5h6l

From Proteopedia

(Difference between revisions)

Revision as of 07:25, 9 August 2023

DNA targeting ADP-ribosyltransferase Pierisin-1 in complex with beta-NAD+

Structural highlights

5h6l is a 2 chain structure with sequence from Pieris rapae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PRSN_PIERA ADP-ribosylates double-stranded DNA by targeting the N2 amino group of dG residues; 10-fold less active on tRNA. Induces apoptosis in a range of human cell lines (PubMed:10485873, PubMed:11592983). May play a role in removing unnecessary or harmful cells during pupation (PubMed:15528160) (Probable). May play a role in defense against parasitic wasps; its habitual predator Cotesia glomerata is only susceptible after removal of its eggshell or the surface of the larval caudal vesicle, while other wasps are damaged by this protein (PubMed:23637752) (Probable). The wild-type catalytic domain (residues 1-233) cannot be expressed in E.coli as it is unstable probably due to its toxicity. A catalytic domain fragment (Glu-165 mutated to Gln) binds dsDNA but not ssDNA; the presence of the linker inhibits DNA-binding (PubMed:28765284).^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

ADP-ribosyltransferases transfer the ADP-ribose moiety of betaNAD+ to an acceptor molecule, usually a protein that modulates the function of the acceptor. Pierisin-1 is an ADP-ribosyltransferase from the cabbage butterfly Pieris rapae and is composed of N-terminal catalytic and C-terminal ricin B-like domains. Curiously, it ADP-ribosylates the DNA duplex, resulting in apoptosis of various cancer cells, which has raised interest in pierisin-1 as an anti-cancer agent. However, both the structure and the mechanism of DNA ADP-ribosylation are unclear. Here, we report the crystal structures of the N-terminal catalytic domain of pierisin-1, its complex with betaNAD+, and the catalytic domain with the linker connecting it to the ricin B-like domains. We found that the catalytic domain possesses a defined, positively charged region on the molecular surface but that its overall structure is otherwise similar to those of protein-targeting ADP-ribosyltransferases. Electrophoretic mobility shift assays and site-directed mutagenesis indicated that pierisin-1 binds double-stranded but not single-stranded DNA and that Lys122, Lys123, and Lys124, which are found in a loop, and Arg181 and Arg187, located in a basic cleft near the loop, are required for DNA binding. Furthermore, the structure of the catalytic domain with the linker revealed an autoinhibitory mechanism in which the linker occupies and blocks both the betaNAD+- and DNA-binding sites, suggesting that proteolytic cleavage to remove the linker is necessary for enzyme catalysis. Our study provides a structural basis for the DNA-acceptor specificity of pierisin-1 and reveals that a self-regulatory mechanism is required for its activity.

Structural basis of autoinhibition and activation of the DNA-targeting ADP-ribosyltransferase pierisin-1.,Oda T, Hirabayashi H, Shikauchi G, Takamura R, Hiraga K, Minami H, Hashimoto H, Yamamoto M, Wakabayashi K, Shimizu T, Sato M J Biol Chem. 2017 Sep 15;292(37):15445-15455. doi: 10.1074/jbc.M117.776641. Epub , 2017 Aug 1. PMID:28765284^[6]

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

References

↑ Watanabe M, Kono T, Matsushima-Hibiya Y, Kanazawa T, Nishisaka N, Kishimoto T, Koyama K, Sugimura T, Wakabayashi K. Molecular cloning of an apoptosis-inducing protein, pierisin, from cabbage butterfly: possible involvement of ADP-ribosylation in its activity. Proc Natl Acad Sci U S A. 1999 Sep 14;96(19):10608-13. PMID:10485873 doi:10.1073/pnas.96.19.10608
↑ Takamura-Enya T, Watanabe M, Totsuka Y, Kanazawa T, Matsushima-Hibiya Y, Koyama K, Sugimura T, Wakabayashi K. Mono(ADP-ribosyl)ation of 2'-deoxyguanosine residue in DNA by an apoptosis-inducing protein, pierisin-1, from cabbage butterfly. Proc Natl Acad Sci U S A. 2001 Oct 23;98(22):12414-9. PMID:11592983 doi:10.1073/pnas.221444598
↑ Oda T, Hirabayashi H, Shikauchi G, Takamura R, Hiraga K, Minami H, Hashimoto H, Yamamoto M, Wakabayashi K, Shimizu T, Sato M. Structural basis of autoinhibition and activation of the DNA-targeting ADP-ribosyltransferase pierisin-1. J Biol Chem. 2017 Sep 15;292(37):15445-15455. doi: 10.1074/jbc.M117.776641. Epub , 2017 Aug 1. PMID:28765284 doi:http://dx.doi.org/10.1074/jbc.M117.776641
↑ Watanabe M, Nakano T, Shiotani B, Matsushima-Hibiya Y, Kiuchi M, Yukuhiro F, Kanazawa T, Koyama K, Sugimura T, Wakabayashi K. Developmental stage-specific expression and tissue distribution of pierisin-1, a guanine-specific ADP-ribosylating toxin, in Pieris rapae. Comp Biochem Physiol A Mol Integr Physiol. 2004 Oct;139(2):125-31. PMID:15528160 doi:10.1016/j.cbpb.2004.07.010
↑ Takahashi-Nakaguchi A, Matsumoto Y, Yamamoto M, Iwabuchi K, Totsuka Y, Sugimura T, Wakabayashi K. Demonstration of cytotoxicity against wasps by pierisin-1: a possible defense factor in the cabbage white butterfly. PLoS One. 2013 Apr 23;8(4):e60539. PMID:23637752 doi:10.1371/journal.pone.0060539
↑ Oda T, Hirabayashi H, Shikauchi G, Takamura R, Hiraga K, Minami H, Hashimoto H, Yamamoto M, Wakabayashi K, Shimizu T, Sato M. Structural basis of autoinhibition and activation of the DNA-targeting ADP-ribosyltransferase pierisin-1. J Biol Chem. 2017 Sep 15;292(37):15445-15455. doi: 10.1074/jbc.M117.776641. Epub , 2017 Aug 1. PMID:28765284 doi:http://dx.doi.org/10.1074/jbc.M117.776641

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5h6l"

@@ Line 3: / Line 3: @@
 <StructureSection load='5h6l' size='340' side='right'caption='[[5h6l]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5h6l]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H6L OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5H6L FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5h6l]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pieris_rapae Pieris rapae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H6L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H6L FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 2.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5h6j|5h6j]], [[5h6k|5h6k]], [[5h6m|5h6m]], [[5h6n|5h6n]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5h6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h6l OCA], [http://pdbe.org/5h6l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h6l RCSB], [http://www.ebi.ac.uk/pdbsum/5h6l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h6l ProSAT]</span></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=5h6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h6l OCA], [https://pdbe.org/5h6l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h6l RCSB], [https://www.ebi.ac.uk/pdbsum/5h6l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h6l ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PRSN_PIERA PRSN_PIERA] ADP-ribosylates double-stranded DNA by targeting the N2 amino group of dG residues; 10-fold less active on tRNA. Induces apoptosis in a range of human cell lines (PubMed:10485873, PubMed:11592983). May play a role in removing unnecessary or harmful cells during pupation (PubMed:15528160) (Probable). May play a role in defense against parasitic wasps; its habitual predator Cotesia glomerata is only susceptible after removal of its eggshell or the surface of the larval caudal vesicle, while other wasps are damaged by this protein (PubMed:23637752) (Probable). The wild-type catalytic domain (residues 1-233) cannot be expressed in E.coli as it is unstable probably due to its toxicity. A catalytic domain fragment (Glu-165 mutated to Gln) binds dsDNA but not ssDNA; the presence of the linker inhibits DNA-binding (PubMed:28765284).<ref>PMID:10485873</ref> <ref>PMID:11592983</ref> <ref>PMID:28765284</ref> <ref>PMID:15528160</ref> <ref>PMID:23637752</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Hashimoto, H]]
+[[Category: Pieris rapae]]
-[[Category: Hirabayashi, H]]
+[[Category: Hashimoto H]]
-[[Category: Hiraga, K]]
+[[Category: Hirabayashi H]]
-[[Category: Minami, H]]
+[[Category: Hiraga K]]
-[[Category: Oda, T]]
+[[Category: Minami H]]
-[[Category: Sato, M]]
+[[Category: Oda T]]
-[[Category: Shikauchi, G]]
+[[Category: Sato M]]
-[[Category: Shimizu, T]]
+[[Category: Shikauchi G]]
-[[Category: Sugimura, T]]
+[[Category: Shimizu T]]
-[[Category: Takamura, R]]
+[[Category: Sugimura T]]
-[[Category: Wakabayashi, K]]
+[[Category: Takamura R]]
-[[Category: Yamamoto, M]]
+[[Category: Wakabayashi K]]
-[[Category: Dna-targeting adp-ribosyltransferase]]
+[[Category: Yamamoto M]]
-[[Category: Transferase]]

5h6l

From Proteopedia

Revision as of 07:25, 9 August 2023

DNA targeting ADP-ribosyltransferase Pierisin-1 in complex with beta-NAD+

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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