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| | ==Crystal structure of DNPH1 (RCL) with 6-CYCLOPENTYL-AMP== | | ==Crystal structure of DNPH1 (RCL) with 6-CYCLOPENTYL-AMP== |
| - | <StructureSection load='4kxl' size='340' side='right' caption='[[4kxl]], [[Resolution|resolution]] 1.69Å' scene=''> | + | <StructureSection load='4kxl' size='340' side='right'caption='[[4kxl]], [[Resolution|resolution]] 1.69Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4kxl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KXL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KXL FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4kxl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KXL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KXL FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6C6:N-CYCLOPENTYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>6C6</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.69Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4fyi|4fyi]], [[4kxm|4kxm]], [[4kxn|4kxn]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6C6:N-CYCLOPENTYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>6C6</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Dnph1, Rcl ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</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=4kxl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kxl OCA], [https://pdbe.org/4kxl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kxl RCSB], [https://www.ebi.ac.uk/pdbsum/4kxl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kxl 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=4kxl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kxl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kxl RCSB], [http://www.ebi.ac.uk/pdbsum/4kxl PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DNPH1_RAT DNPH1_RAT]] Catalyzes the cleavage of the N-glycosidic bond of deoxyribonucleoside 5'-monophosphates to yield deoxyribose 5-phosphate and a purine or pyrimidine base. Deoxyribonucleoside 5'-monophosphates containing purine bases are preferred to those containing pyrimidine bases.<ref>PMID:17234634</ref> | + | [https://www.uniprot.org/uniprot/DNPH1_RAT DNPH1_RAT] Catalyzes the cleavage of the N-glycosidic bond of deoxyribonucleoside 5'-monophosphates to yield deoxyribose 5-phosphate and a purine or pyrimidine base. Deoxyribonucleoside 5'-monophosphates containing purine bases are preferred to those containing pyrimidine bases.<ref>PMID:17234634</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4kxl" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Buffalo rat]] | + | [[Category: Large Structures]] |
| - | [[Category: Kaminski, P A]] | + | [[Category: Rattus norvegicus]] |
| - | [[Category: Labesse, G]] | + | [[Category: Kaminski PA]] |
| - | [[Category: Padilla, A]] | + | [[Category: Labesse G]] |
| - | [[Category: Deoxyribonucleoside 5'-monophosphate n-glycosidase]] | + | [[Category: Padilla A]] |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
DNPH1_RAT Catalyzes the cleavage of the N-glycosidic bond of deoxyribonucleoside 5'-monophosphates to yield deoxyribose 5-phosphate and a purine or pyrimidine base. Deoxyribonucleoside 5'-monophosphates containing purine bases are preferred to those containing pyrimidine bases.[1]
Publication Abstract from PubMed
The gene dnph1 (or rcl) encodes a hydrolase that cleaves the 2'-deoxyribonucleoside 5'-monophosphate (dNMP) N-glycosidic bond to yield a free nucleobase and 2-deoxyribose 5-phosphate. Recently, the crystal structure of rat DNPH1, a potential target for anti-cancer therapies, suggested that various analogs of AMP may inhibit this enzyme. From this result, we asked whether N (6)-substituted AMPs, and among them, cytotoxic cytokinin riboside 5'-monophosphates, may inhibit DNPH1. Here, we characterized the structural and thermodynamic aspects of the interactions of these various analogs with DNPH1. Our results indicate that DNPH1 is inhibited by cytotoxic cytokinins at concentrations that inhibit cell growth.
N (6)-substituted AMPs inhibit mammalian deoxynucleotide N-hydrolase DNPH1.,Amiable C, Pochet S, Padilla A, Labesse G, Kaminski PA PLoS One. 2013 Nov 19;8(11):e80755. doi: 10.1371/journal.pone.0080755., eCollection 2013. PMID:24260472[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ghiorghi YK, Zeller KI, Dang CV, Kaminski PA. The c-Myc target gene Rcl (C6orf108) encodes a novel enzyme, deoxynucleoside 5'-monophosphate N-glycosidase. J Biol Chem. 2007 Mar 16;282(11):8150-6. Epub 2007 Jan 18. PMID:17234634 doi:http://dx.doi.org/10.1074/jbc.M610648200
- ↑ Amiable C, Pochet S, Padilla A, Labesse G, Kaminski PA. N (6)-substituted AMPs inhibit mammalian deoxynucleotide N-hydrolase DNPH1. PLoS One. 2013 Nov 19;8(11):e80755. doi: 10.1371/journal.pone.0080755., eCollection 2013. PMID:24260472 doi:http://dx.doi.org/10.1371/journal.pone.0080755
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