AC PRU00405; DC Domain; TR PROSITE; PS50878; RT_POL; 1; level=0 XX Names: Reverse transcriptase (RT) catalytic domain Function: The RT domain exhibits two enzymatic activities: RNA-dependent DNA polymerase and DNA-dependent DNA polymerase. XX case DE + RecName: EC=2.7.7.49; DE EC=2.7.7.7; end case case and CC -!- FUNCTION: RT is a multifunctional enzyme that converts the viral CC dimeric RNA genome into dsDNA in the cytoplasm, shortly after virus CC entry into the cell. This enzyme displays a DNA polymerase activity CC that can copy either DNA or RNA templates, and a ribonuclease H (RNAse CC H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a CC partially processive 3' to 5' endonucleasic mode. Conversion of viral CC genomic RNA into dsDNA requires many steps. A tRNA(3)-Lys binds to the CC primer-binding site (PBS) situated at the 5' end of the viral RNA. RT CC uses the 3' end of the tRNA primer to perfom a short round of RNA- CC dependent minus-strand DNA synthesis. The reading proceeds through the CC U5 region and ends after the repeated (R) region which is present at CC both ends of viral RNA. The portion of the RNA-DNA heteroduplex is CC digested by the RNase H, resulting in a ssDNA product attached to the CC tRNA primer. This ssDNA/tRNA hybridizes with the identical R region CC situated at the 3' end of viral RNA. This template exchange, known as CC minus-strand DNA strong stop transfer, can be either intra- or CC intermolecular. RT uses the 3' end of this newly synthetized short CC ssDNA to perfom the RNA-dependent minus-strand DNA synthesis of the CC whole template. RNase H digests the RNA template except for two CC polypurine tracts (PPTs) situated at the 5' end and near the center of CC the genome. It is not clear if both polymerase and RNase H activities CC are simultaneous. RNase H probably can proceed both in a polymerase- CC dependent (RNA cut into small fragments by the same RT performing DNA CC synthesis) and a polymerase-independent mode (cleavage of remaining RNA CC fragments by free RTs). Secondly, RT performs DNA-directed plus-strand CC DNA synthesis using the PPTs that have not been removed by RNase H as CC primers. PPTs and tRNA primers are then removed by RNAse H. The 3' and CC 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. CC Strand displacement synthesis by RT to the PBS and PPT ends produces a CC blunt ended, linear dsDNA copy of the viral genome that includes long CC terminal repeats (LTRs) at both ends. else case and CC -!- FUNCTION: RT is a multifunctional enzyme that converts the viral CC dimeric RNA genome into dsDNA in the cytoplasm, shortly after virus CC entry into the cell. This enzyme displays a DNA polymerase activity CC that can copy either DNA or RNA templates, and a ribonuclease H (RNAse CC H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a CC partially processive 3' to 5' endonucleasic mode. Conversion of viral CC genomic RNA into dsDNA requires many steps. A tRNA-Trp binds to the CC primer-binding site (PBS) situated at the 5' end of the viral RNA. RT CC uses the 3' end of the tRNA primer to perfom a short round of RNA- CC dependent minus-strand DNA synthesis. The reading proceeds through the CC U5 region and ends after the repeated (R) region which is present at CC both ends of viral RNA. The portion of the RNA-DNA heteroduplex is CC digested by the RNase H, resulting in a ssDNA product attached to the CC tRNA primer. This ssDNA/tRNA hybridizes with the identical R region CC situated at the 3' end of viral RNA. This template exchange, known as CC minus-strand DNA strong stop transfer, can be either intra- or CC intermolecular. RT uses the 3' end of this newly synthetized short CC ssDNA to perfom the RNA-dependent minus-strand DNA synthesis of the CC whole template. RNase H digests the RNA template except for a CC polypurine tract (PPT) situated at the 5' end of the genome. It is not CC clear if both polymerase and RNase H activities are simultaneous. RNase CC H probably can proceed both in a polymerase-dependent (RNA cut into CC small fragments by the same RT performing DNA synthesis) and a CC polymerase-independent mode (cleavage of remaining RNA fragments by CC free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis CC using the PPT that has not been removed by RNase H as primers. PPT and CC tRNA primers are then removed by RNAse H. The 3' and 5' ssDNA PBS CC regions hybridize to form a circular dsDNA intermediate. Strand CC displacement synthesis by RT to the PBS and PPT ends produces a blunt CC ended, linear dsDNA copy of the viral genome that includes long CC terminal repeats (LTRs) at both ends. else case or or or and CC -!- FUNCTION: RT is a multifunctional enzyme that converts the viral CC dimeric RNA genome into dsDNA in the cytoplasm, shortly after virus CC entry into the cell. This enzyme displays a DNA polymerase activity CC that can copy either DNA or RNA templates, and a ribonuclease H (RNAse CC H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a CC partially processive 3' to 5' endonucleasic mode. Conversion of viral CC genomic RNA into dsDNA requires many steps. A tRNA binds to the primer- CC binding site (PBS) situated at the 5' end of the viral RNA. RT uses the CC 3' end of the tRNA primer to perfom a short round of RNA-dependent CC minus-strand DNA synthesis. The reading proceeds through the U5 region CC and ends after the repeated (R) region which is present at both ends of CC viral RNA. The portion of the RNA-DNA heteroduplex is digested by the CC RNase H, resulting in a ssDNA product attached to the tRNA primer. This CC ssDNA/tRNA hybridizes with the identical R region situated at the 3' CC end of viral RNA. This template exchange, known as minus-strand DNA CC strong stop transfer, can be either intra- or intermolecular. RT uses CC the 3' end of this newly synthetized short ssDNA to perfom the RNA- CC dependent minus-strand DNA synthesis of the whole template. RNase H CC digests the RNA template except for a polypurine tract (PPT) situated CC at the 5' end of the genome. It is not clear if both polymerase and CC RNase H activities are simultaneous. RNase H probably can proceed both CC in a polymerase-dependent (RNA cut into small fragments by the same RT CC performing DNA synthesis) and a polymerase-independent mode (cleavage CC of remaining RNA fragments by free RTs). Secondly, RT performs DNA- CC directed plus-strand DNA synthesis using the PPT that has not been CC removed by RNase H as primers. PPT and tRNA primers are then removed by CC RNAse H. The 3' and 5' ssDNA PBS regions hybridize to form a circular CC dsDNA intermediate. Strand displacement synthesis by RT to the PBS and CC PPT ends produces a blunt ended, linear dsDNA copy of the viral genome CC that includes long terminal repeats (LTRs) at both ends. else case and CC -!- FUNCTION: RT is a multifunctional enzyme that converts the viral CC dimeric RNA genome into dsDNA in the cytoplasm, shortly after virus CC entry into the cell. This enzyme displays a DNA polymerase activity CC that can copy either DNA or RNA templates, and a ribonuclease H (RNAse CC H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a CC partially processive 3' to 5' endonucleasic mode. Conversion of viral CC genomic RNA into dsDNA requires many steps. A tRNA-Pro binds to the CC primer-binding site (PBS) situated at the 5' end of the viral RNA. RT CC uses the 3' end of the tRNA primer to perfom a short round of RNA- CC dependent minus-strand DNA synthesis. The reading proceeds through the CC U5 region and ends after the repeated (R) region which is present at CC both ends of viral RNA. The portion of the RNA-DNA heteroduplex is CC digested by the RNase H, resulting in a ssDNA product attached to the CC tRNA primer. This ssDNA/tRNA hybridizes with the identical R region CC situated at the 3' end of viral RNA. This template exchange, known as CC minus-strand DNA strong stop transfer, can be either intra- or CC intermolecular. RT uses the 3' end of this newly synthetized short CC ssDNA to perfom the RNA-dependent minus-strand DNA synthesis of the CC whole template. RNase H digests the RNA template except for a CC polypurine tract (PPT) situated at the 5' end of the genome. It is not CC clear if both polymerase and RNase H activities are simultaneous. RNase CC H probably can proceed both in a polymerase-dependent (RNA cut into CC small fragments by the same RT performing DNA synthesis) and a CC polymerase-independent mode (cleavage of remaining RNA fragments by CC free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis CC using the PPT that has not been removed by RNase H as primers. PPT and CC tRNA primers are then removed by RNAse H. The 3' and 5' ssDNA PBS CC regions hybridize to form a circular dsDNA intermediate. Strand CC displacement synthesis by RT to the PBS and PPT ends produces a blunt CC ended, linear dsDNA copy of the viral genome that includes long CC terminal repeats (LTRs) at both ends. end case XX case CC -!- CATALYTIC ACTIVITY: CC Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = CC diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339, CC Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560, CC ChEBI:CHEBI:173112; EC=2.7.7.49; CC -!- CATALYTIC ACTIVITY: CC Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = CC diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339, CC Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560, CC ChEBI:CHEBI:173112; EC=2.7.7.7; end case XX case CC -!- COFACTOR: CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; CC Note=The RT polymerase active site binds 2 magnesium ions.; end case XX case CC -!- SUBUNIT: The reverse transcriptase is a heterodimer of p66 RT and p51 CC RT (RT p66/p51). Heterodimerization of RT is essential for DNA CC polymerase activity. Despite the sequence identities, p66 RT and p51 RT CC have distinct folding. else case CC -!- SUBUNIT: The reverse transcriptase forms a heterodimer of alpha and CC beta subunits. else case CC -!- SUBUNIT: The reverse transcriptase is a monomer. end case XX case CC -!- DOMAIN: The p66 RT is structured in five subdomains: finger, palm, CC thumb, connection and RNase H. Within the palm subdomain, the 'primer CC grip' region is thought to be involved in the positioning of the primer CC terminus for accomodating the incoming nucleotide. The RNase H domain CC stabilizes the association of RT with primer-template. end case XX case CC -!- PTM: Specific enzymatic cleavages by the viral protease yield mature CC proteins. The protease is released by autocatalytic cleavage. The CC polyprotein is cleaved during and after budding, this process is termed CC maturation. Proteolytic cleavage of p66 RT removes the RNase H domain CC to yield the p51 RT subunit. end case XX case CC -!- MISCELLANEOUS: The reverse transcriptase is an error-prone enzyme that CC lacks a proof-reading function. High mutations rate is a direct CC consequence of this characteristic. RT also displays frequent template CC swiching leading to high recombination rate. Recombination mostly CC occurs between homologous regions of the two copackaged RNA genomes. If CC these two RNA molecules derive from different viral strains, reverse CC transcription will give rise to highly recombinated proviral DNAs. end case XX XX GO GO:0016740; F:transferase activity GO GO:0016779; F:nucleotidyltransferase activity GO GO:0003964; F:RNA-directed DNA polymerase activity GO GO:0003887; F:DNA-directed DNA polymerase activity XX KW Transferase KW Nucleotidyltransferase KW RNA-directed DNA polymerase KW DNA-directed DNA polymerase KW Multifunctional enzyme KW DNA-binding KW RNA-binding KW DNA recombination KW Metal-binding KW Magnesium XX FT From: PS50878 FT DOMAIN from..to FT /note="Reverse transcriptase #" FT BINDING 66 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_note="catalytic" FT Group: 1; Condition: D FT BINDING 130 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_note="catalytic" FT Group: 1; Condition: D FT BINDING 131 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_note="catalytic" FT Group: 1; Condition: D XX Chop: Nter=0; Cter=0; Size: 140-285; Related: None; Repeats: 1; Topology: Undefined; Example: O14746; Scope: Eukaryota Bacteria Viruses Comments: None XX # Revision 1.23 2022/11/19 //