|
|
| Line 1: |
Line 1: |
| | | | |
| | ==ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with inosine diphosphate ribose (IDPr)== | | ==ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with inosine diphosphate ribose (IDPr)== |
| - | <StructureSection load='6hoz' size='340' side='right' caption='[[6hoz]], [[Resolution|resolution]] 1.77Å' scene=''> | + | <StructureSection load='6hoz' size='340' side='right'caption='[[6hoz]], [[Resolution|resolution]] 1.77Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6hoz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Latch Latch]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HOZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HOZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6hoz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Latimeria_chalumnae Latimeria chalumnae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HOZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6HOZ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=R5I:inosine+diphosphate+ribose'>R5I</scene>, <scene name='pdbligand=R7I:inosine+diphosphate+ribose'>R7I</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]] 1.77Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ADPRHL2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7897 LATCH])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=R5I:inosine+diphosphate+ribose'>R5I</scene>, <scene name='pdbligand=R7I:inosine+diphosphate+ribose'>R7I</scene></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=6hoz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hoz OCA], [http://pdbe.org/6hoz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hoz RCSB], [http://www.ebi.ac.uk/pdbsum/6hoz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hoz 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=6hoz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hoz OCA], [https://pdbe.org/6hoz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6hoz RCSB], [https://www.ebi.ac.uk/pdbsum/6hoz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6hoz ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/ADPRS_LATCH ADPRS_LATCH] ADP-ribosylhydrolase that preferentially hydrolyzes the scissile alpha-O-linkage attached to the anomeric C1'' position of ADP-ribose and acts on different substrates, such as proteins ADP-ribosylated on serine and threonine, free poly(ADP-ribose) and O-acetyl-ADP-D-ribose (PubMed:30472116). Specifically acts as a serine mono-ADP-ribosylhydrolase by mediating the removal of mono-ADP-ribose attached to serine residues on proteins, thereby playing a key role in DNA damage response (PubMed:30472116). Serine ADP-ribosylation of proteins constitutes the primary form of ADP-ribosylation of proteins in response to DNA damage (By similarity). Does not hydrolyze ADP-ribosyl-arginine, -cysteine, -diphthamide, or -asparagine bonds (By similarity). Also able to degrade protein free poly(ADP-ribose), which is synthesized in response to DNA damage: free poly(ADP-ribose) acts as a potent cell death signal and its degradation by ADPRHL2 protects cells from poly(ADP-ribose)-dependent cell death, a process named parthanatos (PubMed:30472116). Also hydrolyzes free poly(ADP-ribose) in mitochondria (By similarity). Specifically digests O-acetyl-ADP-D-ribose, a product of deacetylation reactions catalyzed by sirtuins (By similarity). Specifically degrades 1''-O-acetyl-ADP-D-ribose isomer, rather than 2''-O-acetyl-ADP-D-ribose or 3''-O-acetyl-ADP-D-ribose isomers (By similarity).[UniProtKB:Q9NX46]<ref>PMID:30472116</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 21: |
Line 23: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Latch]] | + | [[Category: Large Structures]] |
| - | [[Category: Ariza, A]] | + | [[Category: Latimeria chalumnae]] |
| - | [[Category: Adp-ribose]] | + | [[Category: Ariza A]] |
| - | [[Category: Adp-ribosylation]]
| + | |
| - | [[Category: Adp-ribosylhydrolase like 2]]
| + | |
| - | [[Category: Adprhl2]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Idpr]]
| + | |
| - | [[Category: Inosine diphosphate ribose]]
| + | |
| Structural highlights
6hoz is a 2 chain structure with sequence from Latimeria chalumnae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.77Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
ADPRS_LATCH ADP-ribosylhydrolase that preferentially hydrolyzes the scissile alpha-O-linkage attached to the anomeric C1 position of ADP-ribose and acts on different substrates, such as proteins ADP-ribosylated on serine and threonine, free poly(ADP-ribose) and O-acetyl-ADP-D-ribose (PubMed:30472116). Specifically acts as a serine mono-ADP-ribosylhydrolase by mediating the removal of mono-ADP-ribose attached to serine residues on proteins, thereby playing a key role in DNA damage response (PubMed:30472116). Serine ADP-ribosylation of proteins constitutes the primary form of ADP-ribosylation of proteins in response to DNA damage (By similarity). Does not hydrolyze ADP-ribosyl-arginine, -cysteine, -diphthamide, or -asparagine bonds (By similarity). Also able to degrade protein free poly(ADP-ribose), which is synthesized in response to DNA damage: free poly(ADP-ribose) acts as a potent cell death signal and its degradation by ADPRHL2 protects cells from poly(ADP-ribose)-dependent cell death, a process named parthanatos (PubMed:30472116). Also hydrolyzes free poly(ADP-ribose) in mitochondria (By similarity). Specifically digests O-acetyl-ADP-D-ribose, a product of deacetylation reactions catalyzed by sirtuins (By similarity). Specifically degrades 1-O-acetyl-ADP-D-ribose isomer, rather than 2-O-acetyl-ADP-D-ribose or 3-O-acetyl-ADP-D-ribose isomers (By similarity).[UniProtKB:Q9NX46][1]
Publication Abstract from PubMed
Protein ADP-ribosylation is a highly dynamic post-translational modification. The rapid turnover is achieved, among others, by ADP-(ribosyl)hydrolases (ARHs), an ancient family of enzymes that reverses this modification. Recently ARHs came into focus due to their role as regulators of cellular stresses and tumor suppressors. Here we present a comprehensive structural analysis of the enzymatically active family members ARH1 and ARH3. These two enzymes have very distinct substrate requirements. Our data show that binding of the adenosine ribose moiety is highly diverged between the two enzymes, whereas the active sites harboring the distal ribose closely resemble each other. Despite this apparent similarity, we elucidate the structural basis for the selective inhibition of ARH3 by the ADP-ribose analogues ADP-HPD and arginine-ADP-ribose. Together, our biochemical and structural work provides important insights into the mode of enzyme-ligand interaction, helps to understand differences in their catalytic behavior, and provides useful tools for targeted drug design.
(ADP-ribosyl)hydrolases: Structural Basis for Differential Substrate Recognition and Inhibition.,Rack JGM, Ariza A, Drown BS, Henfrey C, Bartlett E, Shirai T, Hergenrother PJ, Ahel I Cell Chem Biol. 2018 Nov 16. pii: S2451-9456(18)30389-1. doi:, 10.1016/j.chembiol.2018.11.001. PMID:30472116[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Rack JGM, Ariza A, Drown BS, Henfrey C, Bartlett E, Shirai T, Hergenrother PJ, Ahel I. (ADP-ribosyl)hydrolases: Structural Basis for Differential Substrate Recognition and Inhibition. Cell Chem Biol. 2018 Nov 16. pii: S2451-9456(18)30389-1. doi:, 10.1016/j.chembiol.2018.11.001. PMID:30472116 doi:http://dx.doi.org/10.1016/j.chembiol.2018.11.001
- ↑ Rack JGM, Ariza A, Drown BS, Henfrey C, Bartlett E, Shirai T, Hergenrother PJ, Ahel I. (ADP-ribosyl)hydrolases: Structural Basis for Differential Substrate Recognition and Inhibition. Cell Chem Biol. 2018 Nov 16. pii: S2451-9456(18)30389-1. doi:, 10.1016/j.chembiol.2018.11.001. PMID:30472116 doi:http://dx.doi.org/10.1016/j.chembiol.2018.11.001
|
