3l3p: Difference between revisions

Latest revision as of 16:20, 1 November 2023

Crystal structure of the C-terminal domain of Shigella type III effector IpaH9.8, with a novel domain swap

Structural highlights

3l3p is a 1 chain structure with sequence from Shigella flexneri. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.2Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

IPA9_SHIFL Effector proteins function to alter host cell physiology and promote bacterial survival in host tissues. This protein is an E3 ubiquitin ligase that interferes with host's ubiquitination pathway and modulates the acute inflammatory responses, thus facilitating bacterial colonization within the host cell. Interacts with IKBKG (NEMO) and TNIP1 (ABIN-1), an ubiquitin-binding adapter protein, which results in TNIP1-dependent 'Lys-27'-linked polyubiquitination of IKBKG. Consequently, polyubiquitinated IKBKG undergoes proteasome-dependent degradation, which perturbs NF-kappa-B activation during bacterial infection. Uses UBE2D2 (UBCH5B) as an E2 ubiquitin-conjugating enzyme.^[1] ^[2] ^[3]

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

We show that the monomeric form of Shigella IpaH9.8 E3 ligase catalyses the ubiquitination of human U2AF35 in vitro, providing a molecular mechanism for the observed in vivo effect. We further discover that under non-reducing conditions IpaH9.8 undergoes a domain swap driven by the formation of a disulfide bridge involving the catalytic cysteine and that this dimer is unable to catalyse the ubiquitination of U2AF35. The crystal structure of the domain-swapped dimer is presented. The redox inactivation of IpaH9.8 could be a mechanism of regulating the activity of the IpaH9.8 E3 ligase in response to cell damage so that the host cell in which the bacteria resides is maintained in a benign state suitable for bacterial survival.

A disulfide driven domain swap switches off the activity of Shigella IpaH9.8 E3 ligase.,Seyedarabi A, Sullivan JA, Sasakawa C, Pickersgill RW FEBS Lett. 2010 Oct 8;584(19):4163-8. Epub 2010 Sep 8. PMID:20831869^[4]

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

References

↑ Okuda J, Toyotome T, Kataoka N, Ohno M, Abe H, Shimura Y, Seyedarabi A, Pickersgill R, Sasakawa C. Shigella effector IpaH9.8 binds to a splicing factor U2AF(35) to modulate host immune responses. Biochem Biophys Res Commun. 2005 Jul 29;333(2):531-9. PMID:15950937 doi:10.1016/j.bbrc.2005.05.145
↑ Rohde JR, Breitkreutz A, Chenal A, Sansonetti PJ, Parsot C. Type III secretion effectors of the IpaH family are E3 ubiquitin ligases. Cell Host Microbe. 2007 Mar 15;1(1):77-83. PMID:18005683 doi:10.1016/j.chom.2007.02.002
↑ Ashida H, Kim M, Schmidt-Supprian M, Ma A, Ogawa M, Sasakawa C. A bacterial E3 ubiquitin ligase IpaH9.8 targets NEMO/IKKgamma to dampen the host NF-kappaB-mediated inflammatory response. Nat Cell Biol. 2010 Jan;12(1):66-73; sup pp 1-9. doi: 10.1038/ncb2006. Epub 2009 , Dec 13. PMID:20010814 doi:10.1038/ncb2006
↑ Seyedarabi A, Sullivan JA, Sasakawa C, Pickersgill RW. A disulfide driven domain swap switches off the activity of Shigella IpaH9.8 E3 ligase. FEBS Lett. 2010 Oct 8;584(19):4163-8. Epub 2010 Sep 8. PMID:20831869 doi:10.1016/j.febslet.2010.09.006

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OCA

[1] Okuda J, Toyotome T, Kataoka N, Ohno M, Abe H, Shimura Y, Seyedarabi A, Pickersgill R, Sasakawa C. Shigella effector IpaH9.8 binds to a splicing factor U2AF(35) to modulate host immune responses. Biochem Biophys Res Commun. 2005 Jul 29;333(2):531-9. PMID:15950937 doi:10.1016/j.bbrc.2005.05.145

[2] Rohde JR, Breitkreutz A, Chenal A, Sansonetti PJ, Parsot C. Type III secretion effectors of the IpaH family are E3 ubiquitin ligases. Cell Host Microbe. 2007 Mar 15;1(1):77-83. PMID:18005683 doi:10.1016/j.chom.2007.02.002

[3] Ashida H, Kim M, Schmidt-Supprian M, Ma A, Ogawa M, Sasakawa C. A bacterial E3 ubiquitin ligase IpaH9.8 targets NEMO/IKKgamma to dampen the host NF-kappaB-mediated inflammatory response. Nat Cell Biol. 2010 Jan;12(1):66-73; sup pp 1-9. doi: 10.1038/ncb2006. Epub 2009 , Dec 13. PMID:20010814 doi:10.1038/ncb2006

[4] Seyedarabi A, Sullivan JA, Sasakawa C, Pickersgill RW. A disulfide driven domain swap switches off the activity of Shigella IpaH9.8 E3 ligase. FEBS Lett. 2010 Oct 8;584(19):4163-8. Epub 2010 Sep 8. PMID:20831869 doi:10.1016/j.febslet.2010.09.006

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[2]

[3]

[4]

@@ Line 1: / Line 1: @@
 ==Crystal structure of the C-terminal domain of Shigella type III effector IpaH9.8, with a novel domain swap==
-<StructureSection load='3l3p' size='340' side='right' caption='[[3l3p]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+<StructureSection load='3l3p' size='340' side='right'caption='[[3l3p]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3l3p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"shigella_paradysenteriae"_weldin_1927 "shigella paradysenteriae" weldin 1927]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L3P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3L3P FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3l3p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Shigella_flexneri Shigella flexneri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L3P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3L3P FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ckd|3ckd]], [[3cvr|3cvr]]</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]] 3.2&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ipaH9.8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=623 "Shigella paradysenteriae" Weldin 1927])</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=3l3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l3p OCA], [https://pdbe.org/3l3p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3l3p RCSB], [https://www.ebi.ac.uk/pdbsum/3l3p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3l3p ProSAT]</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=3l3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l3p OCA], [http://pdbe.org/3l3p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3l3p RCSB], [http://www.ebi.ac.uk/pdbsum/3l3p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3l3p ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/IPA9_SHIFL IPA9_SHIFL]] Effector proteins function to alter host cell physiology and promote bacterial survival in host tissues. This protein is an E3 ubiquitin ligase that interferes with host's ubiquitination pathway and modulates the acute inflammatory responses, thus facilitating bacterial colonization within the host cell. Interacts with IKBKG (NEMO) and TNIP1 (ABIN-1), an ubiquitin-binding adapter protein, which results in TNIP1-dependent 'Lys-27'-linked polyubiquitination of IKBKG. Consequently, polyubiquitinated IKBKG undergoes proteasome-dependent degradation, which perturbs NF-kappa-B activation during bacterial infection. Uses UBE2D2 (UBCH5B) as an E2 ubiquitin-conjugating enzyme.<ref>PMID:15950937</ref> <ref>PMID:18005683</ref> <ref>PMID:20010814</ref>
+[https://www.uniprot.org/uniprot/IPA9_SHIFL IPA9_SHIFL] Effector proteins function to alter host cell physiology and promote bacterial survival in host tissues. This protein is an E3 ubiquitin ligase that interferes with host's ubiquitination pathway and modulates the acute inflammatory responses, thus facilitating bacterial colonization within the host cell. Interacts with IKBKG (NEMO) and TNIP1 (ABIN-1), an ubiquitin-binding adapter protein, which results in TNIP1-dependent 'Lys-27'-linked polyubiquitination of IKBKG. Consequently, polyubiquitinated IKBKG undergoes proteasome-dependent degradation, which perturbs NF-kappa-B activation during bacterial infection. Uses UBE2D2 (UBCH5B) as an E2 ubiquitin-conjugating enzyme.<ref>PMID:15950937</ref> <ref>PMID:18005683</ref> <ref>PMID:20010814</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Shigella paradysenteriae weldin 1927]]
+[[Category: Large Structures]]
-[[Category: Ubiquitin--protein ligase]]
+[[Category: Shigella flexneri]]
-[[Category: Pickersgill, R W]]
+[[Category: Pickersgill RW]]
-[[Category: Sasakawa, C]]
+[[Category: Sasakawa C]]
-[[Category: Seyedarabi, A]]
+[[Category: Seyedarabi A]]
-[[Category: Sullivan, J A]]
+[[Category: Sullivan JA]]
-[[Category: Cxd motif]]
-[[Category: Domain swap]]
-[[Category: E3 ligase]]
-[[Category: Ligase]]

3l3p: Difference between revisions

Latest revision as of 16:20, 1 November 2023

Crystal structure of the C-terminal domain of Shigella type III effector IpaH9.8, with a novel domain swap

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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