5UNB

Crystal structure of putative Putative deoxyribonuclease-2 from Burkholderia thailandensis in complex with copper

Summary for 5UNB

• Entry DOI: 10.2210/pdb5unb/pdb
• Related: 5I3E
• Descriptor: Putative deoxyribonuclease-2, COPPER (II) ION, 1,2-ETHANEDIOL, ... (4 entities in total)
• Functional Keywords: ssgcid, putative deoxyribonuclease-2, inhitition, structural genomics, seattle structural genomics center for infectious disease, hydrolase
• Biological source: Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264)
• Total number of polymer chains: 2
• Total formula weight: 79864.53

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID) (deposition date: 2017-01-30, release date: 2017-02-15, Last modification date: 2023-10-04)

Primary citation

Varela-Ramirez, A.,Abendroth, J.,Mejia, A.A.,Phan, I.Q.,Lorimer, D.D.,Edwards, T.E.,Aguilera, R.J.
Structure of acid deoxyribonuclease.
Nucleic Acids Res., 45:6217-6227, 2017

PubMed Abstract: Deoxyribonuclease II (DNase II) is also known as acid deoxyribonuclease because it has optimal activity at the low pH environment of lysosomes where it is typically found in higher eukaryotes. Interestingly, DNase II has also been identified in a few genera of bacteria and is believed to have arisen via horizontal transfer. Here, we demonstrate that recombinant Burkholderia thailandensis DNase II is highly active at low pH in the absence of divalent metal ions, similar to eukaryotic DNase II. The crystal structure of B. thailandensis DNase II shows a dimeric quaternary structure which appears capable of binding double-stranded DNA. Each monomer of B. thailandensis DNase II exhibits a similar overall fold as phospholipase D (PLD), phosphatidylserine synthase (PSS) and tyrosyl-DNA phosphodiesterase (TDP), and conserved catalytic residues imply a similar mechanism. The structural and biochemical data presented here provide insights into the atomic structure and catalytic mechanism of DNase II.

PubMed: 28369538
DOI: 10.1093/nar/gkx222

Experimental method

X-RAY DIFFRACTION (1.75 Å)