1MH9

Crystal Structure Analysis of deoxyribonucleotidase

Summary for 1MH9

• Entry DOI: 10.2210/pdb1mh9/pdb
• Descriptor: deoxyribonucleotidase, PHOSPHATE ION, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: rossmann fold, 4-helix bundle, hydrolase
• Biological source: Homo sapiens (human)
• Cellular location: Mitochondrion : Q9NPB1
• Total number of polymer chains: 1
• Total formula weight: 22960.40

Authors

Rinaldo-Matthis, A.,Rampazzo, C.,Reichard, P.,Bianchi, V.,Nordlund, P. (deposition date: 2002-08-19, release date: 2002-10-30, Last modification date: 2024-03-13)

Primary citation

Rinaldo-Matthis, A.,Rampazzo, C.,Reichard, P.,Bianchi, V.,Nordlund, P.
Crystal structure of a human mitochondrial deoxyribonucleotidase.
Nat.Struct.Biol., 9:779-787, 2002

PubMed Abstract: 5' nucleotidases are ubiquitous enzymes that dephosphorylate nucleoside monophosphates and participate in the regulation of nucleotide pools. The mitochondrial 5'-(3') deoxyribonucleotidase (dNT-2) specifically dephosphorylates dUMP and dTMP, thereby protecting mitochondrial DNA replication from excess dTTP. We have solved the structure of dNT-2, the first of a mammalian 5' nucleotidase. The structure reveals a relationship to the HAD family, members of which use an aspartyl nucleophile as their common catalytic strategy, with a phosphoserine phosphatase as the most similar neighbor. A structure-based sequence alignment of dNT-2 with other 5' nucleotidases also suggests a common origin for these enzymes. Here we study the structures of dNT-2 in complex with bound phosphate and beryllium trifluoride plus thymidine as model for a phosphoenzyme-product complex. Based on these structures, determinants for substrate specificity recognition and the catalytic action of dNT-2 are outlined.

PubMed: 12352955
DOI: 10.1038/nsb846

Experimental method

X-RAY DIFFRACTION (1.8 Å)