ISDA

Deposition Date 2013-05-27

Release Date 2014-02-05

Last Version Date 2023-09-20

Entry Detail

PDB ID:

4KXN

Keywords:

HYDROLASE

Title:

Crystal structure of DNPH1 (RCL) with kinetine riboside monophosphate

Biological Source:

Source Organism:

Rattus norvegicus (Taxon ID: 10116)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.90 Å

R-Value Free:

0.28

R-Value Work:

0.23

R-Value Observed:

0.23

Space Group:

P 1 21 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:2'-deoxynucleoside 5'-phosphate N-hydrolase 1
Gene (Uniprot):Dnph1
Mutations:D69N
Chain IDs:A, B, C, D
Chain Length:152
Number of Molecules:4
Biological Source:Rattus norvegicus

UniProt ID:O35820 Pfam ID:PF05014

Ligand Molecules

6K6

Primary Citation

N (6)-substituted AMPs inhibit mammalian deoxynucleotide N-hydrolase DNPH1.

Amiable, C, Pochet, S, Padilla, A, Labesse, G, Kaminski, P.A, Padilla, A, Amiable, C, Pochet, S, Kaminski, P.A, Labesse, G.Show

Plos One 8 e80755 e80755 (2013)

PMID: 24260472 DOI: 10.1371/journal.pone.0080755

Abstact

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.

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Primary Citation of related structures