DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.
Feature 1:nucleotide binding site [chemical binding site]
Evidence:
Comment:there are 4 distinct nucleotide binding sites (I-IV) described for 1CY7_A
Comment:site IV is a unique binding site for 3'5'ADP; location of site IV has not been definitively determined but is near site I, and the 2 sites may interfere with each other.
Jiyao W et al.(2023). "The conserved domain database in 2023.",