6aci: Difference between revisions

Latest revision as of 09:25, 22 November 2023

Crystal structure of EPEC effector NleB in complex with FADD death domain

Structural highlights

6aci is a 2 chain structure with sequence from Escherichia coli O127:H6 str. E2348/69 and Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.87Å
Ligands:	MN, UDP
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NLEB1_ECO27 Protein-arginine N-acetylglucosaminyltransferase effector that disrupts TNF signaling in infected cells, including NF-kappa-B signaling, apoptosis and necroptosis (PubMed:20126447, PubMed:20485572, PubMed:22144899, PubMed:23955153, PubMed:24025841, PubMed:28138023, PubMed:28522607, PubMed:30979585). Acts by catalyzing the transfer of a single N-acetylglucosamine (GlcNAc) to a conserved arginine residue in the death domain of host proteins FADD, TRADD, FAS, TNFRSF1A/TNFR1, TNFRSF25/DR3 and RIPK1: arginine GlcNAcylation prevents homotypic/heterotypic death domain interactions and assembly of the oligomeric TNF-alpha receptor complex, thereby disrupting TNF signaling (PubMed:23955153, PubMed:24025841, PubMed:26883593, PubMed:28522607, PubMed:28860194, PubMed:30979585). Has preference for host FADD as substrate compared to other death domain-containing proteins (PubMed:28860194). Also acts on host proteins without a death domain: catalyzes arginine GlcNAcylation of HIF1A, thereby regulating host glucose metabolism (PubMed:30125331). Also displays intra-bacterial activity by mediating GlcNAcylation of glutathione synthetase GshB (PubMed:31974499). Catalyzes auto-GlcNAcylation, which is required for activity toward death domain-containing host target proteins (PubMed:32432056). Shows a higher enzymatic activity than NleB2 (PubMed:23955153).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13]

Publication Abstract from PubMed

Enteropathogenic E. coli NleB and related type III effectors catalyze arginine GlcNAcylation of death domain (DD) proteins to block host defense, but the underlying mechanism is unknown. Here we solve crystal structures of NleB alone and in complex with FADD-DD, UDP, and Mn(2+) as well as NleB-GlcNAcylated DDs of TRADD and RIPK1. NleB adopts a GT-A fold with a unique helix-pair insertion to hold FADD-DD; the interface contacts explain the selectivity of NleB for certain DDs. The acceptor arginine is fixed into a cleft, in which Glu253 serves as a base to activate the guanidinium. Analyses of the enzyme-substrate complex and the product structures reveal an inverting sugar-transfer reaction and a detailed catalytic mechanism. These structural insights are validated by mutagenesis analyses of NleB-mediated GlcNAcylation in vitro and its function in mouse infection. Our study builds a structural framework for understanding of NleB-catalyzed arginine GlcNAcylation of host death domain.

Structural and Functional Insights into Host Death Domains Inactivation by the Bacterial Arginine GlcNAcyltransferase Effector.,Ding J, Pan X, Du L, Yao Q, Xue J, Yao H, Wang DC, Li S, Shao F Mol Cell. 2019 Apr 3. pii: S1097-2765(19)30232-1. doi:, 10.1016/j.molcel.2019.03.028. PMID:30979585^[14]

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

References

↑ Nadler C, Baruch K, Kobi S, Mills E, Haviv G, Farago M, Alkalay I, Bartfeld S, Meyer TF, Ben-Neriah Y, Rosenshine I. The type III secretion effector NleE inhibits NF-kappaB activation. PLoS Pathog. 2010 Jan 29;6(1):e1000743. PMID:20126447 doi:10.1371/journal.ppat.1000743
↑ Newton HJ, Pearson JS, Badea L, Kelly M, Lucas M, Holloway G, Wagstaff KM, Dunstone MA, Sloan J, Whisstock JC, Kaper JB, Robins-Browne RM, Jans DA, Frankel G, Phillips AD, Coulson BS, Hartland EL. The type III effectors NleE and NleB from enteropathogenic E. coli and OspZ from Shigella block nuclear translocation of NF-kappaB p65. PLoS Pathog. 2010 May 13;6(5):e1000898. PMID:20485572 doi:10.1371/journal.ppat.1000898
↑ Ruchaud-Sparagano MH, Mühlen S, Dean P, Kenny B. The enteropathogenic E. coli (EPEC) Tir effector inhibits NF-κB activity by targeting TNFα receptor-associated factors. PLoS Pathog. 2011 Dec;7(12):e1002414. PMID:22144899 doi:10.1371/journal.ppat.1002414
↑ Li S, Zhang L, Yao Q, Li L, Dong N, Rong J, Gao W, Ding X, Sun L, Chen X, Chen S, Shao F. Pathogen blocks host death receptor signalling by arginine GlcNAcylation of death domains. Nature. 2013 Sep 12;501(7466):242-6. PMID:23955153 doi:10.1038/nature12436
↑ Pearson JS, Giogha C, Ong SY, Kennedy CL, Kelly M, Robinson KS, Lung TW, Mansell A, Riedmaier P, Oates CV, Zaid A, Mühlen S, Crepin VF, Marches O, Ang CS, Williamson NA, O'Reilly LA, Bankovacki A, Nachbur U, Infusini G, Webb AI, Silke J, Strasser A, Frankel G, Hartland EL. A type III effector antagonizes death receptor signalling during bacterial gut infection. Nature. 2013 Sep 12;501(7466):247-51. PMID:24025841 doi:10.1038/nature12524
↑ Wong Fok Lung T, Giogha C, Creuzburg K, Ong SY, Pollock GL, Zhang Y, Fung KY, Pearson JS, Hartland EL. Mutagenesis and Functional Analysis of the Bacterial Arginine Glycosyltransferase Effector NleB1 from Enteropathogenic Escherichia coli. Infect Immun. 2016 Apr 22;84(5):1346-1360. PMID:26883593 doi:10.1128/IAI.01523-15
↑ Pollock GL, Oates CVL, Giogha C, Wong Fok Lung T, Ong SY, Pearson JS, Hartland EL. Distinct Roles of the Antiapoptotic Effectors NleB and NleF from Enteropathogenic Escherichia coli. Infect Immun. 2017 Mar 23;85(4):e01071-16. PMID:28138023 doi:10.1128/IAI.01071-16
↑ El Qaidi S, Chen K, Halim A, Siukstaite L, Rueter C, Hurtado-Guerrero R, Clausen H, Hardwidge PR. NleB/SseK effectors from Citrobacter rodentium, Escherichia coli, and Salmonella enterica display distinct differences in host substrate specificity. J Biol Chem. 2017 Jul 7;292(27):11423-11430. PMID:28522607 doi:10.1074/jbc.M117.790675
↑ Scott NE, Giogha C, Pollock GL, Kennedy CL, Webb AI, Williamson NA, Pearson JS, Hartland EL. The bacterial arginine glycosyltransferase effector NleB preferentially modifies Fas-associated death domain protein (FADD). J Biol Chem. 2017 Oct 20;292(42):17337-17350. PMID:28860194 doi:10.1074/jbc.M117.805036
↑ Xu C, Liu X, Zha H, Fan S, Zhang D, Li S, Xiao W. A pathogen-derived effector modulates host glucose metabolism by arginine GlcNAcylation of HIF-1α protein. PLoS Pathog. 2018 Aug 20;14(8):e1007259. PMID:30125331 doi:10.1371/journal.ppat.1007259
↑ Ding J, Pan X, Du L, Yao Q, Xue J, Yao H, Wang DC, Li S, Shao F. Structural and Functional Insights into Host Death Domains Inactivation by the Bacterial Arginine GlcNAcyltransferase Effector. Mol Cell. 2019 Apr 3. pii: S1097-2765(19)30232-1. doi:, 10.1016/j.molcel.2019.03.028. PMID:30979585 doi:https://dx.doi.org/10.1016/j.molcel.2019.03.028
↑ El Qaidi S, Scott NE, Hays MP, Geisbrecht BV, Watkins S, Hardwidge PR. An intra-bacterial activity for a T3SS effector. Sci Rep. 2020 Jan 23;10(1):1073. PMID:31974499 doi:10.1038/s41598-020-58062-y
↑ Xue J, Pan X, Peng T, Duan M, Du L, Zhuang X, Cai X, Yi X, Fu Y, Li S. Auto Arginine-GlcNAcylation Is Crucial for Bacterial Pathogens in Regulating Host Cell Death. Front Cell Infect Microbiol. 2020 May 5;10:197. PMID:32432056 doi:10.3389/fcimb.2020.00197
↑ Ding J, Pan X, Du L, Yao Q, Xue J, Yao H, Wang DC, Li S, Shao F. Structural and Functional Insights into Host Death Domains Inactivation by the Bacterial Arginine GlcNAcyltransferase Effector. Mol Cell. 2019 Apr 3. pii: S1097-2765(19)30232-1. doi:, 10.1016/j.molcel.2019.03.028. PMID:30979585 doi:https://dx.doi.org/10.1016/j.molcel.2019.03.028

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OCA

[1] Nadler C, Baruch K, Kobi S, Mills E, Haviv G, Farago M, Alkalay I, Bartfeld S, Meyer TF, Ben-Neriah Y, Rosenshine I. The type III secretion effector NleE inhibits NF-kappaB activation. PLoS Pathog. 2010 Jan 29;6(1):e1000743. PMID:20126447 doi:10.1371/journal.ppat.1000743

[2] Newton HJ, Pearson JS, Badea L, Kelly M, Lucas M, Holloway G, Wagstaff KM, Dunstone MA, Sloan J, Whisstock JC, Kaper JB, Robins-Browne RM, Jans DA, Frankel G, Phillips AD, Coulson BS, Hartland EL. The type III effectors NleE and NleB from enteropathogenic E. coli and OspZ from Shigella block nuclear translocation of NF-kappaB p65. PLoS Pathog. 2010 May 13;6(5):e1000898. PMID:20485572 doi:10.1371/journal.ppat.1000898

[3] Ruchaud-Sparagano MH, Mühlen S, Dean P, Kenny B. The enteropathogenic E. coli (EPEC) Tir effector inhibits NF-κB activity by targeting TNFα receptor-associated factors. PLoS Pathog. 2011 Dec;7(12):e1002414. PMID:22144899 doi:10.1371/journal.ppat.1002414

[4] Li S, Zhang L, Yao Q, Li L, Dong N, Rong J, Gao W, Ding X, Sun L, Chen X, Chen S, Shao F. Pathogen blocks host death receptor signalling by arginine GlcNAcylation of death domains. Nature. 2013 Sep 12;501(7466):242-6. PMID:23955153 doi:10.1038/nature12436

[5] Pearson JS, Giogha C, Ong SY, Kennedy CL, Kelly M, Robinson KS, Lung TW, Mansell A, Riedmaier P, Oates CV, Zaid A, Mühlen S, Crepin VF, Marches O, Ang CS, Williamson NA, O'Reilly LA, Bankovacki A, Nachbur U, Infusini G, Webb AI, Silke J, Strasser A, Frankel G, Hartland EL. A type III effector antagonizes death receptor signalling during bacterial gut infection. Nature. 2013 Sep 12;501(7466):247-51. PMID:24025841 doi:10.1038/nature12524

[6] Wong Fok Lung T, Giogha C, Creuzburg K, Ong SY, Pollock GL, Zhang Y, Fung KY, Pearson JS, Hartland EL. Mutagenesis and Functional Analysis of the Bacterial Arginine Glycosyltransferase Effector NleB1 from Enteropathogenic Escherichia coli. Infect Immun. 2016 Apr 22;84(5):1346-1360. PMID:26883593 doi:10.1128/IAI.01523-15

[7] Pollock GL, Oates CVL, Giogha C, Wong Fok Lung T, Ong SY, Pearson JS, Hartland EL. Distinct Roles of the Antiapoptotic Effectors NleB and NleF from Enteropathogenic Escherichia coli. Infect Immun. 2017 Mar 23;85(4):e01071-16. PMID:28138023 doi:10.1128/IAI.01071-16

[8] El Qaidi S, Chen K, Halim A, Siukstaite L, Rueter C, Hurtado-Guerrero R, Clausen H, Hardwidge PR. NleB/SseK effectors from Citrobacter rodentium, Escherichia coli, and Salmonella enterica display distinct differences in host substrate specificity. J Biol Chem. 2017 Jul 7;292(27):11423-11430. PMID:28522607 doi:10.1074/jbc.M117.790675

[9] Scott NE, Giogha C, Pollock GL, Kennedy CL, Webb AI, Williamson NA, Pearson JS, Hartland EL. The bacterial arginine glycosyltransferase effector NleB preferentially modifies Fas-associated death domain protein (FADD). J Biol Chem. 2017 Oct 20;292(42):17337-17350. PMID:28860194 doi:10.1074/jbc.M117.805036

[10] Xu C, Liu X, Zha H, Fan S, Zhang D, Li S, Xiao W. A pathogen-derived effector modulates host glucose metabolism by arginine GlcNAcylation of HIF-1α protein. PLoS Pathog. 2018 Aug 20;14(8):e1007259. PMID:30125331 doi:10.1371/journal.ppat.1007259

[11] Ding J, Pan X, Du L, Yao Q, Xue J, Yao H, Wang DC, Li S, Shao F. Structural and Functional Insights into Host Death Domains Inactivation by the Bacterial Arginine GlcNAcyltransferase Effector. Mol Cell. 2019 Apr 3. pii: S1097-2765(19)30232-1. doi:, 10.1016/j.molcel.2019.03.028. PMID:30979585 doi:https://dx.doi.org/10.1016/j.molcel.2019.03.028

[12] El Qaidi S, Scott NE, Hays MP, Geisbrecht BV, Watkins S, Hardwidge PR. An intra-bacterial activity for a T3SS effector. Sci Rep. 2020 Jan 23;10(1):1073. PMID:31974499 doi:10.1038/s41598-020-58062-y

[13] Xue J, Pan X, Peng T, Duan M, Du L, Zhuang X, Cai X, Yi X, Fu Y, Li S. Auto Arginine-GlcNAcylation Is Crucial for Bacterial Pathogens in Regulating Host Cell Death. Front Cell Infect Microbiol. 2020 May 5;10:197. PMID:32432056 doi:10.3389/fcimb.2020.00197

[14] Ding J, Pan X, Du L, Yao Q, Xue J, Yao H, Wang DC, Li S, Shao F. Structural and Functional Insights into Host Death Domains Inactivation by the Bacterial Arginine GlcNAcyltransferase Effector. Mol Cell. 2019 Apr 3. pii: S1097-2765(19)30232-1. doi:, 10.1016/j.molcel.2019.03.028. PMID:30979585 doi:https://dx.doi.org/10.1016/j.molcel.2019.03.028

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@@ Line 3: / Line 3: @@
 <StructureSection load='6aci' size='340' side='right'caption='[[6aci]], [[Resolution|resolution]] 1.87&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6aci]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Eco27 Eco27] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ACI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ACI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6aci]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O127:H6_str._E2348/69 Escherichia coli O127:H6 str. E2348/69] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ACI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ACI FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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]] 1.87&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6e66|6e66]], [[6ac0|6ac0]], [[6ac5|6ac5]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">E2348C_3231 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=574521 ECO27]), FADD, MORT1, GIG3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6aci FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aci OCA], [https://pdbe.org/6aci PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6aci RCSB], [https://www.ebi.ac.uk/pdbsum/6aci PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6aci ProSAT]</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=6aci FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aci OCA], [http://pdbe.org/6aci PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6aci RCSB], [http://www.ebi.ac.uk/pdbsum/6aci PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6aci ProSAT]</span></td></tr>
 </table>
-== Disease ==
-[[http://www.uniprot.org/uniprot/FADD_HUMAN FADD_HUMAN]] Defects in FADD are the cause of infections recurrent associated with encephalopathy hepatic dysfunction and cardiovascular malformations (IEHDCM) [MIM:[http://omim.org/entry/613759 613759]]. A condition with biological features of autoimmune lymphoproliferative syndrome such as high-circulating CD4(-)CD8(-)TCR-alpha-beta(+) T-cell counts, and elevated IL10 and FASL levels. Affected individuals suffer from recurrent, stereotypical episodes of fever, encephalopathy, and mild liver dysfunction sometimes accompanied by generalized seizures. The episodes can be triggered by varicella zoster virus (VZV), measles mumps rubella (MMR) attenuated vaccine, parainfluenza virus, and Epstein-Barr virus (EBV).<ref>PMID:21109225</ref>
 == Function ==
-[[http://www.uniprot.org/uniprot/FADD_HUMAN FADD_HUMAN]] Apoptotic adaptor molecule that recruits caspase-8 or caspase-10 to the activated Fas (CD95) or TNFR-1 receptors. The resulting aggregate called the death-inducing signaling complex (DISC) performs caspase-8 proteolytic activation. Active caspase-8 initiates the subsequent cascade of caspases mediating apoptosis. Involved in interferon-mediated antiviral immune response, playing a role in the positive regulation of interferon signaling.<ref>PMID:21109225</ref> <ref>PMID:16762833</ref> <ref>PMID:19118384</ref> <ref>PMID:20935634</ref>
+[https://www.uniprot.org/uniprot/NLEB1_ECO27 NLEB1_ECO27] Protein-arginine N-acetylglucosaminyltransferase effector that disrupts TNF signaling in infected cells, including NF-kappa-B signaling, apoptosis and necroptosis (PubMed:20126447, PubMed:20485572, PubMed:22144899, PubMed:23955153, PubMed:24025841, PubMed:28138023, PubMed:28522607, PubMed:30979585). Acts by catalyzing the transfer of a single N-acetylglucosamine (GlcNAc) to a conserved arginine residue in the death domain of host proteins FADD, TRADD, FAS, TNFRSF1A/TNFR1, TNFRSF25/DR3 and RIPK1: arginine GlcNAcylation prevents homotypic/heterotypic death domain interactions and assembly of the oligomeric TNF-alpha receptor complex, thereby disrupting TNF signaling (PubMed:23955153, PubMed:24025841, PubMed:26883593, PubMed:28522607, PubMed:28860194, PubMed:30979585). Has preference for host FADD as substrate compared to other death domain-containing proteins (PubMed:28860194). Also acts on host proteins without a death domain: catalyzes arginine GlcNAcylation of HIF1A, thereby regulating host glucose metabolism (PubMed:30125331). Also displays intra-bacterial activity by mediating GlcNAcylation of glutathione synthetase GshB (PubMed:31974499). Catalyzes auto-GlcNAcylation, which is required for activity toward death domain-containing host target proteins (PubMed:32432056). Shows a higher enzymatic activity than NleB2 (PubMed:23955153).<ref>PMID:20126447</ref> <ref>PMID:20485572</ref> <ref>PMID:22144899</ref> <ref>PMID:23955153</ref> <ref>PMID:24025841</ref> <ref>PMID:26883593</ref> <ref>PMID:28138023</ref> <ref>PMID:28522607</ref> <ref>PMID:28860194</ref> <ref>PMID:30125331</ref> <ref>PMID:30979585</ref> <ref>PMID:31974499</ref> <ref>PMID:32432056</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Eco27]]
+[[Category: Escherichia coli O127:H6 str. E2348/69]]
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Ding, J]]
+[[Category: Ding J]]
-[[Category: Shao, F]]
+[[Category: Shao F]]
-[[Category: Glycosyltransferase]]
-[[Category: Toxin]]

6aci: Difference between revisions

Latest revision as of 09:25, 22 November 2023

Crystal structure of EPEC effector NleB in complex with FADD death domain

Structural highlights

Function

Publication Abstract from PubMed

References

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