5zj5
From Proteopedia
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<StructureSection load='5zj5' size='340' side='right' caption='[[5zj5]], [[Resolution|resolution]] 1.57Å' scene=''> | <StructureSection load='5zj5' size='340' side='right' caption='[[5zj5]], [[Resolution|resolution]] 1.57Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[5zj5]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZJ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZJ5 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5zj5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Strco Strco]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZJ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZJ5 FirstGlance]. <br> |
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SCO5461 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=100226 STRCO])</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=5zj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zj5 OCA], [http://pdbe.org/5zj5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zj5 RCSB], [http://www.ebi.ac.uk/pdbsum/5zj5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zj5 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=5zj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zj5 OCA], [http://pdbe.org/5zj5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zj5 RCSB], [http://www.ebi.ac.uk/pdbsum/5zj5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zj5 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | ScARP from the bacterium Streptomyces coelicolor belongs to the pierisin family of DNA-targeting ADP-ribosyltransferases (ARTs). These enzymes ADP-ribosylate the N(2) amino groups of guanine residues in DNA to yield N(2)-(ADP-ribos-1-yl)-2'-deoxyguanosine. Although the structures of pierisin-1 and Scabin were revealed recently, the substrate recognition mechanisms remain poorly understood because of the lack of a substrate-binding structure. Here, we report the apo structure of ScARP and of ScARP bound to NADH and its GDP substrate at 1.50 and 1.57 A resolutions, respectively. The bound structure revealed that the guanine of GDP is trapped between N-ribose of NADH and Trp159. Interestingly, N(2) and N(3) of guanine formed hydrogen bonds with the OE1 and NE2 atoms of Gln162, respectively. We directly observed that the ADP-ribosylating toxin turn-turn (ARTT)-loop including Trp159 and Gln162 plays a key role in the specificity of DNA-targeting guanine-specific ART as well as protein-targeting ARTs such as C3 exoenzyme. We propose that the ARTT-loop recognition is a common substrate recognition mechanism in the pierisin family. Furthermore, this complex structure sheds light on similarities and differences among two subclasses that are distinguished by conserved structural motifs: H-Y-E in the ARTD subfamily and R-S-E in the ARTC subfamily. The spatial arrangements of the electrophile and nucleophile were the same, providing the first evidence for a common reaction mechanism in these ARTs. ARTC (including ScARP) uses the ARTT-loop for substrate recognition, whereas ARTD (represented by Arr) uses the C-terminal helix instead of the ARTT-loop. These observations could help inform efforts to improve ART inhibitors. | ||
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| + | Substrate N(2) atom recognition mechanism in pierisin family DNA-targeting guanine-specific ADP-ribosyltransferase ScARP.,Yoshida T, Tsuge H J Biol Chem. 2018 Aug 2. pii: AC118.004412. doi: 10.1074/jbc.AC118.004412. PMID:30072382<ref>PMID:30072382</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 5zj5" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Strco]] | ||
[[Category: Tsuge, H]] | [[Category: Tsuge, H]] | ||
[[Category: Yoshida, T]] | [[Category: Yoshida, T]] | ||
Revision as of 10:24, 5 September 2018
Guanine-specific ADP-ribosyltransferase with NADH and GDP
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