This entry represents flap endonucleases from eukaryotes, bacteria, viruses and archaea. Flap endonucleases (FENs) catalyse the exonucleolytic hydrolysis of blunt-ended duplex DNA substrates and the endonucleolytic cleavage of 5'-bifurcated nucleic acids at the junction formed between single and double-stranded DNA [ (PUBMED:17559871) ].
In prokaryotes, the essential FEN reaction can be performed by the N-terminal 5'-3' exonuclease domain present on DNA polymerase I. Some eubacteria, however, possess a second gene encoding a 5'-3' exonuclease domain [ (PUBMED:19000038) (PUBMED:23821668) ]. Two distinct classes of these independent bacterial FENs exist: Xni (ExoIXI) from Escherichia coli and SaFEN (Staphylococcus aureus FEN). SaFEN has both FEN and 5'-3' exonuclease activities. Xni (ExoIX) was previously identified as a 3'-5' exonuclease and named exonuclease IX (exonuclease 9) [ (PUBMED:9592142) (PUBMED:9840179) ] but subsequently found to possess flap endonuclease activity, but not exonuclease activity [ (PUBMED:17567612) (PUBMED:19000038) (PUBMED:23821668) ].
Archaea, eukaryotes, bacteriophages and some viruses encode a separate FEN enzyme but lack FEN domains on their DNA polymerases [ (PUBMED:23821668) ]. Escherichia phage T5 encodes the flap endonuclease D15, which catalyzes both the 5'-exonucleolytic and structure-specific endonucleolytic hydrolysis of DNA branched nucleic acid molecules [ (PUBMED:9874768) (PUBMED:15077103) (PUBMED:10364212) ]. In bacteriophage T4, disruption of the rnh gene (which encodes a FEN, known historically as T4 RNase H) results in slower, less accurate DNA replication. Bacteriophage T4 has both 5' nuclease and flap endonuclease activities [ (PUBMED:17693399) ].
Crystal structure of Thermus aquaticus DNA polymerase.
Nature. 1995; 376: 612-6
Display abstract
The DNA polymerase from Thermus aquaticus (Taq polymerase), famous for its use in the polymerase chain reaction, is homologous to Escherichia coli DNA polymerase I (pol I) Like pol I, Taq polymerase has a domain at its amino terminus (residues 1-290) that has 5' nuclease activity and a domain at its carboxy terminus that catalyses the polymerase reaction. Unlike pol I, the intervening domain in Taq polymerase has lost the editing 3'-5' exonuclease activity. Although the structure of the Klenow fragment of pol I has been known for ten years, that of the intact pol I has proved more elusive. The structure of Taq polymerase determined here at 2.4 A resolution shows that the structures of the polymerase domains of the thermostable enzyme and of the Klenow fragment are nearly identical, whereas the catalytically critical carboxylate residues that bind two metal ions are missing from the remnants of the 3'-5' exonuclease active site of Taq polymerase. The first view of the 5' nuclease domain, responsible for excising the Okazaki RNA in lagging-strand DNA replication, shows a cluster of conserved divalent metal-ion-binding carboxylates at the bottom of a cleft. The location of this 5'-nuclease active site some 70 A from the polymerase active site in this crystal form highlights the unanswered question of how this domain works in concert with the polymerase domain to produce a duplex DNA product that contains only a nick.
This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with 53EXOc domain which could be assigned to a KEGG orthologous group, and not all proteins containing 53EXOc domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.
