6k4k: Difference between revisions

Latest revision as of 10:41, 27 March 2024

Crystal structure of SidJ-CaM binary complex at 2.71 A

Structural highlights

6k4k is a 4 chain structure with sequence from Homo sapiens and Legionella pneumophila subsp. pneumophila str. Philadelphia 1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.715Å
Ligands:	CA
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SIDJ_LEGPH Glutamylase that mediates the covalent attachment of glutamate moieties to SdeA on one of the catalytic residues that is required for its mono-ADP-ribosyltransferase activity (PubMed:31330532, PubMed:31330531). In turn, inhibits SdeA ubiquitinating activity. Glutamylates also related SdeB, SdeC and SidE (PubMed:31330531, PubMed:31123136). Glutamylase activity only occurs in the host since it requires host calmodulin (PubMed:28497808, PubMed:31330532, PubMed:31330531, PubMed:31123136). May also reverse the SdeA-mediated substrate ubiquitination by cleaving the phosphodiester bond that links phosphoribosylated ubiquitin to protein substrates via its deubiquitinase activity (PubMed:28497808).^[1] ^[2] ^[3] ^[4]

References

↑ Qiu J, Yu K, Fei X, Liu Y, Nakayasu ES, Piehowski PD, Shaw JB, Puvar K, Das C, Liu X, Luo ZQ. A unique deubiquitinase that deconjugates phosphoribosyl-linked protein ubiquitination. Cell Res. 2017 Jul;27(7):865-881. PMID:28497808 doi:10.1038/cr.2017.66
↑ Black MH, Osinski A, Gradowski M, Servage KA, Pawlowski K, Tomchick DR, Tagliabracci VS. Bacterial pseudokinase catalyzes protein polyglutamylation to inhibit the SidE-family ubiquitin ligases. Science. 2019 May 24;364(6442):787-792. doi: 10.1126/science.aaw7446. PMID:31123136 doi:https://dx.doi.org/10.1126/science.aaw7446
↑ Gan N, Zhen X, Liu Y, Xu X, He C, Qiu J, Liu Y, Fujimoto GM, Nakayasu ES, Zhou B, Zhao L, Puvar K, Das C, Ouyang S, Luo ZQ. Regulation of phosphoribosyl ubiquitination by a calmodulin-dependent glutamylase. Nature. 2019 Jul 22. pii: 10.1038/s41586-019-1439-1. doi:, 10.1038/s41586-019-1439-1. PMID:31330531 doi:https://dx.doi.org/10.1038/s41586-019-1439-1
↑ Bhogaraju S, Bonn F, Mukherjee R, Adams M, Pfleiderer MM, Galej WP, Matkovic V, Lopez-Mosqueda J, Kalayil S, Shin D, Dikic I. Inhibition of bacterial ubiquitin ligases by SidJ-calmodulin-catalysed glutamylation. Nature. 2019 Jul 22. pii: 10.1038/s41586-019-1440-8. doi:, 10.1038/s41586-019-1440-8. PMID:31330532 doi:https://dx.doi.org/10.1038/s41586-019-1440-8

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OCA

[1] Qiu J, Yu K, Fei X, Liu Y, Nakayasu ES, Piehowski PD, Shaw JB, Puvar K, Das C, Liu X, Luo ZQ. A unique deubiquitinase that deconjugates phosphoribosyl-linked protein ubiquitination. Cell Res. 2017 Jul;27(7):865-881. PMID:28497808 doi:10.1038/cr.2017.66

[2] Black MH, Osinski A, Gradowski M, Servage KA, Pawlowski K, Tomchick DR, Tagliabracci VS. Bacterial pseudokinase catalyzes protein polyglutamylation to inhibit the SidE-family ubiquitin ligases. Science. 2019 May 24;364(6442):787-792. doi: 10.1126/science.aaw7446. PMID:31123136 doi:https://dx.doi.org/10.1126/science.aaw7446

[3] Gan N, Zhen X, Liu Y, Xu X, He C, Qiu J, Liu Y, Fujimoto GM, Nakayasu ES, Zhou B, Zhao L, Puvar K, Das C, Ouyang S, Luo ZQ. Regulation of phosphoribosyl ubiquitination by a calmodulin-dependent glutamylase. Nature. 2019 Jul 22. pii: 10.1038/s41586-019-1439-1. doi:, 10.1038/s41586-019-1439-1. PMID:31330531 doi:https://dx.doi.org/10.1038/s41586-019-1439-1

[4] Bhogaraju S, Bonn F, Mukherjee R, Adams M, Pfleiderer MM, Galej WP, Matkovic V, Lopez-Mosqueda J, Kalayil S, Shin D, Dikic I. Inhibition of bacterial ubiquitin ligases by SidJ-calmodulin-catalysed glutamylation. Nature. 2019 Jul 22. pii: 10.1038/s41586-019-1440-8. doi:, 10.1038/s41586-019-1440-8. PMID:31330532 doi:https://dx.doi.org/10.1038/s41586-019-1440-8

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[4]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6k4k is ON HOLD
+==Crystal structure of SidJ-CaM binary complex at 2.71 A==
+<StructureSection load='6k4k' size='340' side='right'caption='[[6k4k]], [[Resolution|resolution]] 2.71&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6k4k]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [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=6K4K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K4K FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.715&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=6k4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4k OCA], [https://pdbe.org/6k4k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k4k RCSB], [https://www.ebi.ac.uk/pdbsum/6k4k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4k ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SIDJ_LEGPH SIDJ_LEGPH] Glutamylase that mediates the covalent attachment of glutamate moieties to SdeA on one of the catalytic residues that is required for its mono-ADP-ribosyltransferase activity (PubMed:31330532, PubMed:31330531). In turn, inhibits SdeA ubiquitinating activity. Glutamylates also related SdeB, SdeC and SidE (PubMed:31330531, PubMed:31123136). Glutamylase activity only occurs in the host since it requires host calmodulin (PubMed:28497808, PubMed:31330532, PubMed:31330531, PubMed:31123136). May also reverse the SdeA-mediated substrate ubiquitination by cleaving the phosphodiester bond that links phosphoribosylated ubiquitin to protein substrates via its deubiquitinase activity (PubMed:28497808).<ref>PMID:28497808</ref> <ref>PMID:31123136</ref> <ref>PMID:31330531</ref> <ref>PMID:31330532</ref>
-Authors:
+==See Also==
+*[[Calmodulin 3D structures|Calmodulin 3D structures]]
-Description:
+== References ==
-[[Category: Unreleased Structures]]
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Legionella pneumophila subsp. pneumophila str. Philadelphia 1]]
+[[Category: Ouyang SY]]

6k4k: Difference between revisions

Latest revision as of 10:41, 27 March 2024

Crystal structure of SidJ-CaM binary complex at 2.71 A

Structural highlights

Function

See Also

References

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