EC Number   |
General Information |
Reference |
|---|
   2.4.2.6 | evolution |
a strict classification of CtNDTas either a type I or a type II NDT is not possible |
-, 758684 |
| 2.4.2.6 | evolution |
enzyme LaNDT can be classified as 98 NDT type II |
-, 759530 |
| 2.4.2.6 | evolution |
NDTs are classified into two classes depending on their substrate specificity: NDT type I (PDT), specific for purine exchange, and NDT type II (NDT), which catalyzes the transfer between purines and/or pyrimidines. LhNDT is classified as a NDT type II |
-, 759340 |
| 2.4.2.6 | more |
enzyme structure homology modeling, catalytic mechanism, overview. Glu88 is the catalytic residue whose carboxylate attacks the C1' of the nucleoside, is firmly positioned by the phenol of Tyr7. The carboxamide nitrogen of Asn118# and the Asp82 carboxylate recognize the O5' of the 2'-deoxyribose.Pro11 and Pro40 play a prominent role in making up the active site cavity. The heteroaromatic ring of the nucleobase is sandwiched between the phenyl rings of Phe14 and Phe41 on one side and the hydrophobic side chains of Val58 and Leu119# on the opposite side. The Met120# side chain sulfur appears close to the H1' atom, which suggests that it likely plays a role in transition state stabilization, together with the carboxylate of Asp62. The side chains of Tyr115' and possibly Asp53 can establish direct or water-bridged hydrogen bonds with the N7 of purines and the substituent on C6, be it an amino or a keto group. Asp62 of CtNDT plays a role in cytosine recognition, together with Arg43 and a protonated Asn44 |
-, 758684 |
| 2.4.2.6 | more |
homologous modeling submitting the three-dimensional structure of LlNDT (PDB ID 1F8X), and ligand interaction analysis, modeling of active site involved in the enzyme-substrate interaction |
759526 |
| 2.4.2.6 | more |
molecular dynamics simulations. TbPDT is a homodimer which displays the typical 2'-deoxyribose binding site motif made up of two acidic residues from one subunit (Asp76 and Glu82) and one polar residue from the characteristic NLM motif in the neighboring monomer (Asn126#). The 5'-hydroxyl group of the incoming 2'-deoxynucleoside hydrogen bonds to the carboxylate of Asp76 and is hydrogen bonded by the carboxamide of Asn126#. The nucleophilic attack on C1' of the sugar is effected by the sidechain carboxylate of Glu82, which is held in position by hydrogen bonds donated by the phenol group of Tyr5 and the 3'-hydroxyl of the sugar. In the near-attack conformation one of the lone pairs of the M128# sulfur is poised to interact with the developing positive charge on the oxocarbenium ion of the transition state. The purine ring is sandwiched between the hydrophobic side chains of Val11 and Phe12, on one side, and those of Ile49 and Leu127# on the other side, whereas the nucleobase's N-3 atom is recognized by the carboxamide nitrogen of Asn53 |
-, 759065 |
| 2.4.2.6 | more |
reaction mechanism of nucleoside 2'-deoxyribosyltransferases, a free-energy landscape supports an oxocarbenium ion as the reaction intermediate. Structure-function analysis of wild-type and mutant enzymes using enzyme crystal structures (PDB IDs 1F8X and 1F8Y), QM/MM MD simulations, overview |
759892 |
| 2.4.2.6 | more |
structure modeling of LaNDT |
-, 759530 |
| 2.4.2.6 | physiological function |
N-deoxyribosyltransferases catalyze the direct transfer of the 2'-deoxyribosyl moiety from a 2'-deoxynucleoside donor to a nucleobase acceptor through a one-step reaction |
-, 758681 |
| 2.4.2.6 | physiological function |
nucleoside deoxyribosyltransferase II (NDT) catalyzes the transglycosylation reaction of the 2'-deoxyribose moiety between purine and/or pyrimidine bases |
759526 |
