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| | ==Legionella pneumophila effector== | | ==Legionella pneumophila effector== |
| - | <StructureSection load='4iik' size='340' side='right' caption='[[4iik]], [[Resolution|resolution]] 1.60Å' scene=''> | + | <StructureSection load='4iik' size='340' side='right'caption='[[4iik]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4iik]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Legph Legph]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IIK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IIK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4iik]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Legionella_pneumophila_subsp._pneumophila_str._Philadelphia_1 Legionella pneumophila subsp. pneumophila str. Philadelphia 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IIK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IIK FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4iip|4iip]]</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=4iik FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iik OCA], [https://pdbe.org/4iik PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4iik RCSB], [https://www.ebi.ac.uk/pdbsum/4iik PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4iik ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">sidD, lpg2465 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272624 LEGPH])</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=4iik FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iik OCA], [http://pdbe.org/4iik PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4iik RCSB], [http://www.ebi.ac.uk/pdbsum/4iik PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4iik ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/SIDD_LEGPH SIDD_LEGPH]] Virulence effector that plays a role in hijacking the host vesicular trafficking by recruiting the small guanosine triphosphatase (GTPase) Rab1 to the cytosolic face of the Legionella-containing vacuole (LCVs). Acts as an adenosine monophosphate-protein hydrolase (de-AMPylase) by mediating the hydrolysis of adenosine 5'-monophosphate (AMP) to 'Tyr-77' of host RAB1B, thereby releasing RAB1B from bacterial phagosomes and rendering RAB1B accessible for inactivation by LepB. De-AMPylation of RAB1B cannot take place when LidA is bound to RAB1B.<ref>PMID:21734656</ref> <ref>PMID:21680813</ref> <ref>PMID:22228731</ref> | + | [https://www.uniprot.org/uniprot/SIDD_LEGPH SIDD_LEGPH] Virulence effector that plays a role in hijacking the host vesicular trafficking by recruiting the small guanosine triphosphatase (GTPase) Rab1 to the cytosolic face of the Legionella-containing vacuole (LCVs). Acts as an adenosine monophosphate-protein hydrolase (de-AMPylase) by mediating the hydrolysis of adenosine 5'-monophosphate (AMP) to 'Tyr-77' of host RAB1B, thereby releasing RAB1B from bacterial phagosomes and rendering RAB1B accessible for inactivation by LepB. De-AMPylation of RAB1B cannot take place when LidA is bound to RAB1B.<ref>PMID:21734656</ref> <ref>PMID:21680813</ref> <ref>PMID:22228731</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Legph]] | + | [[Category: Large Structures]] |
| - | [[Category: Chen, Y]] | + | [[Category: Legionella pneumophila subsp. pneumophila str. Philadelphia 1]] |
| - | [[Category: Hierro, A]] | + | [[Category: Chen Y]] |
| - | [[Category: Machner, M P]] | + | [[Category: Hierro A]] |
| - | [[Category: Neunuebel, M R]] | + | [[Category: Machner MP]] |
| - | [[Category: Rojas, A L]] | + | [[Category: Neunuebel MR]] |
| - | [[Category: Tascon, I]] | + | [[Category: Rojas AL]] |
| - | [[Category: Beta sandwich]]
| + | [[Category: Tascon I]] |
| - | [[Category: De-ampylation]]
| + | |
| - | [[Category: Hydrolase]]
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| - | [[Category: Legionella containing vacuole surface]]
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| - | [[Category: Rab1]]
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| Structural highlights
Function
SIDD_LEGPH Virulence effector that plays a role in hijacking the host vesicular trafficking by recruiting the small guanosine triphosphatase (GTPase) Rab1 to the cytosolic face of the Legionella-containing vacuole (LCVs). Acts as an adenosine monophosphate-protein hydrolase (de-AMPylase) by mediating the hydrolysis of adenosine 5'-monophosphate (AMP) to 'Tyr-77' of host RAB1B, thereby releasing RAB1B from bacterial phagosomes and rendering RAB1B accessible for inactivation by LepB. De-AMPylation of RAB1B cannot take place when LidA is bound to RAB1B.[1] [2] [3]
Publication Abstract from PubMed
The covalent attachment of adenosine monophosphate (AMP) to proteins, a process called AMPylation (adenylylation), has recently emerged as a novel theme in microbial pathogenesis. Although several AMPylating enzymes have been characterized, the only known virulence protein with de-AMPylation activity is SidD from the human pathogen Legionella pneumophila. SidD de-AMPylates mammalian Rab1, a small GTPase involved in secretory vesicle transport, thereby targeting the host protein for inactivation. The molecular mechanisms underlying Rab1 recognition and de-AMPylation by SidD are unclear. Here, we report the crystal structure of the catalytic region of SidD at 1.6 A resolution. The structure reveals a phosphatase-like fold with additional structural elements not present in generic PP2C-type phosphatases. The catalytic pocket contains a binuclear metal-binding site characteristic of hydrolytic metalloenzymes, with strong dependency on magnesium ions. Subsequent docking and molecular dynamics simulations between SidD and Rab1 revealed the interface contacts and the energetic contribution of key residues to the interaction. In conjunction with an extensive structure-based mutational analysis, we provide in vivo and in vitro evidence for a remarkable adaptation of SidD to its host cell target Rab1 which explains how this effector confers specificity to the reaction it catalyses.
Structural Basis for Rab1 De-AMPylation by the Legionella pneumophila Effector SidD.,Chen Y, Tascon I, Neunuebel MR, Pallara C, Brady J, Kinch LN, Fernandez-Recio J, Rojas AL, Machner MP, Hierro A PLoS Pathog. 2013 May;9(5):e1003382. doi: 10.1371/journal.ppat.1003382. Epub 2013, May 16. PMID:23696742[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Tan Y, Luo ZQ. Legionella pneumophila SidD is a deAMPylase that modifies Rab1. Nature. 2011 Jul 6;475(7357):506-9. doi: 10.1038/nature10307. PMID:21734656 doi:http://dx.doi.org/10.1038/nature10307
- ↑ Neunuebel MR, Chen Y, Gaspar AH, Backlund PS Jr, Yergey A, Machner MP. De-AMPylation of the small GTPase Rab1 by the pathogen Legionella pneumophila. Science. 2011 Jul 22;333(6041):453-6. doi: 10.1126/science.1207193. Epub 2011 Jun, 16. PMID:21680813 doi:http://dx.doi.org/10.1126/science.1207193
- ↑ Neunuebel MR, Mohammadi S, Jarnik M, Machner MP. Legionella pneumophila LidA affects nucleotide binding and activity of the host GTPase Rab1. J Bacteriol. 2012 Mar;194(6):1389-400. doi: 10.1128/JB.06306-11. Epub 2012 Jan 6. PMID:22228731 doi:http://dx.doi.org/10.1128/JB.06306-11
- ↑ Chen Y, Tascon I, Neunuebel MR, Pallara C, Brady J, Kinch LN, Fernandez-Recio J, Rojas AL, Machner MP, Hierro A. Structural Basis for Rab1 De-AMPylation by the Legionella pneumophila Effector SidD. PLoS Pathog. 2013 May;9(5):e1003382. doi: 10.1371/journal.ppat.1003382. Epub 2013, May 16. PMID:23696742 doi:10.1371/journal.ppat.1003382
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