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1Q92

Crystal structure of human mitochondrial deoxyribonucleotidase in complex with the inhibitor PMcP-U

Summary for 1Q92
Entry DOI10.2210/pdb1q92/pdb
Related1MH9 1Q91
Descriptor5(3)-deoxyribonucleotidase, MAGNESIUM ION, {[(1R,2S)-2-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)CYCLOPENTYL]OXY}METHYLPHOSPHONIC ACID, ... (5 entities in total)
Functional Keywordsalpha-beta rossman fold, hydrolase
Biological sourceHomo sapiens (human)
Cellular locationMitochondrion: Q9NPB1
Total number of polymer chains1
Total formula weight23247.73
Authors
Rinaldo-Matthis, A.,Rampazzo, C.,Balzarini, J.,Reichard, P.,Bianchi, V.,Nordlund, P. (deposition date: 2003-08-22, release date: 2004-04-20, Last modification date: 2023-10-25)
Primary citationRinaldo-Matthis, A.,Rampazzo, C.,Balzarini, J.,Reichard, P.,Bianchi, V.,Nordlund, P.
Crystal structures of the mitochondrial deoxyribonucleotidase in complex with two specific inhibitors
Mol.Pharmacol., 65:860-867, 2004
Cited by
PubMed Abstract: Monophosphate nucleotidases are enzymes that dephosphorylate nucleotides to their corresponding nucleosides. They play potentially important roles in controlling the activation of nucleotide-based drugs targeted against viral infections or cancer cells. The human mitochondrial deoxyribonucleotidase (dNT-2) dephosphorylates thymidine and deoxyuridine monophosphates. We describe the high resolution structures of the dNT-2 enzyme in complex with two potent nucleoside phosphonate inhibitors, (S)-1-[2'-deoxy-3',5'-O-(1-phosphono) benzylidene-beta-d-threo-pentofuranosyl]thymine (DPB-T) at 1.6-A resolution and (+/-)-1-trans-(2-phosphonomethoxycyclopentyl)uracil (PMcP-U) at 1.4-A resolution. The mixed competitive inhibitor DPB-T and the competitive inhibitor PMcP-U both bind in the active site of dNT-2 but in distinctly different binding modes, explaining their different kinetics of inhibition. The pyrimidine part of the inhibitors binds with very similar hydrogen bond interactions to the protein but with their phosphonate moieties in different binding sites compared with each other and to the previously determined position of phosphate bound to dNT-2. Together, these phosphate/phosphonate binding sites describe what might constitute a functionally relevant phosphate entrance tunnel to the active site. The structures of the inhibitors in complex with dNT-2, being the first such complexes of any nucleotidase, might provide important information for the design of more specific inhibitors to control the activation of nucleotide-based drugs.
PubMed: 15044615
DOI: 10.1124/mol.65.4.860
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (1.4 Å)
Structure validation

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