+B+601'>AC2</scene>, <scene name='pdbsite=AC3:Gol+Binding+Site+For+Residue+C+602'>AC3</scene>, <scene name='pdbsite=AC4:Gol+Binding+Site+For+Residue+C+603'>AC4</scene>, <scene name='pdbsite=AC5:Gol+Binding+Site+For+Residue+C+604'>AC5</scene> and <scene name='pdbsite=AC6:Peg+Binding+Site+For+Residue+C+605'>AC6</scene>
== Structural highlights ==
|LIGAND= <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
<table><tr><td colspan='2'>[[3ckd]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Shigella_flexneri_2a_str._301 Shigella flexneri 2a str. 301]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CKD FirstGlance]. <br>
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </span>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.65&#8491;</td></tr>
|GENE= ipaH1.4, CP0265 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=198214 Shigella flexneri 2a str. 301])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG4886 COG4886]</span>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ckd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ckd OCA], [https://pdbe.org/3ckd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ckd RCSB], [https://www.ebi.ac.uk/pdbsum/3ckd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ckd ProSAT], [https://www.topsan.org/Proteins/MCSG/3ckd TOPSAN]</span></td></tr>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ckd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ckd OCA], [http://www.ebi.ac.uk/pdbsum/3ckd PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=3ckd RCSB]</span>
</table>
}}
== 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/ck/3ckd_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3ckd ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
IpaH proteins are E3 ubiquitin ligases delivered by the type III secretion apparatus into host cells upon infection of humans by the Gram-negative pathogen Shigella flexneri. These proteins comprise a variable leucine-rich repeat-containing N-terminal domain and a conserved C-terminal domain harboring an invariant cysteine residue that is crucial for activity. IpaH homologs are encoded by diverse animal and plant pathogens. Here we demonstrate that the IpaH C-terminal domain carries the catalytic activity for ubiquitin transfer and that the N-terminal domain carries the substrate specificity. The structure of the IpaH C-terminal domain, determined to 2.65-A resolution, represents an all-helical fold bearing no resemblance to previously defined E3 ubiquitin ligases. The conserved and essential cysteine residue lies on a flexible, surface-exposed loop surrounded by conserved acidic residues, two of which are crucial for IpaH activity.


'''Crystal structure of the C-terminal domain of the Shigella type III effector IpaH'''
Structure of the Shigella T3SS effector IpaH defines a new class of E3 ubiquitin ligases.,Singer AU, Rohde JR, Lam R, Skarina T, Kagan O, Dileo R, Chirgadze NY, Cuff ME, Joachimiak A, Tyers M, Sansonetti PJ, Parsot C, Savchenko A Nat Struct Mol Biol. 2008 Dec;15(12):1293-301. Epub 2008 Nov 9. PMID:18997778<ref>PMID:18997778</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==About this Structure==
</div>
3CKD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Shigella_flexneri_2a_str._301 Shigella flexneri 2a str. 301]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CKD OCA].
<div class="pdbe-citations 3ckd" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Shigella flexneri 2a str. 301]]
[[Category: Shigella flexneri 2a str. 301]]
[[Category: Single protein]]
[[Category: Cuff ME]]
[[Category: Ubiquitin--protein ligase]]
[[Category: DiLeo R]]
[[Category: Cuff, M E.]]
[[Category: Edwards AM]]
[[Category: DiLeo, R.]]
[[Category: Joachimiak A]]
[[Category: Edwards, A M.]]
[[Category: Kagan O]]
[[Category: Joachimiak, A.]]
[[Category: Lam R]]
[[Category: Kagan, O.]]
[[Category: Savchenko A]]
[[Category: Lam, R.]]
[[Category: Singer AU]]
[[Category: MCSG, Midwest Center for Structural Genomics.]]
[[Category: Skarina T]]
[[Category: Savchenko, A.]]
[[Category: Singer, A U.]]
[[Category: Skarina, T.]]
[[Category: e3 ubiquitin ligase]]
[[Category: helical]]
[[Category: mcsg]]
[[Category: midwest center for structural genomic]]
[[Category: plasmid]]
[[Category: protein structure initiative]]
[[Category: psi-2]]
[[Category: structural genomic]]
[[Category: type iii effector]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 26 10:00:44 2008''

Latest revision as of 04:41, 21 November 2024

Crystal structure of the C-terminal domain of the Shigella type III effector IpaHCrystal structure of the C-terminal domain of the Shigella type III effector IpaH

Structural highlights

3ckd is a 3 chain structure with sequence from Shigella flexneri 2a str. 301. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.65Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Evolutionary Conservation

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

Publication Abstract from PubMed

IpaH proteins are E3 ubiquitin ligases delivered by the type III secretion apparatus into host cells upon infection of humans by the Gram-negative pathogen Shigella flexneri. These proteins comprise a variable leucine-rich repeat-containing N-terminal domain and a conserved C-terminal domain harboring an invariant cysteine residue that is crucial for activity. IpaH homologs are encoded by diverse animal and plant pathogens. Here we demonstrate that the IpaH C-terminal domain carries the catalytic activity for ubiquitin transfer and that the N-terminal domain carries the substrate specificity. The structure of the IpaH C-terminal domain, determined to 2.65-A resolution, represents an all-helical fold bearing no resemblance to previously defined E3 ubiquitin ligases. The conserved and essential cysteine residue lies on a flexible, surface-exposed loop surrounded by conserved acidic residues, two of which are crucial for IpaH activity.

Structure of the Shigella T3SS effector IpaH defines a new class of E3 ubiquitin ligases.,Singer AU, Rohde JR, Lam R, Skarina T, Kagan O, Dileo R, Chirgadze NY, Cuff ME, Joachimiak A, Tyers M, Sansonetti PJ, Parsot C, Savchenko A Nat Struct Mol Biol. 2008 Dec;15(12):1293-301. Epub 2008 Nov 9. PMID:18997778[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Singer AU, Rohde JR, Lam R, Skarina T, Kagan O, Dileo R, Chirgadze NY, Cuff ME, Joachimiak A, Tyers M, Sansonetti PJ, Parsot C, Savchenko A. Structure of the Shigella T3SS effector IpaH defines a new class of E3 ubiquitin ligases. Nat Struct Mol Biol. 2008 Dec;15(12):1293-301. Epub 2008 Nov 9. PMID:18997778 doi:10.1038/nsmb.1511

3ckd, resolution 2.65Å

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