5EWY
Scabin toxin from Streptomyces Scabies in complex with inhibitor P6E
Summary for 5EWY
| Entry DOI | 10.2210/pdb5ewy/pdb |
| Related | 5EWK |
| Descriptor | Putative ADP-Ribosyltransferase Scabin, 4-(8-fluoranyl-6-oxidanylidene-1,3,4,5-tetrahydrobenzo[c][1,6]naphthyridin-2-yl)butanoic acid (3 entities in total) |
| Functional Keywords | transferase, inhibitor, transferase-transferase inhibitor complex, transferase/transferase inhibitor |
| Biological source | Streptomyces scabiei 87.22 |
| Total number of polymer chains | 1 |
| Total formula weight | 22296.92 |
| Authors | Ravulapalli, R.,Lyons, B.,Merrill, A.R. (deposition date: 2015-11-22, release date: 2016-03-23, Last modification date: 2024-11-20) |
| Primary citation | Lyons, B.,Ravulapalli, R.,Lanoue, J.,Lugo, M.R.,Dutta, D.,Carlin, S.,Merrill, A.R. Scabin, a Novel DNA-acting ADP-ribosyltransferase from Streptomyces scabies. J.Biol.Chem., 291:11198-11215, 2016 Cited by PubMed Abstract: A bioinformatics strategy was used to identify Scabin, a novel DNA-targeting enzyme from the plant pathogen 87.22 strain of Streptomyces scabies Scabin shares nearly 40% sequence identity with the Pierisin family of mono-ADP-ribosyltransferase toxins. Scabin was purified to homogeneity as a 22-kDa single-domain enzyme and was shown to possess high NAD(+)-glycohydrolase (Km (NAD) = 68 ± 3 μm; kcat = 94 ± 2 min(-1)) activity with an RSQXE motif; it was also shown to target deoxyguanosine and showed sigmoidal enzyme kinetics (K0.5(deoxyguanosine) = 302 ± 12 μm; kcat = 14 min(-1)). Mass spectrometry analysis revealed that Scabin labels the exocyclic amino group on guanine bases in either single-stranded or double-stranded DNA. Several small molecule inhibitors were identified, and the most potent compounds were found to inhibit the enzyme activity with Ki values ranging from 3 to 24 μm PJ34, a well known inhibitor of poly-ADP-ribosyltransferases, was shown to be the most potent inhibitor of Scabin. Scabin was crystallized, representing the first structure of a DNA-targeting mono-ADP-ribosyltransferase enzyme; the structures of the apo-form (1.45 Å) and with two inhibitors (P6-E, 1.4 Å; PJ34, 1.6 Å) were solved. These x-ray structures are also the first high resolution structures of the Pierisin subgroup of the mono-ADP-ribosyltransferase toxin family. A model of Scabin with its DNA substrate is also proposed. PubMed: 27002155DOI: 10.1074/jbc.M115.707653 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.4 Å) |
Structure validation
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