4L6A

Structure of human mitochondrial 5'(3')-deoxyribonucleotidase

Summary for 4L6A

• Entry DOI: 10.2210/pdb4l6a/pdb
• Related: 4L6C
• Descriptor: 5'(3')-deoxyribonucleotidase, mitochondrial, MAGNESIUM ION, PHOSPHATE ION, ... (7 entities in total)
• Functional Keywords: protein conformation, sequence homology, had-like, hydrolase, dephosphorylation, phosphorylation
• Biological source: Homo sapiens (human)
• Cellular location: Mitochondrion : Q9NPB1
• Total number of polymer chains: 1
• Total formula weight: 24683.23

Authors

Pachl, P.,Brynda, J.,Rezacova, P. (deposition date: 2013-06-12, release date: 2014-02-12, Last modification date: 2024-02-28)

Primary citation

Pachl, P.,Fabry, M.,Rosenberg, I.,Simak, O.,Rezacova, P.,Brynda, J.
Structures of human cytosolic and mitochondrial nucleotidases: implications for structure-based design of selective inhibitors.
Acta Crystallogr. D Biol. Crystallogr., 70:461-470, 2014

PubMed Abstract: The human 5'(3')-deoxyribonucleotidases catalyze the dephosphorylation of deoxyribonucleoside monophosphates to the corresponding deoxyribonucleosides and thus help to maintain the balance between pools of nucleosides and nucleotides. Here, the structures of human cytosolic deoxyribonucleotidase (cdN) at atomic resolution (1.08 Å) and mitochondrial deoxyribonucleotidase (mdN) at near-atomic resolution (1.4 Å) are reported. The attainment of an atomic resolution structure allowed interatomic distances to be used to assess the probable protonation state of the phosphate anion and the side chains in the enzyme active site. A detailed comparison of the cdN and mdN active sites allowed the design of a cdN-specific inhibitor.

PubMed: 24531480
DOI: 10.1107/S1399004713030502

Experimental method

X-RAY DIFFRACTION (1.4 Å)