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| | ==Crystal structure of the C-terminal domain of the Shigella type III effector IpaH== | | ==Crystal structure of the C-terminal domain of the Shigella type III effector IpaH== |
| - | <StructureSection load='3ckd' size='340' side='right' caption='[[3ckd]], [[Resolution|resolution]] 2.65Å' scene=''> | + | <StructureSection load='3ckd' size='340' side='right'caption='[[3ckd]], [[Resolution|resolution]] 2.65Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3ckd]] is a 3 chain structure with 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CKD FirstGlance]. <br> | + | <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> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.65Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <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> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ipaH1.4, CP0265 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=198214 Shigella flexneri 2a str. 301])</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=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> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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://pdbe.org/3ckd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ckd RCSB], [http://www.ebi.ac.uk/pdbsum/3ckd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ckd ProSAT], [http://www.topsan.org/Proteins/MCSG/3ckd TOPSAN]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ck/3ckd_consurf.spt"</scriptWhenChecked> | | <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/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Shigella flexneri 2a str. 301]] | | [[Category: Shigella flexneri 2a str. 301]] |
| - | [[Category: Ubiquitin--protein ligase]]
| + | [[Category: Cuff ME]] |
| - | [[Category: Cuff, M E]] | + | [[Category: DiLeo R]] |
| - | [[Category: DiLeo, R]] | + | [[Category: Edwards AM]] |
| - | [[Category: Edwards, A M]] | + | [[Category: Joachimiak A]] |
| - | [[Category: Joachimiak, A]] | + | [[Category: Kagan O]] |
| - | [[Category: Kagan, O]] | + | [[Category: Lam R]] |
| - | [[Category: Lam, R]] | + | [[Category: Savchenko A]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Singer AU]] |
| - | [[Category: Savchenko, A]] | + | [[Category: Skarina T]] |
| - | [[Category: Singer, A U]] | + | |
| - | [[Category: Skarina, T]] | + | |
| - | [[Category: E3 ubiquitin ligase]]
| + | |
| - | [[Category: Helical]]
| + | |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Mcsg]]
| + | |
| - | [[Category: PSI, Protein structure initiative]]
| + | |
| - | [[Category: Type iii effector]]
| + | |
| 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
- ↑ 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
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